DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claim Status
Claims 1-16 are pending.
Claims 11 and 16 are objected to.
Claims 1-16 are rejected.
Priority
This application is a CON of 16002468 filed Jun 7 2018 (now USP 11,401,551), which claims priority to as early as 61/258,567, filed Nov 5 2009.
However, 61/258,567 and 61/259,075 do not provide support for determining a cutoff value for a number of predicted counts of the respective first allele at the specific locus as recited in claim 3, solution phase capture as recited in claim 7, determining the number of molecules to be analyzed at a first locus of the one or more first loci using an assumed value of fractional concentration of fetal DNA and a target probability of detecting the respective first allele at the first locus as recited in claim 10, and
PNG
media_image1.png
46
120
media_image1.png
Greyscale
in claim 13.
Accordingly, each of claims 1-2, 8-9, 11-12, and 14-16 are afforded the effective filing date of Jun 11 2009 and claims 3-7, 10, and 13 are afforded the effective filing date of Sep 10 2010.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Mar 20 2023 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Drawings
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Nucleotide and/or Amino Acid Sequence Disclosures
The sequence listing filed Jun 14 2022 has been accepted.
Specification
The disclosure is objected to for the following informalities. It is noted that for purposes of the instant Office Action, any reference to the specification pertains to the specification as originally filed on Jun 14 2022.
Title
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed. The claims of the instant child application are no longer drawn to identifying a de novo fetal mutation.
The following title is suggested: “DETERMINING A FRACTIONAL CONCENTRATION OF FETAL DNA FROM A MATERNAL BIOLOGICAL SAMPLE” or similar.
Hyperlinks
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Non-limiting examples include paragraphs [0066; 0075-0076; 0110; 0206]. Applicant will note that this is exemplary and other instances may exist. It is requested that all instances be corrected.
Trade Names
The use of the terms Nimblegen sequence capture system, Agilent SureSelect Target Enrichment System, and RainDance, as examples, which are trade names or marks used in commerce, have been noted in this application. Each term should be accompanied by corresponding generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, ™ , or ® following the terms. Applicant is requested to review the Specification and Drawings for all instances.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) is permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Appropriate correction for all objections to the specification is required.
Claim Objections
The claims are objected to for the following informalities:
In claim 11, the comma after “value” on line 3 should be changed to a semicolon.
Claim 16, line 4, recites “nucleic molecules”, which should be amended to recite “nucleic acid molecules”.
Claim Rejections - 35 USC § 112
35 U.S.C. 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-16 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1, limitation 3, recites “identify a location of the nucleic acid molecule”. However, the claim previously recites only “nucleic acid molecules”. It is therefore not clear which of the nucleic acid molecules is intended to be further limited in limitation 3, or if each of the nucleic acid molecules are intended to be further limited. For compact examination, it is assumed that the claim should read ““identify a location of each [[the]] nucleic acid molecule of the nucleic acid molecules; determine a respective allele of each [[the]] nucleic acid molecule of the nucleic acid molecules”. The rejection may be overcome by clarifying the metes and bounds of the claim. Claims 14 and 16 and similarly rejected. Claims 2-13 and 15 are rejected based on their dependency from claims 1 and 14.
Claim 1, lines 9-12, recites “wherein the sequencing results are analyzed to: identify a location of the nucleic acid molecule in the target region of the human genome; and determine a respective allele of the nucleic acid molecule”. It is unclear whether the wherein clause is intended to require analyzing the sequencing results within the metes and bounds of the claimed invention, or if it is only further limiting the sequencing results such that performing the analyzing is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of analyzing the sequencing results, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the analyzing the sequencing results is required to be performed. The rejection may be overcome by clarifying what steps are required to be performed. Claims 14 and 16 and similarly rejected. Claims 2-13 and 15 are rejected based on their dependency from claims 1 and 14.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a method, a computer product comprising a non-transitory computer readable medium, and a system, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
The claims also recite a law of nature or a natural phenomenon. The MPEP at 2106.04(b) further explains that laws of nature and natural phenomena include naturally occurring principles/relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) as well as a law of nature or a natural phenomenon are as follows:
Independent claims 1, 14, and 16: wherein the sequencing results are analyzed to: identify a location of the nucleic acid molecule in the target region of the human genome; and determine a respective allele of the nucleic acid molecule;
determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele;
for at least one of the first loci:
determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and
determining the fractional concentration based on the first and second numbers.
Dependent claim 10: determining the number of molecules to be analyzed at a first locus of the one or more first loci using an assumed value of fractional concentration of fetal DNA and a target probability of detecting the respective first allele at the first locus.
Dependent claim 11: for a specific locus: comparing counts of the respective first allele to a cutoff value, and categorizing, using the comparison of the counts to the cutoff value, the locus as a locus where the mother is homozygous in the first allele and the fetus is heterozygous; the mother is heterozygous and the fetus is heterozygous; or the mother is heterozygous and the fetus is homozygous.
Dependent claims 2-6 and 12-13 recite further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claim 2 further limits determining the one or more first loci; claims 3-6 further limits determining a specific locus; and claims 12-13 further limit determining the fractional concentration to specific formulas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually determine the fractional concentration of fetal DNA in a biological sample. Without further detail as to the methodology involved in “analyzing”, “identifying”, and “determining”, under the BRI, one may simply, for example, use pen and paper to: identify a location of the nucleic acid molecule in the target region of the human genome; determine an allele of the nucleic acid molecule; determine how many molecules to analyze at a locus based on an assumed fractional concentration of fetal DNA and a target probability of detecting an allele; determine loci where the fetal genome is heterozygous, the maternal genome is homozygous, and the paternal genome is homozygous for the other allele by comparing counts to cutoff values and categorizing them based on the comparison; and determine the fractional concentration of the fetal DNA based on at least one of those identified loci. Some of these steps, such as determining loci which are homozygous or heterozygous and determining the fractional concentration of the fetal DNA require mathematical techniques as the only supported embodiments, as comparing values to cutoff values, as recited in claim 11, describes a mathematical process in words, and claims 12-13 explicitly recite mathematical formulas. Further support for the mathematical nature of the claims is disclosed in the specification at: [0140-0150].
Therefore, claims 1, 14, and 16 and those claims dependent therefrom recite an abstract idea and a law of nature/natural phenomenon [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 1: enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region; and
sequencing a plurality of nucleic acid molecules from the enriched biological sample to obtain sequencing results, the sequencing being specific to the target region.
Independent claim 14: receiving sequencing results of a sequencing of a plurality of nucleic acid molecules from an enriched biological sample, the enriched biological sample being enriched for nucleic acid molecules in a target region, the sequencing being specific to the target region.
Independent claim 16: receiving sequencing results from the sequencing device of a sequencing of a plurality of nucleic acid molecules from the enriched biological sample from the enrichment system, the enriched biological sample being enriched for nucleic acid molecules in the target region, the sequencing being specific to the target region.
