DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Please note: The examiner handling this application has changed. The new examiner on this case is Kailey Cash (kailey.cash@uspto.gov) in AU1683. Any correspondence relating to the instant application should be directed to this examiner.
Election/Restrictions
Applicant’s election without traverse of Group V (claim 53) in the reply filed on 10/3/2025 is acknowledged. Claims 54-78 are new and depend from claim 53.
Claims 53-78 are pending and being examined on the merits.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
The substitute specification provided does not adequately overcome the sequence disclosure deficiencies noted in the Requirement for Restriction/Election of 7/3/2025.
In paragraph [0021], 7 SEQ ID NOs are supplied for Figure 22, however there are 8 sequences in the figure. Additionally, there are 4 sequences supplied for Figure 23 but there are 5 sequences in the figure.
In paragraph [0022], 8 sequences are provided for Figure 26, but there are 9 sequences present.
In paragraph [0023], 9 sequences are provided for Figure 29 but there are 10 present in the figure. Additionally, there are 5 sequences provided for Figure 30, but there are 6 present in the figure.
It is unclear what sequences are missing from this disclosure. Additionally, the format of “in order of appearance” does not make it perfectly clear which sequence is being referred to, especially in instances such as Figure 29. Is the appearance of sequences top down through the left column and then through the right column or is it top down and then left to right through the rows?
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: Paragraphs [0020-0023] contain references to “SEQ ID NOS X-Y”. The proper notation for sequence identification numbers is “SEQ ID NO: X” or “SEQ ID NOs: X-Y”.
Appropriate correction is required.
The use of the term “Q5 Polymerase” (paragraph [00124 and 00127]) and “FAM” (paragraph [00126]), which are trade names or marks used in commerce, have been noted in this application. These terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are 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.
Claim Objections
Claims 53, 62, and 74 are objected to because of the following informalities:
Claim 53 reads “a variation region having a nucleotide sequence with sequence dissimilarity to the target sequence” and should read “a variation region having a second nucleotide sequence with sequence dissimilarity to the target sequence region”.
Claims 62 and 74 read “wherein determining the abundance of the target comprises determining the presence or absence of an aneuploidy based on the computed ratios” and should read “wherein determining the abundance of the target comprises determining the presence or absence of an aneuploidy based on the computed chromosome-specific ratios” to maintain consistent claim terminology throughout the claims, since claims 62 and 74 involve generating “a chromosome-specific ratio”.
Claim 74 reads “and for each length of a set of discrete lengths, adding a tail with the discrete length” and should read “and for each discrete length of a set of discrete lengths, adding a tail with the discrete length” to maintain claim consistency.
Appropriate correction is required.
Claim Rejections - 35 USC § 112b - Indefiniteness
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 53-78 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 53 recites the limitation “wherein each of the plurality of spike-in molecules further comprises: a target region having a first nucleotide sequence with sequence similarity to a target sequence region; a variation region having a nucleotide sequence with sequence dissimilarity to the target sequence”. This does not impart adequate structural information regarding the sequence of the spike-in molecules. It is unclear how this spike-in molecule would 1) differ from the endogenous target while still being able to be co-amplified by the same target-specific primers, and 2) how the spike-in molecule amplicon peak would be differentiated from its associated endogenous target amplicon peak. This is especially unclear given that no information is provided as to how peak data is calculated before being received (i.e., no information regarding the methodology to generate said peak data is provided). Further clarification is required.
Claim 53 contains the limitation “co-amplifying the mixture with target-specific primers to create a co-amplified mixture”. It is unclear if the target-specific primers are meant to amplify both the endogenous target (target-specific), or if these target specific primers would also amplify the spike-in molecules associated with each target. There is no limitation that the target-specific primers would also amplify the spike-in molecules. Co-amplification could mean that each endogenous target of a set of endogenous targets is being amplified at the same time with each of their own target-specific primers. For purposes of examination, it is being interpreted that the target-specific primers would also amplify the associated spike-in molecules, to be consistent with the depiction of the methodology in Figure 4. However, further clarification is required.
