DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
The Track One Request, filed 01/15/2025, was granted 02/25/2025. Therefore, this application is accorded special status.
Amendments and Status of the Claims
This action is in response to papers filed 10th Dec 2025, in which claims 1-2, 4, 12, and 14-15 were amended, claim 5 was canceled, and new claims 21 -25 were added. All of the amendments have been thoroughly reviewed and entered.
Applicant has amended:
i) claims 1-2, 4, 12, and 14-15 to overcome objections and 112(b) and (d) rejections; the objections and 112(b) and (d) rejections are withdrawn.
ii) specification to include verbiage from previous incorporated by reference statements; the denial of earliest possible priority date has been withdrawn.
Applicant’s arguments, see Pgs. 14 onwards, filed 26th June 2025, with respect to:
rejections of claims 1-20 under 35 USC § 103 have been fully considered and are persuasive. The 35 USC § 103 rejections are withdrawn. However, in view of:
new IDS, new BRI of claims, and newly added independent claim 21 and its dependent claims a new 102 and 103 rejection of claims 1-25, not necessitated by amendment, is made in this Office action.
Objections and Rejections not reiterated here are withdrawn.
Claims 1-25 are under consideration.
Priority
This application is a continuation of U.S. patent application Ser. No. 18/643,870 filed on Apr. 23, 2024 which is a continuation of U.S. patent application Ser. No. 16/551,638, filed on Aug. 26, 2019, now U.S. Pat. No. 11970737, which is a continuation of U.S. patent application Ser. No. 16/219,553, filed on Dec. 13, 2018, now U.S. Pat. No. 10,392,661, which is a continuation of U.S. patent application Ser. No. 16/038,832, filed on Jul. 18, 2018, now U.S. Pat. No. 10,202,646, which is a continuation of U.S. patent application Ser. No. 15/224,460, filed on Jul. 29, 2016, now U.S. Pat. No. 10,047,394, which is a continuation of U.S. patent application Ser. No. 14/281,706, filed on May 19, 2014, now U.S. Pat. No. 9,816,137, which is a continuation of U.S. patent application Ser. No. 12/969,581, filed on Dec. 15, 2010, now U.S. Pat. No. 8,835,358, which claims priority to U.S. Provisional Application No. 61/286,768, filed on Dec. 15, 2009.
Accordingly, claims 1 - 25 have an effective filing date of Dec. 15, 2009, which is the filing date of the earliest priority document.
Claim Interpretation
Wherein and that clause:
It is noted that the subject matter of a properly construed claim is defined by the terms that limit its scope. It is this subject matter that must be examined. As a general matter, the grammar and intended meaning of terms used in a claim will dictate whether the language limits the claim scope. Language that suggests or makes optional but does not require steps to be performed or does not limit a claim to a particular structure does not limit the scope of a claim or claim limitation. “Wherein” and “that” clauses are examples of language that may raise a question as to the limiting effect of the language in a claim. See MPEP 2103 I.C. and MPEP § 2111.04.
It is also noted that a “wherein” and “that” clause, such as that in (claim 1 and 21), must give “meaning and purpose to the manipulative steps.” See, MPEP § 2111.04.
In the instant claims, the “wherein” and “that” clauses are followed by functional language: two or more enzymes capable of modifying both ends of fragmented DNA to generate ends that are compatible for ligation with said cohesive end …wherein a phosphate transfer enzyme is capable of transferring a phosphate group from ATP to a 5'-OH terminus of a nucleic acid rather than a structural limitation. Thus, the “that” and “wherein” clauses recite an inherent function which will flow from the structural limitations of the claims they depend from. See, MPEP § 2112.01: II. COMPOSITION CLAIMS — IF THE COMPOSITION IS PHYSICALLY THE SAME, IT MUST HAVE THE SAME PROPERTIES.
Product-by-Process:
Claim 11 recites wherein n1 and n2 are numbers of occurrences of the first target molecule and the second target molecule and wherein the ratio of the greater of n1 and n2 to m (number of different label sequences) is smaller than 0.2. Since ratio is understood to be the result of a calculation ( a step that is performed) the claim is being interpreted as a product-by-process claim which it depends from a composition claim.