Dependent claims 7-9 recite steps that further limit the recited additional elements in the claims. For example, claim 7 further limits enriching the biological sample to performing solution phase capture, microarray capture, or targeted amplification; claim 8 further limits sequencing the plurality of nucleic acid molecules to sequencing both ends of each nucleic acid molecule of the plurality of nucleic acid molecules; claim 9 further limits sequencing the plurality of nucleic acid molecules to random sequencing of the enriched biological sample.
The claims also include non-abstract computing elements. For example, independent claim 14 includes a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system; claim 15 includes a system comprising the computer product of claim 14 and one or more processors for executing instructions stored on the computer readable medium; and independent claim 16 includes a system comprising: an enrichment system configured to enrich a biological sample for nucleic acid molecules in a target region to form an enriched biological sample; a sequencing device configured to sequence a plurality of nucleic molecules in the enriched biological sample; and a computer system comprising: a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system; and one or more processors for executing instructions stored on the computer readable medium.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “enriching” and “sequencing” in claims 1 and 7-9 and “receiving” in claims 14-16, perform functions of collecting the data needed to carry out the judicial exceptions. Further, in claim 16, the enrichment system performs the enrichment of the biological sample and the sequencing device performs the sequencing, thereby also performing functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract computer elements in claims 14-16 do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the specification as published discloses that commercial systems exist to perform enrichment of biological samples and sequencing [0075; 0237]. The prior art to Bohmer (WO 2004/078999; IDS reference; p. 3, line 34 through p. 4, line 1), Quake (US 2007/0202525; IDS reference; [0033; 0060; 0067; 0084; 0120-0121]), Stoughton (US 2008/0070792; IDS reference; [0085]), and Lo (US 2009/0087847; IDS reference; [0273]) disclose that enrichment for nucleic acid molecules of a target region (as recited in claim 1; via targeted amplification, as recited in claim 7) followed by sequencing (as recited in claim 1; via random sequencing, as recited in claim 9) are data gathering elements that are routine, well-understood and conventional in the art. Further, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 14-16 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at 225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The specification as published also notes that computer processors and systems, as example, are commercially available or widely used at [0260-0263]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
(c) he has abandoned the invention.
(d) the invention was first patented or caused to be patented, or was the subject of an inventor’s certificate, by the applicant or his legal representatives or assigns in a foreign country prior to the date of the application for patent in this country on an application for patent or inventor’s certificate filed more than twelve months before the filing of the application in the United States.
(e) the invention was described in (1) an application for patent, published under section 122(b), by another filed in the United States before the invention by the applicant for patent or (2) a patent granted on an application for patent by another filed in the United States before the invention by the applicant for patent, except that an international application filed under the treaty defined in section 351(a) shall have the effects for purposes of this subsection of an application filed in the United States only if the international application designated the United States and was published under Article 21(2) of such treaty in the English language.
(f) he did not himself invent the subject matter sought to be patented.
(g)(1) during the course of an interference conducted under section 135 or section 291, another inventor involved therein establishes, to the extent permitted in section 104, that before such person’s invention thereof the invention was made by such other inventor and not abandoned, suppressed, or concealed, or (2) before such person’s invention thereof, the invention was made in this country by another inventor who had not abandoned, suppressed, or concealed it. In determining priority of invention under this subsection, there shall be considered not only the respective dates of conception and reduction to practice of the invention, but also the reasonable diligence of one who was first to conceive and last to reduce to practice, from a time prior to conception by the other.
A. Claims 1, 7-10, and 14-16 are rejected under pre-AIA 35 U.S.C. 102(e) as being anticipated by Lo et al. (US 2009/0087847; IDS Reference; priority to Jul 23 2007; filed Jul 23 2008).
The applied reference has a common assignee and joint inventor with the instant application. Based upon the pre-AIA 35 U.S.C. 102(e) date of the reference, it constitutes prior art. This rejection under pre-AIA 35 U.S.C. 102(e) might be overcome either by a showing under 37 CFR 1.132 that any invention disclosed but not claimed in the reference was derived from the inventor or joint inventors (i.e., the inventive entity) of this application and is thus not the invention “by another,” or if the same invention is not being claimed, by an appropriate showing under 37 CFR 1.131(a).
Claim 1 discloses a method. Claim 14 discloses a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system. Claim 15 discloses a system comprising the computer product of claim 14 and one or more processors for executing instructions stored on the computer readable medium. Claim 16 discloses a system comprising: an enrichment system configured to enrich a biological sample for nucleic acid molecules in a target region to form an enriched biological sample; a sequencing device configured to sequence a plurality of nucleic molecules in the enriched biological sample; and a computer system comprising: a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system; and one or more processors for executing instructions stored on the computer readable medium. The method of claim 1 and the instructions of claims 14-16 are for determining a fractional concentration of fetal DNA in a biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids.
US 2009/0087847 discloses methods (claim 1), systems, and apparatus for determining whether a nucleic acid sequence imbalance exists within a biological sample (abstract). US 2009/0087847 teaches computer readable media encoded with the program code (claims 14-16) and computer systems with processors (claims 15-16) for performing the method [0307-0309]. US 2009/0087847 teaches oligonucleotide arrays for hybridization based techniques (i.e., an enrichment system as in claim 16) [0273]. US 2009/0087847 teaches platforms for sequencing (i.e., a sequencing device as in claim 16) [0176; 0262]. US 2009/0087847 teaches that the sample may be maternal plasma containing fetal DNA (abstract).
The method of claim 1 comprises:
enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region;
sequencing a plurality of nucleic acid molecules from the enriched biological sample to obtain sequencing results, the sequencing being specific to the target region.
US 2009/0087847 teaches that a fraction of the nucleic acid pool that is sequenced in a run is further sub-selected prior to sequencing, by for example, hybridization based techniques such as oligonucleotide array to first sub-select for nucleic acid sequences from certain chromosomes [0273; see 0262-0264; 0269].
The instructions of claims 14-16 comprise:
receiving sequencing results of a sequencing of a plurality of nucleic acid molecules from an enriched biological sample, the enriched biological sample being enriched for nucleic acid molecules in a target region, the sequencing being specific to the target region.
US 2009/0087847 teaches that a fraction of the nucleic acid pool that is sequenced in a run is further sub-selected prior to sequencing, by for example, hybridization based techniques such as oligonucleotide array to first sub-select for nucleic acid sequences from certain chromosomes [0273; 0269].
The method of claim 1 and the instructions of claims 14-16 further comprise:
wherein the sequencing results are analyzed to: identify a location of the nucleic acid molecule in the target region of the human genome; and determine a respective allele of the nucleic acid molecule;
US 2009/0087847 teaches a bioinformatics procedure to locate each DNA sequence to the human genome [0265]. As US 2009/0087847 teaches using fetal-specific alleles at [0278] (see below), it is considered that US 2009/0087847 fairly teaches determining a respective allele of the nucleic acid molecule as instantly recited.
determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele; for at least one of the first loci: determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and determining the fractional concentration based on the first and second numbers.