Claim 53 contains the limitation “labeling the co-amplified mixture by fluorescently labeled primers”. It is unclear what in the co-amplified mixture is being labeled. Are these primers specific for endogenous targets? Primers that anneal to the “dissimilar” sequence of the spike-in molecule? Primers that will anneal to both the spike-in molecule and its associated endogenous target? For purposes of examination, it is being interpreted that the fluorescently labeled primers are target/spike-in pair specific, meaning that each spike-in molecule and its associated endogenous target would be bound by the same fluorescently labeled primer. However, further clarification is required.
Claims 54-78 depend from claim 53, inherit these deficiencies, and are rejected on the same basis.
Claims 54, 62, 67, and 74 recite the limitation “determining the abundance of the target comprises determining the presence or absence of an aneuploidy based on the computed ratios”. It is unclear how the computed ratio between an endogenous target and its associated spike-in molecule would enable determination of an aneuploidy. “the computed ratios” as recited in this claim, depend from claim 53 in which “a computed ratio” is calculated between the spike-in molecule peak and its associated target peak. This would not provide the necessary information to determine an aneuploidy. Indeed, in the specification the example of determining an aneuploidy involves the comparison of individual computed ratios between two chromosomes (see specification paragraphs [0090-0091]). For the purposes of examination this claim is being interpreted to mean that the computed ratio between two different chromosome/spike-in molecule pairs are being compared to determine an aneuploidy, however clarification is required to render this claim definite.
Claims 55-57 depend from claim 54, inherit this deficiency, and are rejected on the same basis. Claims 63-66 depend from claim 62, inherit this deficiency, and are rejected on the same basis. Claims 68-73 depend from claim 67, inherit this deficiency, and are rejected on the same basis. Claims 75-78 depend from claim 74, inherit this deficiency, and are rejected on the same basis.
Claim 61 recites the limitation "the one or more fluorescently labeled primers". There is insufficient antecedent basis for this limitation in the claim.
Claim 67 recites the limitation “wherein co-amplifying the mixture comprises co-amplifying the mixture with one or more chromosome-specific primers to create a co-amplified mixture, wherein the one or more chromosome-specific primers are fluorescently labeled primers”. This limitation of the fluorescently labeled primers that are chromosome-specific is a further limitation of the target-specific primers used to generate the co-amplified mixture in claim 53, from which this claim depends. Claim 53 contains a step in which the co-amplified mixture is labeled with fluorescently labeled primers after amplification by target-specific primers has occurred. It is unclear if this step of labeling the co-amplified mixture occurs after using fluorescently labeled chromosome-specific primers, and if they are different fluorescently labeled primers or more of the same fluorescently labeled chromosome-specific primers being added in after amplification. For purposes of examination, the examiner is interpreting this to mean that the fluorescently labeled primers from claim 53 are the same as those being used for the co-amplification step, therefore obviating the need for the labeling of the co-amplification mixture in a separate step. However, this is not consonant with the dependence of claim 67 from claim 53, wherein the target-specific primers (genus to the species of chromosome-specific primers) are separate and distinct from the fluorescently labeled primers in claim 53. Clarification is required.
Claims 68-73 depend from claim 67, inherit this deficiency, and are rejected on the same basis.
Claim 70 recites the limitation "the aggregated genomic peak intensity". There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 53-54, 58-61, 67 and 71-73 are rejected under 35 U.S.C. 103 as being unpatentable over Tsao (Tsao et al., US 2019/0095577 A1; cited on IDS of 8/2/2023) in view of Holck (Holck et al., European Food Research and Technology 2011).
Claim 53: Tsao teaches a method of determining abundance metrics of endogenous targets through computing ratios between the amplicons of endogenous targets and amplicons of target-associated molecules (reads on spike-in molecules; Abstract and paragraph [0018]). Tsao teaches mixing a nucleic acid sample of a subject and a plurality of spike-in molecules to create a mixture, each of the plurality of spike-in molecules are associated with an endogenous target or targets of a set of targets (paragraph [0023]). Tsao teaches that the plurality of spike-in molecules further comprise a target region having a first nucleotide sequence with sequence similarity to a target sequence region and a variation region having a nucleotide sequence with sequence dissimilarity to the target sequence (paragraph [0023]). Tsao teaches co-amplifying the mixture with target-specific primers to create a co-amplified mixture (paragraph [0023]). Tsao teaches receiving peak data from the co-amplified mixture, the peak data including, for each target of the set of targets, peak intensities of the nucleic acid sample and spike-in speak intensities of the spike-in molecules associated with each respective target (paragraph [0023]). Tsao then teaches for each target, computing a ratio between the respective target peak intensity and the respective spike-in peak intensity and determining the abundance of the target based on computed ratios (paragraph [0023]).