The courts have stated:
“even though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985). See MPEP§ 2113.
It is noted that claims 1 and 21 are broad and do not limit the label, universal primer, or biotin-tagged oligonucleotide, by sequence or size or relationship to each other. Furthermore, no limiting definitions are given in the specification. Thus, these limitations are very broad and encompass any number of nucleotides and /or sequence. Furthermore, the use of the word “comprising” indicates that the labels, universal primer, and biotin-tagged oligonucleotides could be directly or indirectly; i.e., via another moiety or bridge, ligated or even hybridized to each other.
The label in claim 1 and 21 is interpreted as: An oligonucleotide comprising two portions (exemplified as 305 and 303 in Fig. 4), wherein:
one portion comprises different sequences (m) that are connected to a second portion. In the absence of a specific recitation for the manner in which a label comprising different sequences and a universal primer are connected, if at all, the different sequences and universal primer that comprise the label could be comprised together by any means possible, for e.g., ligated end-to-end or hybridized via a complementary domain to each other or via a linker moiety.
the second portion comprises a universal primer. In the absence of a limiting definition for universal primer, the universal primer is being interpreted as a sequence of nucleotides that is common to all labels.
Since the label is recited in line 5 of claims 1 and 21 as comprising a cohesive end, it is understood that only one end of the label is capable of being ligated to another nucleotide; i.e., the label does not form a circular structure when ligated to another nucleotide.
Accordingly, claims 1 and 21 are interpreted as: A composition/kit, comprising:
fragmented DNA comprising at least four distinct target molecules comprising SNPs
two sets of oligonucleotides that each “connect” with at least one target nucleic acid sequence to be detected, wherein:
one set (recited as labels), comprises a cohesive DNA end that may ligate with fragmented target sequences,
and the other set (recited as at least four biotin-tagged oligonucleotides) comprises biotin-tagged sequences each with at least one nucleotide complementary to at least one of four distinct target molecules (PIK3R1, MYC, CCND2, or CDKN2A); i.e., this set may hybridize with at least one target.
two or more target DNA-modifying enzymes (to generate ends that are compatible for ligation with said cohesive end), wherein the fragmented DNA comprises four or more distinct target molecules comprising SNP(s), wherein the target DNA-modifying enzymes are exonuclease and/or polymerases or kinases; streptavidin magnetic beads; and one or more ligases.
Claim Rejections - 35 USC § 102
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 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.
This first rejection is based on the BRI wherein the label comprises m different sequences which are hybridized to a “universal primer”.
I. Claim(s) 1 and 21 is/are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Mirkin (US 2005/0037397 A1, IDS dated 12/10/2025), and evidenced by Nannya (Cancer Res 2005;65: (14) July 15, 2005).
Mirkin had taught a screening method for detecting the presence or absence of one or more target analytes, e.g., nucleic acids ([0003], Example 10, [0372]). Such method comprising putting together the following:
DNA sequences comprising a gene sequence and two DNA positive controls [0372] from DNA fragments ([0253], [0290], [0308], claim 44);
two sets of nanoparticle-attached probes that each connect with at least one target nucleic acid sequence to be detected, wherein each probe comprises two parts, wherein one part is a specific binding complement to a specific target analyte
One set is a detection probe. E.g. see recitation [0021] providing one or more types of detection probes, each type of detection probe comprising a nanoparticle having oligonucleotides bound thereto, one or more specific binding complements to a second binding site of the specific target analyte, and one or more DNA barcodes that serve as a marker for the particular target analyte, wherein at least a portion of a sequence of the DNA barcodes is hybridized to at least some of the oligonucleotides bound to the nanoparticles
The other set is a capture probe. E.g. see recitation [0020]: providing one or more types of capture probes bound to a substrate, each type of capture probe comprising a specific binding complement to a first binding site of a specific target analyte.