US 2009/0087847 teaches determining the fractional concentration of fetal DNA through the quantification of polymorphic differences between the pregnant women and the fetus by targeting polymorphic sites at which the pregnant woman is homozygous and the fetus is heterozygous, where the amount of fetal-specific allele (i.e., P) can be compared with the amount of the common allele (i.e., Q) to determine the fractional concentration of fetal DNA [0278].
Regarding claim 7, US 2009/0087847 teaches the method of claim 1 as described above. Claim 7 further adds that enriching the biological sample comprises performing solution phase capture, microarray capture, or targeted amplification.
US 2009/0087847 teaches that a fraction of the nucleic acid pool that is sequenced in a run is further sub-selected prior to sequencing, by for example, hybridization based techniques such as oligonucleotide array to first sub-select for nucleic acid sequences from certain chromosomes (i.e., microarray capture) [0273; see 0262-0264].
Regarding claim 8, US 2009/0087847 teaches the method of claim 1 as described above. Claim 8 further adds that sequencing the plurality of nucleic acid molecules comprises sequencing both ends of each nucleic acid molecule of the plurality of nucleic acid molecules.
US 2009/0087847 teaches paired end sequencing [0272].
Regarding claim 9, US 2009/0087847 teaches the method of claim 1 as described above. Claim 9 further adds that sequencing the plurality of nucleic acid molecules comprises random sequencing of the enriched biological sample.
US 2009/0087847 teaches random sequencing of DNA fragments that are present in the plasma of a pregnant woman [0264; 0279].
Regarding claim 10, US 2009/0087847 teaches the method of claim 1 as described above. Claim 10 further adds determining the number of molecules to be analyzed at a first locus of the one or more first loci using an assumed value of fractional concentration of fetal DNA and a target probability of detecting the respective first allele at the first locus.
US 2009/0087847 teaches that if maternal serum is used, it is expected that more sequences would need to be generated (i.e., determine a number of molecules to be analyzed) for fetal chromosomal aneuploidy to be diagnosed (i.e., a target probability of detecting), when compared with a plasma sample obtained from the same pregnant woman at the same time because it is expected that the fractional concentration of fetal DNA will be lower (i.e., an assumed value of fractional concentration of fetal DNA) in maternal plasma than maternal serum [0277].
B. Claims 1, 7-10, and 14-16 are rejected under pre-AIA 35 U.S.C. 102(e) as being anticipated by Lo et al. (US 2009/0029377; newly cited; priority to Jul 23 2007; filed Jul 23 2008).
The applied reference has a common assignee and joint inventor with the instant application. Based upon the pre-AIA 35 U.S.C. 102(e) date of the reference, it constitutes prior art. This rejection under pre-AIA 35 U.S.C. 102(e) might be overcome either by a showing under 37 CFR 1.132 that any invention disclosed but not claimed in the reference was derived from the inventor or joint inventors (i.e., the inventive entity) of this application and is thus not the invention “by another,” or if the same invention is not being claimed, by an appropriate showing under 37 CFR 1.131(a).
Claim 1 discloses a method. Claim 14 discloses a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system. Claim 15 discloses a system comprising the computer product of claim 14 and one or more processors for executing instructions stored on the computer readable medium. Claim 16 discloses a system comprising: an enrichment system configured to enrich a biological sample for nucleic acid molecules in a target region to form an enriched biological sample; a sequencing device configured to sequence a plurality of nucleic molecules in the enriched biological sample; and a computer system comprising: a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system; and one or more processors for executing instructions stored on the computer readable medium. The method of claim 1 and the instructions of claims 14-16 are for determining a fractional concentration of fetal DNA in a biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids.
US 2009/0029377 discloses methods (claim 1), systems, and apparatus for performing prenatal diagnosis of a fetal chromosomal aneuploidy in a biological sample obtained from a pregnant female subject (abstract). US 2009/0029377 teaches computer readable media encoded with the program code (claims 14-16) and computer systems with processors (claims 15-16) for performing the method [0122-0124]. Lo teaches oligonucleotide arrays for hybridization based techniques (i.e., an enrichment system as in claim 16) [0072]. US 2009/0029377 teaches platforms for sequencing (i.e., a sequencing device as in claim 16) [0056; 0073; 0087]. US 2009/0029377 teaches that the sample may be maternal plasma containing fetal DNA (abstract).
The method of claim 1 comprises:
enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region;
sequencing a plurality of nucleic acid molecules from the enriched biological sample to obtain sequencing results, the sequencing being specific to the target region.
US 2009/0029377 teaches that a fraction of the nucleic acid pool that is sequenced in a run is further sub-selected prior to sequencing, by for example, hybridization based techniques such as oligonucleotide array to first sub-select for nucleic acid sequences from certain chromosomes [0072; 0079].
The instructions of claims 14-16 comprise:
receiving sequencing results of a sequencing of a plurality of nucleic acid molecules from an enriched biological sample, the enriched biological sample being enriched for nucleic acid molecules in a target region, the sequencing being specific to the target region.
US 2009/0029377 teaches that a fraction of the nucleic acid pool that is sequenced in a run is further sub-selected prior to sequencing, by for example, hybridization based techniques such as oligonucleotide array to first sub-select for nucleic acid sequences from certain chromosomes [0072; 0079].
The method of claim 1 and the instructions of claims 14-16 further comprise:
wherein the sequencing results are analyzed to: identify a location of the nucleic acid molecule in the target region of the human genome; and determine a respective allele of the nucleic acid molecule;
US 2009/0029377 teaches a bioinformatics procedure to locate each DNA sequence to the human genome [0058]. As US 2009/0029377 teaches using fetal-specific alleles at [0008; 0107] (see below), it is considered that US 2009/0029377 fairly teaches determining a respective allele of the nucleic acid molecule as instantly recited.
determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele; for at least one of the first loci: determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and determining the fractional concentration based on the first and second numbers.
US 2009/0029377 teaches determining the fractional concentration of fetal DNA through the quantification of polymorphic differences between the pregnant women and the fetus by targeting polymorphic sites at which the pregnant woman is homozygous and the fetus is heterozygous, where the amount of fetal-specific allele (i.e., P) can be compared with the amount of the common allele (i.e., Q) to determine the fractional concentration of fetal DNA [0107].
Regarding claim 7, US 2009/0029377 teaches the method of claim 1 as described above. Claim 7 further adds that enriching the biological sample comprises performing solution phase capture, microarray capture, or targeted amplification.
US 2009/0087847 teaches that a fraction of the nucleic acid pool that is sequenced in a run is further sub-selected prior to sequencing, by for example, hybridization based techniques such as oligonucleotide array to first sub-select for nucleic acid sequences from certain chromosomes (i.e., microarray capture) [0072; 0079].
Regarding claim 8, US 2009/0029377 teaches the method of claim 1 as described above. Claim 8 further adds that sequencing the plurality of nucleic acid molecules comprises sequencing both ends of each nucleic acid molecule of the plurality of nucleic acid molecules.
US 2009/0087847 teaches paired end sequencing [0071].
Regarding claim 9, US 2009/0087847 teaches the method of claim 1 as described above. Claim 9 further adds that sequencing the plurality of nucleic acid molecules comprises random sequencing of the enriched biological sample.