Tsao does not teach labeling the co-amplified mixture by fluorescently labeled primers. However, the use of fluorescently labeled primers to label co-amplified mixtures for subsequent detection and determination of relative abundances is known in the art, as taught by Holck.
Holck teaches a multiplex quantitative PCR method in which target molecules are co-amplified with synthetic competitor molecules (reads on spike-in molecules or “target-associated molecules”; Abstract and Table 3). Holck teaches amplifying the target molecules and the target-associated molecules using this primer set to generate a labeled, co-amplified mixture.
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Tsao, who teaches co-amplification of targets and target-associated molecules, to include fluorescently labeled primers for co-amplification to generate a labeled co-amplification mixture, as taught by Holck. One would be motivated to do so given that Holck teaches that inclusion of fluorescent primers allows the differentiation of fragments through capillary electrophoresis and couples it with fluorescent detection for “high resolution of fragments, high sensitivity and high-throughput capabilities” and “easy identification of amplicons even when the sizes of PCR fragments are almost identical”. One would have a reasonable expectation of success given that Tsao teaches that their method is compatible with capillary electrophoresis (paragraph [0068]). Additionally, Holck teaches that any qualitative PCR approach can easily incorporate the fluorescently labeled primers without changing the primer sets themselves and requires no additional steps be added to the traditional qualitative PCR methodologies (pg 952, col 1 last paragraph into col 2 first paragraph).
Claim 54 and 67: Tsao teaches that the sample is a DNA sample, the target of the set of targets comprises a chromosome of a set of chromosomes, the target-specific primers are chromosome-specific primers, and determining the abundance of the target comprises determining the presence or absence of an aneuploidy based on the computed ratios (paragraph [0023]). As described in the citations and rationale for combining above, Holck teaches using fluorescently labeled primers for amplification of the target, the target in this case being a chromosome-specific target, as taught by Tsao (relevant to claim 67).
Claims 58-59 and 71-72: Tsao teaches that the variation region includes an insertion of base pairs with a of length 1 base pair. Tsao also teaches that the variation region includes a deletion of base pairs with a length of 1 base pairs (“variation regions with one or more insertions…or one or more deletions”, paragraph [0078]). Tsao specifically exemplifies a variation region that is a deletion of 3 base pairs (paragraph [0079]).
Claims 60 and 73: Tsao teaches a respective variation region of a spike-in molecule is in the center of a respective amplicon of the spike-in molecule (Figures 2 and 3).
Claim 61: Holck teaches that each of the fluorescently labeled primers is associated with a color channel (Figure 2 and Table 3).
Claims 55-57, 62, 64-66, 68-70, 74, and 76-78 are rejected under 35 U.S.C. 103 as being unpatentable over Tsao (Tsao et al., US 2019/0095577 A1; cited on IDS of 8/2/2023) in view of Holck (Holck et al., European Food Research and Technology 2011) as applied to claims 53-54, 58-61, 67 and 71-73 above, and further in view of Nygren (US 2012/0264618 A1).
The teachings of Tsao in view of Holck are detailed above. Relevant to the instantly rejected claims, Tsao in view of Holck teach a method of determining the abundance of endogenous targets through the use of computed ratios between amplicons of the endogenous target and target-associated “spike-in” molecules. Tsao in view of Holck teach that separation of amplicon fragments can be achieved through capillary electrophoresis and fluorescently labeled molecules to produce peak data allowing for calculation of said ratios.
Regarding claims 55 and 68: Tsao in view of Holck do not teach co-amplifying endogenous targets and spike-in molecules with target-specific or chromosome-specific primers that have tails to generate amplicons of discrete lengths. However, use of tailed primers for generating amplicons of a discrete length of a set of discrete lengths is known in the art, as taught by Nygren.