Mirkin further taught the following about the detection probe:
[0025]: [T]he detection probe comprises (i) one or more specific binding complements to the second binding site of a specific target analyte, (ii) at least one type of oligonucleotides bound to the nanoparticle, and a DNA barcode having a predetermined sequence that is complementary to at least a portion of at least one type of oligonucleotides, the DNA barcode bound to each type of detection probe serving as a marker for a specific target analyte; [0029]: the DNA barcode is amplified by PCR; [0052]: [T]he nanoparticles are metal nanoparticles such as gold nanoparticles or semiconductor nanoparticles; [0116]: [T]he DNA barcode has a predefined sequence, is also called the reporter probe, and may be further labelled for e.g., with biotin; the DNA barcode can be made into a universal probe as taught in: [0144] These universal probes can be … "tuned" to various single target nucleic acid sequences, by simply substituting or interchanging the target recognition oligonucleotides such that the second portion comprises complementary sequence to the target nucleic acid of interest. Similarly, if multiple target nucleic acid sequences are to be assayed in a single test solution, the reporter oligonucleotides can comprise a sequence that is specific for each target nucleic acid. Thus, detection of the reporter oligonucleotide of known and specific sequence, would indicate the presence of the particular target nucleic acid in the test solution.
Mirkin further taught the following about the capture probe: [0030]: [T]he capture probe is bound to a magnetic substrate such as a magnetic particle.
Mirkin taught the following about the enzymes used in the method: [0150]: Methods of making oligonucleotides of a predetermined sequence are well known. They further cite well-known texts in the field.
Having taught such method, Mirkin inherently taught a composition comprising instant limitations. Specifically, in Mirkin’s method, the detection probe reads on instant label comprising unique sequences and a universal primer and the capture probe reads on instant biotin-tagged oligonucleotides.
While Mirkin does not make mention of the four or more distinct target molecules: PIK3R1, MYC, CCND2, or CDKN2A, Nannya evidences the presence of these four SNP containing target molecules in genomic DNA from one sample. See Nannya Table 1, as well as incorporated by reference in instant application.
Thus, Mirkin anticipates instant claims 1 and 21.
This second rejection is based on the BRI wherein the label comprises m different sequences which are ligated to a “universal primer”.
II. Claim(s) 1, 6 – 10, 12, 15 – 17, 21, and 25 is/are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Brenner (US 2008/0318802 Al), and evidenced by Nannya (Cancer Res 2005;65: (14) July 15, 2005).
Regarding the recitation of “kit” in claim 21, the preamble of this claim recites a “kit.” The specification, however, does not define this term, and so it is being interpreted to encompass any collection of reagents that includes all of the elements of the claims. Any further interpretation of the word is considered an intended use and does not impart any further structural limitation of on the claimed subject matter.
Regarding claims 1 and 21, Brenner had taught a method for detecting the presence or absence of SNPs (polymorphism [0005]; pg. 7, left col., 1st para). Such method comprising putting together the following:
Target DNA sequences comprising a gene sequence from DNA fragments ([0007]; pg. 2, left col., 1st para; [0065]; claim 23: genetic variation); digesting the samples so they are ready for ligation [0038].
Preparing tagged oligonucleotides: Two sets of tagged oligonucleotides are prepared:
One set of tagged oligonucleotide is an adaptor, comprises an oligonucleotide tag comprising: a) one or more unique “words” and b) an RE sequence, such that this set attaches (ligates) to fragmented target sequences of (i) above ([0038]), and optionally c) a spacer (represented as 252 in Fig. 3B, [0041]).
and the other set is referred to as tag complements [0040 - 0041] or anti-tags [0051] which comprises complements to each of the unique oligonucleotide tags and is attached to a solid substrate (labeled copies of oligonucleotide tags can be specifically hybridized to their tag complements on an addressable microarray, [0040]; anti-tags synthesized on a solid phase support, [0056]; for selecting with specific hybridization and differential duplex stability, template-driven ligation, template-driven strand extension, and exonuclease digestion, claim 25).