US 2009/0087847 teaches enriching the pool of nucleic acids to be sequenced prior to random sequencing of a fraction of the enriched pool [0077].
Regarding claim 10, US 2009/0087847 teaches the method of claim 1 as described above. Claim 10 further adds determining the number of molecules to be analyzed at a first locus of the one or more first loci using an assumed value of fractional concentration of fetal DNA and a target probability of detecting the respective first allele at the first locus.
US 2009/0087847 teaches that if maternal serum is used, it is expected that more sequences would need to be generated (i.e., determine a number of molecules to be analyzed) for fetal chromosomal aneuploidy to be diagnosed (i.e., a target probability of detecting), when compared with a plasma sample obtained from the same pregnant woman at the same time because it is expected that the fractional concentration of fetal DNA will be lower (i.e., an assumed value of fractional concentration of fetal DNA) in maternal plasma than maternal serum [0106].
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
A1. Claims 2-4, 6, and 11 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over US 2009/0087847 and/or US 2009/0029377, as applied to claim 1 in the above pre-AIA 35 USC 102 rejection, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited).
Regarding claim 2, US 2009/0087847 and/or US 2009/0029377 teach the method of claim 1 as described above. Claim 2 further adds determining the paternal genome is homozygous for the respective first allele at each loci of the one or more first loci and determining the maternal genome is homozygous for the respective second allele at the same locus, which US 2009/0087847 and/or US 2009/0029377 does not teach.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, US 2009/0087847 and/or US 2009/0029377 teaches the method of claim 1 as described above. Claim 3 further adds determining a cutoff value for a number of predicted counts of the respective first allele at the specific locus, the cutoff value predicting whether the maternal genome is homozygous and the fetal genome is heterozygous, wherein the cutoff value is determine based on a statistical distribution of numbers of counts for different combinations of homozygosity and heterozygosity at the specific locus; based on the analysis of the sequencing results, detecting the respective first and second allele at the specific locus; determining a number of actual counts of the respective first allele based on the sequencing of the plurality of nucleic acid molecules from the biological sample; and determining the specific locus is one of the first loci when the number of actual counts is less than the cutoff value, which US 2009/0087847 and/or US 2009/0029377 do not teach.
However, Dhallan teaches possible ratios (i.e., cutoff value) for nucleotides based on an expected percentage of fetal DNA in the sample when the maternal SNP is homozygous and the fetal SNP is heterozygous, when both the maternal and fetal SNP is heterozygous, and when the maternal SNP is heterozygous and the fetal SNP is homozygous (TABLEs II-III). Dhallan teaches examining samples to determine whether the possible ratios are seen [0397].
Regarding claim 4, US 2009/0087847 and/or US 2009/0029377 teaches the method of claims 1 and 3 as described above. Claim 4 further adds that determining the cutoff value includes determining a statistical distribution for a maximum and a minimum fractional concentration, which US 2009/0087847 and/or US 2009/0029377 do not teach.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 6, US 2009/0087847 and/or US 2009/0029377 teaches the method of claims 1 and 3-4 as described above. Claim 6 further adds that the maximum and the minimum fractional concentration depend on the length of the pregnancy, which US 2009/0087847 and/or US 2009/0029377 do not teach.
However, Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 11, US 2009/0087847 and/or US 2009/0029377 teaches the method of claim 1 as described above. Claim 11 further adds, for a specific locus, comparing counts of the respective first allele to a cutoff value, and categorizing, using the comparison of the counts to the cutoff value, the locus as a locus where the mother is homozygous in the first allele and the fetus is heterozygous; the mother is heterozygous and the fetus is heterozygous; or the mother is heterozygous and the fetus is homozygous, which US 2009/0087847 and/or US 2009/0029377 do not teach.
However, Dhallan teaches ratios (i.e., cutoff value) for nucleotides when the maternal SNP is homozygous and the fetal SNP is heterozygous, when both the maternal and fetal SNP is heterozygous, and when the maternal SNP is heterozygous and the fetal SNP is homozygous (TABLE II).
Regarding claims 2-4, 6, and 11, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, US 2009/0087847 and/or US 2009/0029377 with Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method which can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031].
A2. Claim 5 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over US 2009/0087847 and/or US 2009/0029377, as applied to claim 1 in the above pre-AIA 35 USC 102 rejection, and in further view of Dhallan, as applied to claims 3-4 above, and in further view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited). Claim 12 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over US 2009/0087847 and/or US 2009/0029377, as applied to claim 1 in the above 35 USC 102 rejection, and in further view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited). Claim 13 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over US 2009/0087847 and/or US 2009/0029377, as applied to claim 1 in the above 35 USC 102 rejection, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited) and Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited).
Regarding claim 5, US 2009/0087847 and/or US 2009/0029377 teaches the method of claim 1, and in further view of Dhallan, of claims 3-4 as described above. Claim 5 further adds that the statistical distribution is a Poisson distribution, which US 2009/0087847 and/or US 2009/0029377 do not teach.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 12, US 2009/0087847 and/or US 2009/0029377 teaches the method of claim 1 as described above. Claim 12 further adds that the fractional concentration is determined as 2xP/(P+Q), which US 2009/0087847 and/or US 2009/0029377 do not teach.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, US 2009/0087847 and/or US 2009/0029377 teaches the method of claim 1 as described above. Claim 13 further adds that P and Q are determined for a plurality of first loci, and where the fractional concentration f is determined as
PNG
media_image2.png
48
134
media_image2.png
Greyscale
, where pi is the first number for the ith first loci and qi is the second number for the ith first loci, which US 2009/0087847 and/or US 2009/0029377 do not teach.
Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, US 2009/0087847 and/or US 2009/0029377, Dhallan, and Lun because each disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of Dhallan, because Dhallan teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
B1. Claims 1-4, 6-7, 9-11, and 14-16 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over the features of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited).
The prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan, indicated by the open circles, teaches the instant features, indicated by the closed circles, as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 1 discloses a method. Claim 14 discloses a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system. Claim 15 discloses a system comprising the computer product of claim 14 and one or more processors for executing instructions stored on the computer readable medium. Claim 16 discloses a system comprising: an enrichment system configured to enrich a biological sample for nucleic acid molecules in a target region to form an enriched biological sample; a sequencing device configured to sequence a plurality of nucleic molecules in the enriched biological sample; and a computer system comprising: a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system; and one or more processors for executing instructions stored on the computer readable medium. The method of claim 1 and the instructions of claims 14-16 are for determining a fractional concentration of fetal DNA in a biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids.
Dhallan teaches analyzing samples containing fetal DNA and maternal DNA from a pregnant female [0034] and examining genetic contributions from the father [0389].
Dhallan does not teach the computer elements as instantly claimed in claim 14-16. However, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
The method of claim 1 comprises:
enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region;
sequencing a plurality of nucleic acid molecules from the enriched biological sample to obtain sequencing results, the sequencing being specific to the target region.
Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367].
The instructions of claims 14-16 comprise:
wherein the sequencing results are analyzed to: identify a location of the nucleic acid molecule in the target region of the human genome; and determine a respective allele of the nucleic acid molecule.
Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367]. The amplification of the sequence of interest is considered to read on an enrichment system as instantly recited in claim 16.
The method of claim 1 and the instructions of claims 14-16 further comprise:
wherein the sequencing results are analyzed to: identify a location of the nucleic acid molecule in the target region of the human genome; and determine a respective allele of the nucleic acid molecule;
Dhallan teaches determining the sequence of alleles of a locus of interest on template DNA [0033].
determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele; for at least one of the first loci: determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and determining the fractional concentration based on the first and second numbers.
Dhallan teaches determining sequences of multiple loci of interest that are suspected of containing a single nucleotide polymorphism [0060]. Dhallan teaches quantitating a ratio for the alleles at a heterozygous locus of interest that was identified from the locus of interest [0033]. Dhallan teaches that the sequence of the alleles of multiple loci of interest on maternal template DNA is determined to identify homozygous loci of interest [0380]. Dhallan teaches that from the population of homozygous maternal loci of interest, there will be both heterozygous and homozygous loci of interest from the template DNA from the sample from the pregnant female; the heterozygous loci of interest can be further analyzed; at heterozygous loci of interest, the ratio of alleles can be used to determine the number of chromosomes that are present [0383]. Dhallan teaches that the percentage of fetal DNA present in the sample from the pregnant female can be calculated by determining the ratio of alleles at a heterozygous locus of interest on a chromosome that is not typically associated with a chromosomal abnormality [0384-0388]. Dhallan teaches at [0385]: “SNP X is homozygous at the maternal template DNA (A/A). At SNP X, the template DNA from the sample from the pregnant female, which can contain both fetal DNA and maternal DNA, is heterozygous (A/G). The nucleotide guanine represents the fetal DNA because at SNP X the mother is homozygous, and thus the guanine is attributed to the fetal DNA. The guanine at SNP X can be used to calculate the percentage (i.e., fractional concentration) of fetal DNA in the sample.”.
Regarding claim 2, the features of Dhallan teaches the method of claim 1 as described above. Claim 2 further adds determining the paternal genome is homozygous for the respective first allele at each loci of the one or more first loci and determining the maternal genome is homozygous for the respective second allele at the same locus.
Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, the features of Dhallan teaches the method of claim 1 as described above. Claim 3 further adds determining a cutoff value for a number of predicted counts of the respective first allele at the specific locus, the cutoff value predicting whether the maternal genome is homozygous and the fetal genome is heterozygous, wherein the cutoff value is determine based on a statistical distribution of numbers of counts for different combinations of homozygosity and heterozygosity at the specific locus; based on the analysis of the sequencing results, detecting the respective first and second allele at the specific locus; determining a number of actual counts of the respective first allele based on the sequencing of the plurality of nucleic acid molecules from the biological sample; and determining the specific locus is one of the first loci when the number of actual counts is less than the cutoff value.
Dhallan teaches possible ratios (i.e., cutoff value) for nucleotides based on an expected percentage of fetal DNA in the sample when the maternal SNP is homozygous and the fetal SNP is heterozygous, when both the maternal and fetal SNP is heterozygous, and when the maternal SNP is heterozygous and the fetal SNP is homozygous (TABLEs II-III). Dhallan teaches examining samples to determine whether the possible ratios are seen [0397].
Regarding claim 4, the features of Dhallan teaches the method of claims 1 and 3 as described above. Claim 4 further adds that determining the cutoff value includes determining a statistical distribution for a maximum and a minimum fractional concentration.
Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 6, the features of Dhallan teaches the method of claims 1 and 3-4 as described above. Claim 6 further adds that the maximum and the minimum fractional concentration depend on the length of the pregnancy.
Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, the features of Dhallan teaches the method of claim 1 as described above. Claim 7 further adds that enriching the biological sample comprises performing solution phase capture, microarray capture, or targeted amplification.
Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying (i.e., targeted amplification) or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367].
Regarding claim 9, the features of Dhallan teaches the method of claim 1 as described above. Claim 9 further adds that sequencing the plurality of nucleic acid molecules comprises random sequencing of the enriched biological sample.
Dhallan teaches that any method that provides information on the sequence of a nucleic acid can be used including DNA sequencing [0235], which reads on random sequencing as instantly claimed because the DNA sequencing has not been limited to targeted sequencing.
Regarding claim 10, the features of Dhallan teaches the method of claim 1 as described above. Claim 10 further adds determining the number of molecules to be analyzed at a first locus of the one or more first loci using an assumed value of fractional concentration of fetal DNA and a target probability of detecting the respective first allele at the first locus.
Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, the features of Dhallan teaches the method of claim 1 as described above. Claim 11 further adds, for a specific locus, comparing counts of the respective first allele to a cutoff value, and categorizing, using the comparison of the counts to the cutoff value, the locus as a locus where the mother is homozygous in the first allele and the fetus is heterozygous; the mother is heterozygous and the fetus is heterozygous; or the mother is heterozygous and the fetus is homozygous.
Dhallan teaches ratios (i.e., cutoff value) for nucleotides when the maternal SNP is homozygous and the fetal SNP is heterozygous, when both the maternal and fetal SNP is heterozygous, and when the maternal SNP is heterozygous and the fetal SNP is homozygous (TABLE II).
B2. Claims 5 and 12-13 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over the features of Dhallan, as applied to claims 1 and 3-4 as above, and in further view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited).
Regarding claim 5, the features of Dhallan teaches the method of claims 1 and 3-4 as described above. Claim 5 further adds that the statistical distribution is a Poisson distribution, which Dhallan does not teach.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 12, the features of Dhallan teaches the method of claim 1 as described above. Claim 12 further adds that the fractional concentration is determined as 2xP/(P+Q), which Dhallan does not teach.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the features of Dhallan teaches the method of claim 1 as described above. Claim 13 further adds that P and Q are determined for a plurality of first loci, and where the fractional concentration f is determined as
PNG
media_image2.png
48
134
media_image2.png
Greyscale
, where pi is the first number for the ith first loci and qi is the second number for the ith first loci.
Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Dhallan and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of Dhallan, because Dhallan teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
B3. Claim 8 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over the features of Dhallan as applied to claim 1 above, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claim 8, the features of Dhallan teaches the method of claim 1 as described above. Claim 8 further adds that sequencing the plurality of nucleic acid molecules comprises sequencing both ends of each nucleic acid molecule of the plurality of nucleic acid molecules, which Dhallan does not teach.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Dhallan and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by Dhallan, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of Dhallan.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
A. Claims 1-4, 9, 11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, 33-36, and 47 of U.S. Patent No. 10900080. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Claims 5 and 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, 33-36, and 47 of U.S. Patent No. 10900080 in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 6-7 and 10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, 33-36, and 47 of U.S. Patent No. 10900080, as applied to claim 1, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, 33-36, and 47 of U.S. Patent No. 10900080, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the method of reference claims 1 and 33 teach the method of instant claim 1. Reference claims 1 and 33 disclose enriching the biological sample for DNA fragments in a set of chromosomal regions; performing massively parallel sequencing of DNA fragments in the enriched biological sample, thereby analyzing the fetal and maternal cell-free DNA fragments to obtain sequence reads, obtaining data about alleles of the DNA fragments, determining, by the computer system, a genotype of the pregnant female at each of one or more first loci within a first chromosomal region, the pregnant female being homozygous at each of the one or more first loci or being heterozygous at each of the one or more first loci; for each first locus of the one or more first loci: identifying, by the computer system, a primary allele and a secondary allele in the biological sample using the data, wherein the primary allele is more abundant than the secondary allele at the first locus in the biological sample; determining, by the computer system at the one or more first loci, a first amount of the one or more primary alleles and/or a second amount of the one or more secondary alleles in the biological sample using the data, the first amount corresponding to a quantity of DNA fragments having the one or more primary alleles in the biological sample, and the second amount corresponding to a quantity of DNA fragments having the one or more secondary alleles in the biological sample.