Nygren teaches a method of determining the relative amount of a nucleic acid species in a sample (Abstract). Nygren teaches using “competitive PCR” to co-amplify a target and target-associated molecules with the same primer pair, and then using capillary electrophoresis to separate the fragments and determine relative abundance through computation of a ratio between the two (paragraphs [0020, 0106, 0259] and Figure 1). Nygren teaches that “amplified competitors can optionally be further distinguishable from one another through the use of tailed amplification primers” (paragraph [0112]) and that in cases when multiple genomic targets are being amplified in the same reaction “the primers that amplify the genomic DNA target sequences and corresponding competitor oligonucleotides each contain a 5’ tail of the same overall length” (paragraph [0165]). Nygren teaches that “In a multiplex amplification assay, for example, where a plurality of genomic DNA target sequences are co-amplified with a plurality of corresponding competitor oligonucleotides, the genomic DNA target sequences can all be of the same length, and the competitor oligonucleotides can be of the same or different lengths, such that the amplicons generated (through the use of tailed primers of varying length, for example) are distinct for each region assayed. In such cases, each region would be represented by two amplicon lengths (i.e. one amplicon length for the genomic DNA target(s) for that region and another amplicon length for the corresponding competitor oligonucleotide(s))” (paragraph [0184]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Tsao in view of Holck, who teach co-amplification of targets and target-associated molecules using labeled primers, to include tailed primers for co-amplification to generate discrete fragment lengths for both target and target-associated molecules for a given region, as taught by Nygren. One would be motivated to do so given that Nygren teaches that amplifying fragments of the same length and then varying the length with tailed primers allows for the removal of “unnecessary amplification bias” (paragraph [0260]). One would have a reasonable expectation of success given that the methodology of Tsao in view of Holck already employs fragment separation via capillary electrophoresis (thus the length of the amplicons is being used to generate peak data), and the incorporation of the tailed primers for greater control of final amplicon length independent of the length of the target genomic region provides an additional level of controllable multiplex ability.
Claims 56 and 69: Tsao in view of Holck and Nygren teach computing, for each discrete length of the set of discrete lengths, a ratio between the respective target peak intensity and the spike-in peak intensity and then aggregating these individual abundance ratios across each discrete length of the set of discrete lengths (“for each pair, extracting an individual abundance ratio of endogenous to spike-in based on comparing a peak intensity metric…[and] generating an overall abundance ratio based on the individual abundance ratios (e.g., averaging individual abundance ratios for different pairs of target sequence base and target-associated sequence base associated with a plurality of target loci for chromosome 21; averaging abundance ratios across loci; etc.)” Tsao, paragraph [0023]).
Claims 57 and 70: Tsao in view of Holck and Nygren teach computing, for each discrete length of the set of discrete lengths, a ratio between the respective target peak intensity and the spike-in peak intensity and then aggregating these individual abundance ratios across each discrete length of the set of discrete lengths (“for each pair, extracting an individual abundance ratio of endogenous to spike-in based on comparing a peak intensity metric…[and] generating an overall abundance ratio based on the individual abundance ratios (e.g., averaging individual abundance ratios for different pairs of target sequence base and target-associated sequence base associated with a plurality of target loci for chromosome 21; averaging abundance ratios across loci; etc.)” Tsao, paragraph [0023]). Tsao in view of Holck and Nygren do not teach first aggregating the target peak intensity across each discrete length of the set of discrete lengths and aggregating the spike-in peak intensity across each discrete length of the set of discrete lengths and then computing a ratio between the aggregated target peak intensity and aggregated spike-in peak intensities. However, with respect to the order of steps, it is noted that the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959)). See MPEP §2144.04 IV C. Therefore, the claimed order of steps (aggregating prior to determining the ratio vs aggregating after determining individual ratios) is an obvious variant of the steps of the cited prior art.