Brenner had further taught the following about the adaptor: The adaptor is hybridized to biotinylated primers so as to allow for capture on to a solid support [0030] and then amplified. A copy of the adaptored target sequence that is not biotinylated is thus obtained (represented as 212 in Fig. 2A). Adaptor is ligated to this fragment. Thus, an adaptored target sequence is obtained (represented as 220 in Fig. 2A). Capture entities (e.g., biotin), primers, RE sites etc., may continue to be added to obtain tagged target sequences (method described in [0039]). Alternatively, common sequences from the target itself may form part of the tags, as seen in this recitation from [0066]:
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Thus, when the tag comprises a sequence fragment of the target DNA, such as common-sequence fragments, e.g., a restriction fragment from a particular locus, as disclosed in the citation above, ii. b. above is inherently complementary to the target.
Brenner had taught the following about the enzymes used in the method: a kit comprising enzymes for use in the assay is provided [0023]. The method taught above requires polymerase, ligase, exonuclease [0017, 0029, 0039, 0036]. Brenner does not explicitly mention the enzyme kinase. However, the following recitation from Brenner [0029] makes clear that a kinase may be incorporated in reactions to allow for a phosphate addition or removal as needed:
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Brenner had taught that capture of nucleotides via a biotin moiety, to e.g., avidin or streptavidin is a conventional protocol [0041]. Thus, biotinylating either the first or second set of oligonucleotides is common and routine.
Having taught such method, Brenner inherently taught a composition comprising instant limitations. Specifically, in Brenner’s method, the adaptor, comprising “words” and RE sequences/spacer reads on instant label comprising unique sequences and a universal primer respectively, the complement/anti-tag reads on instant biotin-tagged oligonucleotides comprising sequences each complementary to distinct target molecules.
While Brenner does not make mention of the four or more distinct target molecules: PIK3R1, MYC, CCND2, or CDKN2A, Nannya evidences the presence of these four SNP containing target molecules in genomic DNA from one sample. See Nannya Table 1, as well as incorporated by reference in instant application.
Regarding claims 6 - 7 and 25, Brenner had taught that the composition in their method requires labels to be in excess of fragments to be tagged (an example is provided for generating a population of genomic fragments wherein fragments from each different genome have a different oligonucleotide tag attached that is comprised of oligonucleotide subunits, or words., last lines of [0065]; when oligonucleotide tags comprise four such words, a repertoire of 4096 oligonucleotide tags is formed; when oligonucleotide tags comprise five such words, a repertoire of32,768 (=85) oligonucleotide tags is formed; and so on., middle few lines of [0066]). Such teachings read on instant recitation of m is between 100 and 10000 as recited in claims 6 – 7 and m is between 100 and 1000 as recited in claim 25.
Regarding claims 8 - 9, Brenner had taught that the composition in their method requires tags to have a length of up to 12mers (ligation tags of a set each have a length in the range of from 6 to 12 nucleotides, and more preferably, from 8 to 10 nucleotides., [0042]) which reads on the recitation of at least 6 nucleotides in length and 6-15 nucleotides in length.
Regarding claim 10, Brenner had taught that the fragmented DNA in the composition in their method comprises a plurality of target molecules (claims 32 - 33). Such teachings read on instant recitation of plurality of first target molecules and plurality of second target molecules.
Regarding claim 12, Brenner had taught their method incorporates a reverse transcriptase (last few lines of on [0028] on pg. 4).
Regarding claims 15 - 17, Brenner had taught their method requires that the DNA to be detected comes from a sample, is tissue and from human (Biological samples may be animal, including human, fluid, solid (e.g., stool) or tissue, …, [0035]).
Thus, Brenner anticipates instant claims 1, 6 – 10, 12, 15 – 17, 21, and 25.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
III. Claims 2, 4, 13 - 14, 18 - 20, 22, and 24 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Brenner (US 2008/0318802 Al) and evidenced by Nannya (Cancer Res 2005;65: (14) July 15, 2005) as applied to claims 1, 6 – 10, 12, 15 – 17, 21, and 25 above, and further in view of Rittie (J. Cell Commun. Signal. (2008) 2:25–45).
The teachings of Brenner have been discussed in the rejection for claims 1 and 21 above and apply.
Regarding claims 2, 4, 13-14, 18-20, 22, and 24, Brenner had taught wherein the composition comprises enzymes for PCR and oligonucleotide modification.
However, Brenner had not taught the specific polymerases or kinases as recited in instant.