The reference claims do not disclose the computer elements of claims 14-16.
Further, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
Regarding claim 2, reference claims 33-35 and 36 disclose the limitations of instant claim 2.
Regarding claim 3, reference claims 1 and 33 disclose the limitations of instant claim 3.
Regarding claim 4, reference claim 47 discloses the limitations of instant claim 4.
Regarding claim 5, the reference claims do not disclose the limitations of claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of claim 6.
However, The prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, the reference claims do not disclose the limitations of claim 7.
However, Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying (i.e., targeted amplification) or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367].
Regarding claim 8, the reference claims do not disclose the limitations of claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claim 10 discloses the limitations of claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claim 11 discloses the limitations of claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of claim 12.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of claim 13.
Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 6-7 and 10, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031]. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
B. Claims 1-7 and 9-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 8, 10, 14-15, 17, 21, and 49 of U.S. Patent No. 10152568 in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 8, 10, 14-15, 17, 21, and 49 of U.S. Patent No. 10152568 in view of Dhallan, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the method of reference claim 1 and the system of reference claim 49 disclose the statutory categories of the instant claims. Reference claim 21 discloses sequencing the nucleic acid molecules. Reference claim 5 discloses obtaining the percentage of fetal nucleic acid molecules Pf includes: detecting a first allele in the reactions, wherein the first allele is shared by the mother and fetus at a locus where the pregnant female is homozygous and the fetus is either heterozygous or hemizygous.
The reference claims do not disclose enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region as recited in claim 1, receiving the enriched and sequenced nucleic acid sequencing results in claims 14-16, or the enrichment system of claim 16.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367]. The amplification of the sequence of interest is considered to read on an enrichment system as instantly recited in claim 16.
Regarding claim 2, reference claim 8 discloses the limitations of instant claim 2.
Regarding claim 3, reference claims 1 and 49 disclose the limitations of instant claim 3.
Regarding claim 4, reference claim 4 disclose the limitations of instant claim 4 except for a maximum and a minimum fractional concentration.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, reference claims 5, 15, and 17 disclose the limitations of instant claim 5.
Regarding claim 6, the reference claims do not disclose the limitations of instant claim 6.
However, Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, reference claims 15 disclose the limitations of instant claim 7.
Regarding claim 8, the reference claims do not disclose the limitations of instant claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claims 14 and 21 disclose the limitations of instant claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 1, 5, and 49 disclose the limitations of instant claim 11.
Regarding claim 12, reference claim 10 disclose the limitations of instant claim 12.
Regarding claim 13, reference claim 10 disclose the limitations of instant claim 13 except for summing the equation.
However, Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
Regarding claims 1-16, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031]. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
C. Claims 1-7, 9-11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10, 15-16, and 18 copending Application No. 18/656,503 in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10, 15-16, and 18 of copending Application No. 18/656,503 in view of Dhallan, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited). Claims 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10, 15-16, and 18 of copending Application No. 18/656,503 in view of Dhallan, as applied to claim 1, and in further view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited).
This is a provisional nonstatutory double patenting rejection.
Regarding claims 1 and 14-16, the method of reference claim 1 discloses the method of the claims. Reference claim 15 discloses sequencing the nucleic acid molecules. Reference claim 7 discloses that measuring the fetal percentage Pf includes: detecting a first allele in the reactions, wherein the first allele is shared by the pregnant female and the male fetus at a locus where the pregnant female is homozygous and the male fetus is either heterozygous or hemizygous.
The reference claims do not disclose enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region as recited in claim 1, receiving the enriched and sequenced nucleic acid sequencing results in claims 14-16, or the computer elements of claims 14-16.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367]. The amplification of the sequence of interest is considered to read on an enrichment system as instantly recited in claim 16.
Further, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
Regarding claim 2, reference claim 10 discloses the limitations of instant claim 2.
Regarding claim 3, reference claim 1 discloses the limitations of instant claim 3.
Regarding claim 4, reference claim 6 disclose the limitations of instant claim 4 except for a maximum and a minimum fractional concentration.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, reference claims 7 and 18 disclose the limitations of instant claim 5.
Regarding claim 6, the reference claims do not disclose the limitations of instant claim 6.
However, Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, reference claims 16 disclose the limitations of instant claim 7.
Regarding claim 8, the reference claims do not disclose the limitations of instant claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claims 15 discloses the limitations of instant claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 1 and 7 disclose the limitations of instant claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of instant claim 12.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of instant claim 13 except for summing the equation.
However, Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 1-16, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031]. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
Regarding claims 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
D. Claims 1, 3, 7, 9, 11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6-8, 13, 15-16, 19, 21, and 24 of U.S. Patent No. 10208348. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Claims 2, 4, 6, and 10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6-8, 13, 15-16, 19, 21, and 24 of U.S. Patent No. 10208348, as applied to claim 1, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 5 and 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6-8, 13, 15-16, 19, 21, and 24 of U.S. Patent No. 10208348, as applied to claim 1, in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6-8, 13, 15-16, 19, 21, and 24 of U.S. Patent No. 10208348, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the method of reference claims 1 and 19 disclose the statutory categories of the claims. Reference claims 6-8, 15-16, and 24 disclose enriching the biological sample for the one or more clinically relevant nucleic acid sequences and the one or more background nucleic acid sequences. Reference claims 13 and 19 disclose sequencing. Reference claims 1 and 19 disclose measuring a fractional concentration of fetal DNA in a biological sample of a female subject pregnant with a fetus, the biological sample including a mixture of cell-free nucleic acid molecules from the female subject and from the fetus, and wherein the female subject is homozygous at a first locus for a first allele and the fetus is heterozygous at the first locus for the first allele and a second allele different from the first allele and comparing, by the computer system, the first number to the second number to measure the fractional concentration of fetal DNA.
Regarding claim 2, the reference claims do not disclose the limitations of instant claim 2.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, reference claims 3 and 21 discloses the limitations of instant claim 3.
Regarding claim 4, the reference claims do not disclose the limitations of instant claim 4.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, the reference claims do not disclose the limitations of instant claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of instant claim 6.
Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, reference claims 7-8 and 16 disclose the limitations of instant claim 7.
Regarding claim 8, the reference claims do not disclose the limitations of instant claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claims 13 and 29 disclose the limitations of instant claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 3 and 21 discloses the limitations of instant claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of instant claim 10.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 2, 4, 6, and 10, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031]. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Sun for each locus.
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Sun for each locus.
E. Claims 1, 3, 7, 9, 11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 8-11, and 14-17 of U.S. Patent No. 11725245. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Claims 2, 4, 6, and 10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 8-11, and 14-17 of U.S. Patent No. 11725245, as applied to claim 1, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 5 and 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 8-11, and 14-17 of U.S. Patent No. 11725245, as applied to claim 1, in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 8-11, and 14-17 of U.S. Patent No. 11725245, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the method of reference claims 1 disclose the method of claim 1. The reference claims do not disclose computer elements of claims 14-16. However, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
Reference claims 8-11 and 14 discloses enriching the biological sample for the one or more clinically relevant nucleic acid sequences and the one or more background nucleic acid sequences. Reference claim 4 discloses sequencing. Reference claims 15-17 disclose determining a fractional concentration of fetal DNA in the biological sample; and using the fractional concentration of fetal DNA to determine the one or more cutoff values and identifying a target polymorphic site at which the female subject is homozygous and the fetus is heterozygous; and comparing an amount of a fetal-specific allele at the target polymorphic site and an amount of a common allele at the target polymorphic site to determine the fractional concentration of fetal DNA, the common allele not being fetal-specific.
Regarding claim 2, the reference claims do not disclose the limitations of instant claim 2.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, reference claims 1 and 15 discloses the limitations of instant claim 3.
Regarding claim 4, the reference claims do not disclose the limitations of instant claim 4.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, the reference claims do not disclose the limitations of instant claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of instant claim 6.
Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, reference claims 8-11 and 14 disclose the limitations of instant claim 7.
Regarding claim 8, the reference claims do not disclose the limitations of instant claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claim 4 discloses the limitations of instant claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 1 and 15 discloses the limitations of instant claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of instant claim 10.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 2, 4, 6, and 10, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031].
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Sun for each locus.
F. Claims 1-4, 6-7, 9-11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 9-10 13-17 22-23 of U.S. Patent No. 12227804 in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 5 and 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims, as applied to claim 1, in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the reference claims 1 and 26-27 disclose the statutory categories of the claims. Reference claims 10 and 14-17 disclose enriching the biological sample for the one or more clinically relevant nucleic acid sequences and the one or more background nucleic acid sequences. Reference claims 13-14 and 22-23 disclose sequencing. Reference claims 4-7 disclose determining a fractional concentration of tumor DNA in the biological sample and identifying a target polymorphic site at which the non-malignant cells are homozygous and the tumor cells are heterozygous; and comparing an amount of a tumor-specific allele at the target polymorphic site and an amount of a common allele at the target polymorphic site to determine the fractional concentration of tumor DNA, the common allele not being tumor-specific.
The reference claims do not disclose a biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches analyzing samples containing fetal DNA and maternal DNA from a pregnant female [0034] and examining genetic contributions from the father [0389].
Regarding claim 2, the reference claims do not disclose the limitations of instant claim 2.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, reference claims 2-4 discloses the limitations of instant claim 3.
Regarding claim 4, the reference claims do not disclose the limitations of instant claim 4.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, the reference claims do not disclose the limitations of instant claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of instant claim 6.
Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, reference claims 10 and 14-17 disclose the limitations of instant claim 7.
Regarding claim 8, the reference claims do not disclose the limitations of instant claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claim 13-14 and 22-23 discloses the limitations of instant claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 2-4 discloses the limitations of instant claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of instant claim 10.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 1-4, 6-7, 9-11, and 14-16, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031].
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Sun for each locus.
G. Claims 1, 3, 7, 9, 11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 10, and 12-14 of copending application 18/336579. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Claims 2, 4, 6, and 10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 10, and 12-14 of copending application 18/336579, as applied to claim 1, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 5 and 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 10, and 12-14 of copending application 18/336579, as applied to claim 1, in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 10, and 12-14 of copending application 18/336579, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
This is a provisional nonstatutory double patenting rejection.
Regarding claims 1 and 14-16, the method of reference claims 1 disclose the method of claim 1. The reference claims do not disclose computer elements of claims 14-16. However, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
Reference claims 1 and discloses enriching the biological sample for the one or more clinically relevant nucleic acid sequences and the one or more background nucleic acid sequences and sequencing. Reference claims 12-14 disclose determining a fractional concentration of fetal DNA in the biological sample and identifying a target polymorphic site at which the female subject is homozygous and the fetus is heterozygous; and comparing an amount of a fetal-specific allele at the target polymorphic site and an amount of a common allele at the target polymorphic site to determine the fractional concentration of fetal DNA, the common allele not being fetal-specific.
Regarding claim 2, the reference claims do not disclose the limitations of instant claim 2.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, reference claims 10 and 12 discloses the limitations of instant claim 3.
Regarding claim 4, the reference claims do not disclose the limitations of instant claim 4.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, the reference claims do not disclose the limitations of instant claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of instant claim 6.
Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, reference claim 3 discloses the limitations of instant claim 7.
Regarding claim 8, the reference claims do not disclose the limitations of instant claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claim 6 discloses the limitations of instant claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 10 and 12 discloses the limitations of instant claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of instant claim 10.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of instant claim 10.
However, Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 2, 4, 6, and 10, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031].
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Sun for each locus.
H. Claims 1-4, 9, and 11-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 13, 19, 29-33, and 37 of U.S. Patent No. 8467976. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Claims 5 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 13, 19, 29-33, and 37 of U.S. Patent No. 8467976 in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 6-7 and 10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 13, 19, 29-33, and 37 of U.S. Patent No. 8467976, as applied to claim 1, and in further view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 13, 19, 29-33, and 37 of U.S. Patent No. 8467976, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the method of reference claim 29 teaches the method of instant claim 1, and reference claim 33 discloses a computer product comprising a non-transitory computer readable medium of claim 14. Reference claim 29 discloses all of the limitations of the method steps of instant claims 1 and 14-16 except for enriching the biological sample for nucleic acids in a target region of a genome and sequencing, which is discloses by reference claim 19.
The reference claims do not disclose the computer elements of claims 15-16.
However, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
Regarding claim 2, reference claims 33 and 37 disclose the limitations of instant claim 2.
Regarding claim 3, reference claim 29 discloses the limitations of instant claim 3.
Regarding claim 4, reference claim 32 discloses the limitations of instant claim 4.
Regarding claim 5, the reference claims do not disclose the limitations of claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of claim 6.
However, The prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, the reference claims do not disclose the limitations of claim 7.
However, Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying (i.e., targeted amplification) or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367].
Regarding claim 8, the reference claims do not disclose the limitations of claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claim 13 discloses the limitations of claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claim 29 discloses the limitations of claim 11.
Regarding claim 12, reference claim 30 discloses the limitations of claim 12.