Claim 62: Tsao teaches that the sample is a DNA sample and that the target comprises a chromosome of a set of chromosomes (Tsao, paragraph [0023]). As described in the rejection of claims 55 and 58 above, Nygren teaches performing this amplification with primers that add a tail with a discrete length of a set of discrete lengths to an amplicon of the DNA sample and a tail with the discrete length of the set of discrete lengths to an amplicon of the spike-in molecule. The rationale to combine said references is provided in the rejection of claims 55 and 58 above. Tsao teaches aggregating the peak intensity ratios (discrete length-specific ratios) across each of the discrete lengths in the set of discrete lengths to generate a chromosome-specific ratio (Tsao, paragraph [0023]; see also the rejection of claims 56 and 69 above). Tsao teaches determining the abundance of the target comprises determining the presence or absence of an aneuploidy based on the computed ratios (paragraph [0023]).
Claim 64 and 65: Tsao teaches that the variation region includes an insertion of base pairs with a length of 1 base pair. Tsao also teaches that the variation region includes a deletion of base pairs with a length of 1 base pairs (“variation regions with one or more insertions…or one or more deletions”, paragraph [0078]). Tsao specifically exemplifies a variation region that is a deletion of 3 base pairs (paragraph [0079]).
Claim 66: Tsao teaches a respective variation region of a spike-in molecule is in the center of a respective amplicon of the spike-in molecule (Figures 2 and 3).
Claim 74: Tsao teaches that the sample is a DNA sample and that the target comprises a chromosome of a set of chromosomes (Tsao, paragraph [0023]). As described in the rejection of claims 55 and 58 above, Nygren teaches performing this amplification with primers that add a tail with a discrete length of a set of discrete lengths to an amplicon of the DNA sample and a tail with the discrete length of the set of discrete lengths to an amplicon of the spike-in molecule. Nygren teaches that the addition of a tail using a tailed primer can be done to a subset of amplicons (Nygren, Figure 1 molecule 1). The rationale to combine said references is provided in the rejection of claims 55 and 58 above. Tsao teaches aggregating the peak intensity ratios (discrete length-specific ratios) across each of the discrete lengths in the set of discrete lengths to generate a chromosome-specific ratio (Tsao, paragraph [0023]; see also the rejection of claims 56 and 69 above). Tsao teaches determining the abundance of the target comprises determining the presence or absence of an aneuploidy based on the computed ratios (paragraph [0023]).
Claim 76 and 77: Tsao teaches that the variation region includes an insertion of base pairs with a length of 1 base pair. Tsao also teaches that the variation region includes a deletion of base pairs with a length of 1 base pairs (“variation regions with one or more insertions…or one or more deletions”, paragraph [0078]). Tsao specifically exemplifies a variation region that is a deletion of 3 base pairs (paragraph [0079]).
Claim 78: Tsao teaches a respective variation region of a spike-in molecules is in the center of a respective amplicon of the spike-in molecule (Figures 2 and 3).
Claims 63 and 75 are rejected under 35 U.S.C. 103 as being unpatentable over Tsao (Tsao et al., US 2019/0095577 A1; cited on IDS of 8/2/2023) in view of Holck (Holck et al., European Food Research and Technology 2011) and Nygren (US 2012/0264618 A1) as applied to claims 55-57, 62, 64-66, 68-70, 74, and 76-78 above, and further in view of Landry (Landry et al., US 2019/0147980 A1; cited on IDS of 8/2/2023).
The teachings of Tsao in view of Holck and Nygren are detailed above. Relevant to the instantly rejected claims, Tsao in view of Holck and Nygren teach computing a ratio of abundance of a target chromosome relative to the abundance of a target-associated spike-in molecule and using the computed ratios relative to a reference chromosome ratio to determine an aneuploidy (such as Down Syndrome, see Tsao paragraph [0023]).
Tsao in view of Holck and Nygren do not teach determining that the computed ratio is greater than a threshold ratio to determine the presence of aneuploidy. However, comparison of a computed abundance ratio of target chromosomes to reference chromosomes and comparison of this ratio to a threshold to accurately diagnose an aneuploidy is known in the art, as taught by Landry.