However, before the time of the effective filing date, the skilled artisan was aware of various choices of enzymes for PCR and oligonucleotide modification as reviewed in the art of Rittie. Rittie had provided a useful guide to enzymes used in molecular biology. Rittie’s Table 1 describes various polymerases and Table 3 describes various kinases, including recited polymerases and kinases, with advantages and disadvantages of each. Specifically, Rittie had taught that Klenow and T4 DNA polymerase are equivalent (See Rittie, Table 1).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to modify the composition used in the method of Brenner with specific polymerases and kinases as taught by Rittie. One would have been motivated to make such a modification in order to receive the expected benefit of optimal performance to perform PCR and oligonucleotide modification as taught by Rittie. One of ordinary skill in the art would have a reasonable expectation of success since both Brenner and Rittie teach methods for analysis of DNA. The combination of prior art elements according to known methods to yield predictable results supports a conclusion of obviousness. See MPEP 2143(I) A.
Thus, Brenner in view of Rittie makes obvious instant claims 2, 4, 13 - 14, 18 - 20, 22, and 24.
IV. Claims 3, 11, and 23 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Brenner (US 2008/0318802 Al) and evidenced by Nannya (Cancer Res 2005;65: (14) July 15, 2005) as applied to claims 1, 6 – 10, 12, 15 – 17, 21, and 25 above, and further in view of Lockhart (US 6,361,947 B1).
The teachings of Brenner have been discussed in the rejection for claims 1 and 21 above and apply.
Regarding claims 3 and 23, Brenner had taught wherein the target DNA is fragmented, as discussed.
However, Brenner had not taught fragmented DNA is sheared as recited in instant.
However, before the time of the effective filing date, the skilled artisan was aware of various means for fragmenting DNA for PCR, labelling, and oligonucleotide modifications for further analysis, for e.g., as taught in the art of Lockhart. Lockhart had provided methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample (abstract). Lockhart had taught physical fragmentation methods may involve subjecting the DNA to a high shear rate. Further, Lockhart had taught how one may achieve such shearing (column 9, 1st para).
Regarding claim 11, Brenner had taught the recitation of claim 10; i.e., a plurality of target molecules, but had not specifically taught ratios of tags to target DNA as recited in claim 11.
Lockhart had taught their method requires an excess of oligonucleotides to target DNA (biotin-tagged oligonucleotides containing sequences complementary to the regions of desired SNPs were mixed with target DNA in a 1000:1 ratio. (Alternatively, a 10:1, 20:1, 50:1, 250:1 or any other ratio could have been chosen), column 19, 5th para titled SNP Discovery-Method 4). Thus, it is implied that Lockhart had suggested the ratio of the greater of n1 and n2 to m is smaller than 0.2, as recited in claim 11.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to modify the target DNA in the composition used in the method of Brenner with sheared DNA as taught by Lockhart. One would have been motivated to make such a modification in order to receive the expected benefit of low complexity DNA which in turn would enable more efficient PCR and oligonucleotide modification, as taught by Lockhart. Further, one of skill in the art knows, the reason why PCR works is because initially there is a large excess of primer over target DNA, so the hybridizations take place very rapidly. Therefore, one of skill in the art would be motivated to use excess of labels over DNA to achieve higher efficiency of hybridization or ligation. One of ordinary skill in the art would have a reasonable expectation of success since both Brenner and Lockhart teach methods for analysis of DNA. The combination of prior art elements according to known methods to yield predictable results supports a conclusion of obviousness. See MPEP 2143(I) A.
Thus, Brenner in view of Lockhart makes obvious instant claims 3, 11, and 23.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Response to Arguments
Applicant’s arguments with respect to claim(s) 1 - 20 rejected under § 103 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
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.
The rejections below are maintained for reasons of record set forth in the office action of 9-10-2025, and reiterated below.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 26 - 30, 39 – 67, 73 – 118, 124 - 138 of U.S. Patent No.8,835,358 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 26 of the ‘358 patent is drawn to a method that comprises attaching a label from a set of diverse labels to each occurrence of a first target molecule and detecting each molecule by detecting each label present on the new molecule and counting the number of new molecules, wherein the number of label is m, and the number of first molecule is n. Claim 27 from the ‘358 patent further recites that the ratio of m to n is greater than 50.