Regarding claim 13, reference claim 31 discloses the limitations of claim 13.
Regarding claims 6-7 and 10, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031]. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
Regarding claim 5, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation to assume the molecules are in a Poisson distribution would have been to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
I. Claims 1-4, 6-7, 9-11, and 14-16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-45 of U.S. Patent No. 10457990 in view of Dhallan et al. (US 2007/0178478; corresponds to IDS reference WO 2007/075836; newly cited). Claims 5 and 12-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims , as applied to claim 1, and in view of Lun et al. (Clinical Chemistry, Oct 1 2008, 54(10), pp.1664-1672; newly cited), and claim 13 further. Claim 8 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims, as applied to claim 1, and in further view of Ng et al. (Nucleics Acid Research, 2006, 34(12):e84, p. 1-10; newly cited).
Regarding claims 1 and 14-16, the method of reference claims 1-39 teach the method of instant claim 1 and the computer product of claims 40-45 disclose the computer product of claim 14. Reference claims 1-39 disclose all of the limitations of instant claims 1 and 14-16 except for enriching the sample.
However, the prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367].
The reference claims do not disclose the computer elements of claims 15-16.
However, it would have been obvious to include these computing elements to automate the method steps of the invention. The motivation would have been to automate a manual activity, as the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); see MPEP § 2144.04).
Regarding claim 2, the reference claims do not disclose the limitations of claim 2.
However, Dhallan teaches that the biological father can be genotyped to identify a homozygous locus of interest, and the locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA [0403].
Regarding claim 3, reference claims 31-32 disclose the limitations of instant claim 3.
Regarding claim 4, the reference claims do not disclose the limitations of instant claim 4.
However, Dhallan teaches determining possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as described above, based on the differing theoretical amounts of fetal DNA ([0389-0390]; TABLEs II-III). Dhallan teaches that the fetal DNA in the sample can comprise at least 15% to 99.5% [0179] or between different ranges [0180-1081]. Dhallan does not teach calculating a maximum and a minimum fractional concentration as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to calculate the possible ratios for nucleotides at different combinations of maternal and fetal SNP heterozygosities, as taught by Dhallan in TABLEs II-III, for a minimum and maximum amount of fetal DNA in a sample based on the disclosed ranges and amounts disclosed, where those upper and lower bounds of the ranges are considered to read on a minimum and maximum amount of fetal DNA in a sample. Such a modification would be obvious because Dhallan already teaches each of the elements as claimed, and it would be obvious to apply the calculation of the expected ratios to any amount of fetal DNA in a sample.
Regarding claim 5, the reference claims do not disclose the limitations of claim 5.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, where the molecules are assumed to be in a Poisson distribution in order to determine the original number of molecules derived from chromosomes X and Y (p. 1667, col. 1, par. 2; p. 1665, col. 2, par. 4).
Regarding claim 6, the reference claims do not disclose the limitations of claim 6.
However, The prior art to Dhallan discloses a non-invasive method for the detection of chromosomal abnormalities in a fetus, comprising determining the sequence of alleles of a locus of interest, and quantitating a ratio for the alleles at the locus of interest, wherein the ratio indicates the presence or absence of a chromosomal abnormality (abstract). Dhallan teaches that fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy [0030]. Dhallan does not teach a maximum and minimum fractional concentration dependent on the length of the pregnancy as instantly claimed.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, to modify the method of Dhallan to base the possible ratios of SNPs on increasing amounts of fetal DNA based on the length of the pregnancy, as the amount of fetal DNA is known to increase throughout pregnancy [0030].
Regarding claim 7, the reference claims do not disclose the limitations of claim 7.
However, Dhallan teaches obtaining a sample from a pregnant female [0033; 0041-0042] and determining the sequence of alleles of multiple loci of interest on a single chromosome [0045] by amplifying (i.e., targeted amplification) or purifying a sequence of interest and determining the sequence [0047-0048; 0221-0225; 0290-0301] using sequencing [0046; 0058; 0235; 0365; 0367].
Regarding claim 8, the reference claims do not disclose the limitations of claim 8.
However, the prior art to Ng discloses methods for paired-end multiplex sequencing of DNA (abstract; entire document is relevant), which reads on sequencing both ends of each nucleic acid molecule as supported by the instant specification as published at [0071].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Ng because both references disclose methods for DNA sequencing. The motivation would have been to perform paired-end sequencing as taught by Ng would have been to use and efficient and accurate sequencing technique for large-scale genome analysis, as taught by Ng (abstract). The use of paired-end sequencing as taught by Ng is a therefore a simple substitution of one general sequencing technique, as taught by the reference patent, for the more specific technique of paired-end sequencing, the substitution of which one of ordinary skill in the art would have been expected to produce predictable results of sequencing the maternal plasma sample of the reference patent.
Regarding claim 9, reference claim 11 discloses the limitations of claim 9.
Regarding claim 10, the reference claims do not disclose the limitations of claim 10.
However, Dhallan teaches analyzing more SNPs (i.e., determining a number of molecules to be analyzed) by sequencing larger numbers of SNPs for higher accuracy (i.e., a target probability) with samples that contain lower percentages of fetal DNA (i.e., an assumed fraction concentration) [1291].
Regarding claim 11, reference claims 31-32 discloses the limitations of claim 11.
Regarding claim 12, the reference claims do not disclose the limitations of claim 12.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claim 13, the reference claims do not disclose the limitations of claim 13.
Dhallan teaches that the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed [0061; 0375-0376], but does not teach the equation as claimed.
However, the prior art to Lun discloses using digital PCR to measure circulating fetal DNA. Lun teaches counting the number of wells that were positive for ZFY, a Y-linked gene, and ZFX, an X-linked gene, to determine the number of each of the molecules, and, because each male fetal cell contains a copy of the ZFX and ZFY gene and each background maternal cell contains 2 copies of ZFX and no ZFY, calculating the proportion of fetal DNA in a maternal plasma sample based on the equation (2 x ZFY)/(ZFY + ZFX) x 100 (p. 1667, col. 1, par. 2-3; p. 1665, col. 2, par. 4).
Regarding claims 1-4, 6-7, 9-11, and 14-16, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Dhallan because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to use a method for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus, as taught by Dhallan [0031].
Regarding claims 5 and 12-13, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference patent and Lun because both disclose methods for determining the amount of fetal DNA in a maternal plasma sample. The motivation would have been to apply an equation for determining the fraction of molecules attributed to the fetus, as taught by Lun (p. 1667, col. 1, par. 3). It would have been obvious to one of ordinary skill in the art to use the equation taught by Lun for analyzing DNA from the fetus linked only to the Y chromosome to DNA from the fetus throughout the genome using the method of the reference application, because the reference application teaches identifying SNPs from the fetus and not the mother, as described above, to determine the amount of fetal DNA in the sample. Regarding claim 13, as Dhallan teaches summing the ratio of the alleles of interest [0061; 0375-0376], it further would have been obvious to sum the calculated proportion of fetal DNA as calculated using the equation of Lun for each locus.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached on (571)272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685