Landry teaches a method wherein an endogenous DNA target (such as a region on chromosome 21) is co-amplified with target-associated spike-in molecules and a reference target (a chromosome other than chromosome 21) and reference target-associated spike-in molecules (which reads on the plurality of other chromosome-specific ratios; paragraph [0060]). Landry teaches determining a ratio between each target/target associated pair intensity and each reference target/reference target-associated pair intensity (paragraph [0060]). Landry then teaches computing a ratio between the target-associated ratio and the reference-associated ratio, and if the target-associated ratio relative to the reference-associated ratio exceeds a “statistically significant threshold amount”, diagnosing aneuploidy (paragraph [0060]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Tsao in view of Holck and Nygren, who teach comparison of target-associated ratios to reference-associated ratio for diagnosis of an aneuploidy, to include a threshold ratio as taught by Landry. One would be motivated to include a threshold ratio comparison given the teaching by Landry that this allows a “statistically significant” method of determining an aneuploidy based on ratio comparisons (paragraph [0060]). One would have a reasonable expectation of success given that Landry is using this threshold methodology in comparing ratios that are obtained through relative abundance ratios between targets and target-associated molecules, as taught by Tsao.
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.
US 11,430,543 B2
Claims 53-54, 58-61, 67, and 71-73 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 6, and 13 of U.S. Patent No. US 11,430,543 B2 in view of Holck (Holck et al., European Food Research and Technology 2011).
Although the claims are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the same limitations. Any additional limitations of the ‘543 claims are encompassed by the open claim language “comprising” found in the instant claims.
Regarding claims 53, 60-62, 67, and 73: ‘543 teaches determining abundance through generation of a plurality of spike-in molecules associated with an endogenous target wherein the spike-in molecules have a target region with sequence similarity to a target sequence region and a variation region having sequence dissimilarity to the target sequence region, co-amplifying the mixture, receiving peak data from the co-amplified mixture and determining a target-associated abundance metric based on the peak data (reads on computing a ratio). ‘543 does not teach labeling the co-amplified mixture with fluorescently labeled primers (claim 53) or performing the amplification with fluorescently labeled primers (claim 62). Additionally, ‘543 does not teach that the variation sequence is in the center of the spike-in molecule (claims 60 and 73). However, the use of fluorescently labeled primers to label co-amplified mixtures for subsequent detection and determination of relative abundances with variation regions in the center of the molecule is known in the art, as taught by Holck.
Holck teaches a multiplex quantitative PCR method in which target molecules are co-amplified with synthetic competitor molecules (reads on spike-in molecules or “target-associated molecules”; Abstract and Table 3). Holck teaches amplifying the target molecules and the target-associated molecules using this primer set to generate a labeled, co-amplified mixture. Holck teaches that each of the fluorescently labeled primers is associated with a color channel (Figure 2 and Table 3). Holck teaches that the synthetic competitor molecules have variation regions in the center of the molecules (Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘543, who teaches co-amplification of targets and target-associated molecules, to include fluorescently labeled primers for co-amplification to generate a labeled co-amplification mixture, as taught by Holck. One would be motivated to do so given that Holck teaches inclusion of fluorescent primers allows the differentiation of fragments with fluorescent detection for “high resolution of fragments, high sensitivity and high-throughput capabilities” and “easy identification of amplicons even when the sizes of PCR fragments are almost identical”. One would be motivated to have the variation region towards the center of the molecule given the teaching by Holck that this allows for the variation region to be included in the amplicon using the same primers as the target molecule, and thus enable separation of the spike-in molecule and the endogenous target via electrophoresis. One would have a reasonable expectation of success given that Holck teaches that any qualitative PCR approach can easily incorporate the fluorescently labeled primers without changing the primer sets themselves and requires no additional steps be added to the traditional qualitative PCR methodologies (pg 952, col 1 last paragraph into col 2 first paragraph).
US 12,183,437 B2
Although the claims are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the same limitations. Any additional limitations of the ‘437 claims are encompassed by the open claim language “comprising” found in the instant claims.
Claims 53-54, 58-59, 60-61, 67, and 71-73 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-6, 9, 15, 17 and 18 of U.S. Patent No. US 12,183,437 B2 in view of Holck (Holck et al., European Food Research and Technology 2011) according to the citations and rationales provided above.