It would have been obvious to an ordinary skilled in the art to use the claimed composition of the present application in the method of the ‘358 patent because their method requires the attaching of a label to a number of occurrences of a target molecule and counting the new labeled molecules. The ratio of m to n is greater than 50 claimed in claim 27 of the ‘358 patent is same as the ratio of n to m smaller than 0.02 claimed in claim 11 of the present application.
Although the method in claim 26 of the ‘358 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method, this is evidenced by claims 42 and 43 of the ‘358 patent, wherein the method recites additional target molecules are included in the sample.
Therefore, instant claims 1 – 20 would have been obvious to use in the method as claimed in claims 26 - 30, 39 – 67, 73 – 118, 124 - 138 of the ‘358 patent;
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 123, 145 – 155, 157 - 161, 163 – 164, and 172 of U.S. Patent No.9315857 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 123 of the ‘857 patent is drawn to a method that comprises attaching a label from a set of diverse labels to multiple copies of target molecules and detecting each molecule by detecting each label present on the new molecule and counting the number of new molecules, wherein the target is fragmented DNA.
It would have been obvious to an ordinary skilled in the art to use the claimed composition of the present application in the method of the ‘857 patent because their method requires the attaching of a label to a number of occurrences of a target molecule and counting the new labeled molecules.
Although the method in claim 123 of the ‘857 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method, this is evidenced by [0238] of the disclosure that describes preparation of the target which is fragmented DNA from genomic DNA, thus encompassing any target molecules are included in the sample.
Therefore, instant claims 1 – 20 would have been obvious to use in the method as claimed in claims 123, 145 – 155, 157 - 161, 163 – 164, and 172 of the ‘857 patent;
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31 – 66, and 68 - 71 of U.S. Patent No.9816137 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 31 of the ‘137 patent is drawn to a method that comprises attaching a primer wherein the primer comprises a different variable region to multiple copies of nucleic acids, amplifying, and detecting each labelled molecule by detecting each label present on the new molecule and counting the number of new molecules. Dependent claims require the target to be genomic DNA, and the label further comprising a universal primer.
It would have been obvious to an ordinary skilled in the art to use the claimed composition of the present application in the method of the ‘137 patent because their method requires the attaching of a label to a number of occurrences of a target molecule and counting the new labeled molecules; i.e., the components of instant claim.
Although the method in claim 31 of the ‘137 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method, this is evidenced by claim 55 of the reference application that recites the target which is genomic DNA, thus encompassing any target molecules are included in the sample.
Therefore, instant claims 1 – 20 would have been obvious to use in the method as claimed in claims 31 – 66, and 68 - 71 of the ‘137 patent;
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 7 - 15, 17, 19 – 20, 26 - 31 of U.S. Patent No.9,290,809 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements of a composition that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 1 of the ‘809 patent is also drawn to a composition used in a method that comprises attaching a label from a set of diverse labels to each occurrence of a first target molecule and detecting each molecule by detecting each label present on the new molecule and counting the number of new molecules, wherein the number of label is m. Dependent claims further recite the number of first molecule is n. Claim 15 from the ‘809 patent further recites that the ratio of m to n is greater than 5.
It would have been obvious to an ordinary skilled in the art to utilize the claimed composition of the present application in place of the claimed composition of the reference application in a method that requires the attaching of a label to a number of occurrences of a target molecule and counting the new labeled molecules. The ratio of m to n is greater than 5 claimed in claim 15 of the ‘809 patent is same as the ratio of n to m smaller than 0.2 claimed in claim 11 of the present application.
Although the composition of the ‘809 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the method requiring the composition, this is evidenced by claim 29 of the ‘809 patent, wherein the composition requires “two or more different target sequences”.
Therefore, instant claims 1 – 25 are obvious over claims 1, 7 - 15, 17, 19 – 20, 26 - 31 of the ‘809 patent;
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31 – 58, 60, 63 - 67 of U.S. Patent No.10,619,203. Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claims 31 and 34 of the ‘203 patent are drawn to a method of randomly attaching label sequences from a set of m label sequences to first target molecule that comprises a first allele at a first polymorphic site and a second target molecules that comprises a second allele at a second polymorphic site in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art that the claimed method of claims 1 and 34 of the ‘203 patent utilizes the composition of instant claims 1 - 25 (of the present application). The ‘203 patent’s recitation of the target molecule to comprising a first allele at a first polymorphic site and second target molecules comprises a second allele at a second polymorphic site encompasses instant claim’s recitation of:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A.
It would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice of the method and that these targets could be the same as recited in instant claims.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claims 31 and 34 of the ‘203 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31-50 of U.S. Patent No. 10,047,394. Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 31 of the ‘394 patent is drawn to a method of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2, and wherein more than 90% of the new first and second molecules have a label that is different from the labels on the other new first molecules and new second molecules.
It would have been obvious to an ordinary skilled in the art that the claimed method of claim 31 of the ‘394 patent utilizes the composition of instant claims 1 - 25. As such, the composition recited in Claims 1 - 25 of the present application are not patentably distinct from a composition needed to perform the method of claim 31 from the ‘394 patent.
Although the method in claim 31 of the ‘394 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that the first and second target molecules that are present in the sample for practice of the method; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘394 patent, wherein the method described in [0106] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 31 of the ‘394 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 10,202,646. Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 1 of the ‘646 patent is drawn to a method of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2, and wherein more than 90% of the new first and second molecules have a label that is different from the labels on the other new first molecules and new second molecules.
It would have been obvious to an ordinary skilled in the art that the claimed method of claim 1 of the ‘646 patent utilizes the composition of instant claims 1 - 25 of the present application. As such, the composition claimed in Claims 1 - 25 of the present application are not patentably distinct from the composition needed to practice the method of claim 1 from the ‘646 patent.
Although the method in claim 1 of the ‘646 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘646 patent, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 1 of the ‘646 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 10,392,661. Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 1 of the ‘661 patent is drawn to a method of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art that the claimed method of claim 1 of the ‘661 patent utilizes the composition of instant claims 1 - 25. As such, the composition claimed in claims 1 - 25 of the present application are not patentably distinct from the composition used in the method of claim 1 from the ‘661 patent.
Although the method in claim 1 of the ‘661 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘661 patent, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 1 of the ‘661 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31, 33 – 36, 38 - 67 of U.S. Patent No. 10,059,991. Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 31 of the ‘991 patent is drawn to a method of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, amplifying the labeled first and second target molecule to create clonal population of the first and second molecule, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2, and wherein more than 90% of the new first and second molecules have a label that is different from the labels on the other new first molecules and new second molecules.
It would have been obvious to an ordinary skilled in the art that the claimed method of claim 31 of the ‘991 patent utilizes the composition of instant claims 1 - 25 of the present application. As such, the method claimed in Claims 1 - 25 of the present application is not patentably distinct from the method of claim 1 from the ‘991 patent.
Although the method in claim 31 of the ‘991 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘991 patent, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence. Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 1 of the ‘991 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 31-58 of U.S. Patent No. 12,060,607 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 31 of the ‘607 patent is drawn to a method that comprises the steps of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claims of the ‘607 patent. As such, the method claimed in Claims 1 - 25 of the present application is not patentably distinct from the method of claim 1 from the ‘607 patent.
Although the method in claim 31 of the ‘607 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘607 patent, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 31 of the ‘607 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-30 and 39 of Patent No. 11993814 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claims 1 and 39 of the ‘814 patent are drawn to a method that comprises the steps of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claims 1 and 39 of the ‘814 patent. As such, the composition claimed in Claims 1 - 25 of the present application is not patentably distinct from the method of claim 1 from the ‘814 patent.