Claims 55-57, 62, 64-66, 68-70, 74, and 76-78 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-6, 9, 15, 17 and 18 of U.S. Patent No. US 12,183,437 B2 in view of Holck (Holck et al., European Food Research and Technology 2011), as applied to claims 53-54, 58-59, 60-61, 67, and 71-73 above, and further in view of Nygren (US 2012/0264618 A1).
Regarding claims 55, 62, 68, and 74: ‘437 in view of Holck teach a method of determining the abundance of endogenous targets through the use of computed ratios between amplicons of the endogenous target and target-associated “spike-in” molecules. Tsao in view of Holck teach that separation of amplicon fragments can be achieved through capillary electrophoresis and fluorescently labeled molecules to produce peak data allowing for calculation of said ratios.
‘437 in view of Holck do not teach co-amplifying endogenous targets and spike-in molecules with target-specific or chromosome-specific primers that have tails to generate the amplicons of discrete lengths. However, use of tailed primers for generating amplicons of a discrete length of a set of discrete lengths is known in the art, as taught by Nygren.
Nygren teaches a method of determining the relative amount of a nucleic acid species in a sample (Abstract). Nygren teaches using “competitive PCR” to co-amplify a target and a target-associated molecules with the same primer pair, and then using capillary electrophoresis to separate the fragments and determine relative abundance through computation of a ratio between the two (paragraphs [0020, 0106, 0259] and Figure 1). Nygren teaches that “amplified competitors can optionally be further distinguishable from one another through the use of tailed amplification primers” (paragraph [0112]) and that in cases when multiple genomic targets are being amplified in the same reaction “the primers that amplify the genomic DNA target sequences and corresponding competitor oligonucleotides each contain a 5’ tail of the same overall length” (paragraph [0165]). Nygren teaches that “In a multiplex amplification assay, for example, where a plurality of genomic DNA target sequences are co-amplified with a plurality of corresponding competitor oligonucleotides, the genomic DNA target sequences can all be of the same length, and the competitor oligonucleotides can be of the same or different lengths, such that the amplicons generated (through the use of tailed primers of varying length, for example) are distinct for each region assayed. In such cases, each region would be represented by two amplicon lengths (i.e. one amplicon length for the genomic DNA target(s) for that region and another amplicon length for the corresponding competitor oligonucleotide(s))” (paragraph [0184]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘437 in view of Holck, who teaches co-amplification of targets and target-associated molecules using labeled primers, to include tailed primers for co-amplification to generate discrete fragment lengths for both target and target-associated molecules for a given region, as taught by Nygren. One would be motivated to do so given that Nygren teaches that amplifying fragments of the same length and then varying the length with tailed primers allows for the removal of “unnecessary amplification bias” (paragraph [0260]). One would have a reasonable expectation of success given that the methodology of ‘437 in view of Holck already employs fragment separation via capillary electrophoresis (thus the length of the amplicons is being used to generate peak data), and the incorporation of the tailed primers for greater control of final amplicon length independent of the length of the target genomic region provides an additional level of controllable multiplex ability.
Regarding claim 57: ‘437 in view of Holck and Nygren, teaches computing, for each discrete length of the set of discrete lengths, a ratio between the respective target peak intensity and the spike-in peak intensity and then aggregating these individual abundance ratios across each discrete length of the set of discrete lengths (see claim 6 of ‘437). ‘437 in view of Holck and Nygren do not teach first aggregating the target peak intensity across each discrete length of the set of discrete lengths and aggregating the spike-in peak intensity across each discrete length of the set of discrete lengths and then computing a ratio between the aggregated target peak intensity and aggregated spike-in peak intensities. However, with respect to the order of steps, it is noted that the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959)). See MPEP §2144.04 IV C. Therefore, the claimed order of steps (aggregating prior to determining the ratio vs aggregating after determining individual ratios) is an obvious variant of the steps of the cited prior art.
Claims 63 and 75 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-6, 9, 15, 17 and 18 of U.S. Patent No. US 12,183,437 B2 in view of Holck (Holck et al., European Food Research and Technology 2011) and Nygren (US 2012/0264618 A1), as applied to claims 55-57, 62, 64-66, 68-70, 74, and 76-78 above, and further in view of Landry (Landry et al., US 2019/0147980 A1; cited on IDS of 8/2/2023).