Although the method in claims 1 and 39 of the ‘814 patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘814 patent, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 1 and 39 of the ‘814 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31-53 of Patent No. 11,970,737 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 31 of the ‘737 patent is drawn to a method that comprises the steps of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claim 31 of the ‘737 patent because the reference application requires the components of Claims 1 - 25 of the present application except the patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method,; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘737 patent, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence. Therefore, the inclusion of this wherein clause does not make change to the steps of method claimed in claim 1 of reference application. As such, the method claimed in Claims 1 - 25 of the present application is not patentably distinct from the method of claim 31 from the ‘737 patent.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 31 of the ‘737 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 23 - 42 of reference application No. 18771886 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 23 of the ‘886 reference application is drawn to a method that comprises the steps of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claim 23 of the ‘886 reference application because the reference application requires the components of Claims 1 - 25 of the present application except the ‘886 reference application does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘886 reference application, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence. As such, the composition claimed in Claims 1 - 25 of the present application are not patentably distinct from the method of claim 23 from the ‘870 reference application.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 23 of the ‘886 reference application.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 39-58 of Application No. 18/643,870 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 39 of the ‘870 patent is drawn to a method that comprises the steps of randomly attaching diverse label sequences from a set of m different label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claim 31 of the ‘870 application because the reference application requires the components of Claims 1 - 25 of the present application except the reference application does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method,; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘870 reference application, wherein the method described in [0013] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence. As such, the method claimed in Claims 1 - 25 of the present application is not patentably distinct from the method of claim 31 from the ‘870 reference application.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 39 of the ‘870 reference application.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 - 27 of Patent No. 9290808 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 1 of the ‘808 patent is drawn to a method that comprises the steps of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claim 1 of the ‘808 patent because the reference application requires the components of Claims 1 - 25 of the present application except the patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that multiple targets may be present in the sample for practice the same method,; it would have been obvious to an ordinary skilled in the art looking at the disclosure of the ‘808 patent, wherein the method described in [012] discloses that the method can simultaneously count copies of multiple target sequences, without specifically naming any target sequence. As such, the method claimed in Claims 1 - 25 of the present application is not patentably distinct from the method of claim 1 from the ‘808 patent.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 1 of the ‘808 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Claims 1 - 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 308 - 335 of Patent No. 9845502 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because they are both drawn to elements that are used in a method of detecting nucleic acid sequences by attaching diverse sequences (labels) to one end of the sequences to be detected, thus overlapping in scope.
Claims of the present application are drawn to a composition that comprises diverse label sequences and enzymes for attaching these to a plurality of occurrences of at least one target sequence, wherein the number of labels is m, and number of occurrences of first and second target molecules is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
Claim 308 of the ‘502 patent is drawn to a method that comprises the steps of randomly attaching label sequences from a set of m label sequences to first target molecule and a second target molecules in a sample, and detecting the new molecule having label attached to the target sequences by detecting the label sequence, wherein the number of label is m, and number of occurrences of first and second target molecule is n1 and n2 respectively, and the ratio of the greater of n1 and n2 to m is smaller than 0.2.
It would have been obvious to an ordinary skilled in the art to utilize the composition of instant claims 1 - 25 in the claimed method of claim 308 of the ‘502 patent because the reference application requires the components of Claims 1 - 25 of the present application except the patent does not recite:
four or more biotin-tagged oligonucleotides containing sequences each complementary to at least one of the four or more distinct target molecules wherein at least one of the four or more distinct target nucleic acid molecules is PIK3R1, MYC, CCND2, or CDKN2A; it would have been obvious to an ordinary skilled in the art that the “plurality of target molecules present in the single cell” recited in reference claim 308 for practice of the method could encompass the recited genes instant claim 1. As such, the method claimed in Claims 1 - 25 of the present application are not patentably distinct from the method of claim 308 from the ‘502 patent.
Therefore, claims 1 - 25 would have been obvious to use in the method as claimed in claim 308 of the ‘502 patent.
Any additional limitations of the reference application claims are encompassed by the open claim language “comprises” found in the instant claims.
Response to Arguments
It is noted the response requests that double patenting rejections be held in abeyance until the rejections outstanding in the instant application are overcome. All the double patenting rejections are maintained for reasons of record (reiterated above).
Conclusion
No claims are allowed.
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SHABANA S. MEYERING, Ph.D.
Examiner
Art Unit 1635
/SHABANA S MEYERING/ Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635