‘437 in view of Holck and Nygren do not teach determining that the computed ratio is greater than a threshold ratio to determine the presence of aneuploidy/chromosomal abnormality. However, comparison of a computed abundance ratio of target chromosomes to reference chromosomes and comparison of this ratio to a threshold to accurately diagnose an aneuploidy is known in the art, as taught by Landry.
Landry teaches a method wherein an endogenous DNA target (such as a region on chromosome 21) is co-amplified with target-associated spike-in molecules and a reference target (a chromosome other than chromosome 21) and reference target-associated spike-in molecules (which reads on the plurality of other chromosome-specific ratios; paragraph [0060]). Landry teaches determining a ratio between each target/target associated pair intensity and each reference target/reference target-associated pair intensity (paragraph [0060]). Landry then teaches computing a ratio between the target-associated ratio and the reference-associated ratio, and if the target-associated ratio relative to the reference-associated ratio exceeds a “statistically significant threshold amount”, diagnosing aneuploidy (paragraph [0060]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘437 in view of Holck and Nygren, who teach comparison of target-associated ratios to reference-associated ratio for diagnosis of an aneuploidy, to include a threshold ratio as taught by Landry. One would be motivated to include a threshold ratio comparison given the teaching by Landry that this allows a “statistically significant” method of determining an aneuploidy based on ratio comparisons (paragraph [0060]). One would have a reasonable expectation of success given that Landry is using this threshold methodology in comparing ratios that are obtained through relative abundance ratios between targets and target-associated molecules, as taught by ‘437.
US 11,646,100 B2
Although the claims are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the same limitations. Any additional limitations of the ‘100 claims are encompassed by the open claim language “comprising” found in the instant claims.
Claims 53-54, 58, 60-61, 67, and 73 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 8-9, and 12 of U.S. Patent No. US 11,646,100 B2 in view of Holck (Holck et al., European Food Research and Technology 2011) according to citations and rationales provided above.
Regarding claim 58: ‘100 teaches a variation region with sequence dissimilarity to the target sequence region but does not specify that this includes an insertion between 1-20 base pairs. However, Holck teaches incorporation of an insertion of 15 base pairs into a spike-in (“target-associated”) molecule (Figure 1). It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘100 with that of Holck to include an insertion in the variation region of the target-associated molecule. One would be motivated to do so given the teaching by Holck that this allows for differentiation between the spike-in molecules and their associated endogenous targets in addition to the fluorescently labeled primers (Figure 2). One would have a reasonable expectation of success given that incorporation of different sized variable regions in the spike-in molecules would yield the predictable result of amplicons which are distinguishable by peak location/length of the amplicon.
Claims 59, 71, and 72 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 8-9, and 12 of U.S. Patent No. US 11,646,100 B2 in view of Holck (Holck et al., European Food Research and Technology 2011) as applied to claims 53-54, 58, 60-61, 67, and 73 above, and further in view of Tsao (Tsao et al., US 2019/0095577 A1; cited on IDS of 8/2/2023).
‘100 in view of Holck teaches variation regions in spike-in molecules with varying legnths of insertions/deletions added in for differentiation between spike-in molcules and their associated endogenous targets in downstream analysis. ‘100 in view of Holck do not teach an insertion that is between 1-5 base pairs or a delation that is either 1-20 base pairs or 1-5 base pairs long. However, inclusion of insertions/deletions within these ranges for discrimination between targets and target-associated molecules in downstream applications such as capillary electrophoresis is known in the art, as taught by Tsao.
Tsao teaches that the variation region includes an insertion of base pairs with a length of 1 base pair. Tsao also teaches that the variation region includes a deletion of base pairs with a length of 1 base pairs (“variation regions with one or more insertions…or one or more deletions”, paragraph [0078]). Tsao specifically exemplifies a variation region that is a deletion of 3 base pairs (paragraph [0079]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘00 in view of Holck, who teach differentiation of spike-in molecules and their associated targets by inclusion of large insertions/deletions, to include smaller insertions/deletions as taught by Tsao. One would be motivated to do so given that this would reduce amplification bias by maintaining similar lengths of amplicons and would still allow for differentiation via capillary electrophoresis, as taught by Tsao.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683 /STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683