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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on December 22, 2025 has been entered.
Applicant’s amendment filed on December 22, 2025 is acknowledged and has been entered. Claim 1 has been amended. Claims 7-9 have been canceled. Claims 1-6 and 10-22 are pending.
Claims 1-6 and 10-22 are discussed in this Office action.
All of the amendments and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons discussed below. Any rejection not reiterated in this action has been withdrawn as being obviated by the amendment of the claims. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
This action is made NON-FINAL as necessitated by Amendment.
New Grounds of Rejection
Priority
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 61395850, 61398159, 61462972, 61448547, 61675020, 61683331 fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or
more claims of this application. These priority documents of '850, '159 and '547 provide support
for cell-free or free-floating DNA, multiplex amplification but does not provide support for barcodes or barcoding. While each of these priority documents 61448547, 61462972,
61426208, 61398159, 61395850 include support for universal adaptors or universal amplification and mutation detection, none of these priority documents include sufficient (or any) support for the inclusion of barcodes or barcode primers. Finally, the '331 document does not provide support for analysis of cell-free DNA, as claimed.
The earliest priority date with support for the claimed method is April 12, 2011 as provided by priority document 61516996.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on December 22, 2025 was filed in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-6, 10, 12-15, 17, 20-21 is/are rejected under 35 U.S.C. 103 as being unpatentable over May et al. (US PGPub 20140227691; August 2014) in view of McCloskey et al. (PgPub 20070020640; January 2007).
With regard to claim 1, May teaches a method for preparing a non-naturally occurring composition of amplified DNA from a sample, comprising:
tagging isolated cell free DNA with one or more universal tail adaptors to generate tagged products, wherein the isolated cell-free DNA is isolated from a blood sample collected from a pregnant woman, and wherein the isolated cell-free DNA comprises a mixture of fetal cell-free DNA and maternal cell-free DNA (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification);
amplifying the tagged products one or more times to generate final amplification products, wherein one of the amplifications comprises targeted amplification of a plurality of single nucleotide polymorphism (SNP) loci in a single reaction volume (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification);
and sequencing the plurality of SNP loci on the cell free DNA by conducting massively parallel sequencing on the final amplification products, wherein the plurality of SNP loci comprises 50-2,000 SNP loci (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification), wherein the method further comprises determining the likelihood of the presence or absence of a single gene disease in the fetus using sequence reads of the plurality of SNP loci generated from the massively parallel sequencing (abstract; paragraph 202, where the method can be employed in genotyping and diagnosis of disease).
With regard to claim 2, May teaches a method of claim 1, wherein tagging the cell free DNA comprises ligating the one or more universal tail adaptors to the cell free DNA (paragraph 78, where a universal tag is included; see also paragraph 154 where universal priming sites are described).
With regard to claim 3, May teaches a method of claim 2, wherein the one or more universal tail adaptors each comprise a first strand and a second strand, wherein a first end of each of the universal tail adaptors comprises a double-stranded section comprising the 5' portion of the first strand and the 3' portion of the second strand, wherein the first end is ligated to the cell free DNA (paragraph 78, where a universal tag is included; see also paragraph 154 where universal priming sites are described).
With regard to claim 4, May teaches a method of claim 3, wherein amplifying the tagged products comprises a first amplifying step and a second amplifying step, wherein the first amplifying step comprises using a first target-specific primer that specifically anneals to a target sequence and a first adaptor primer having a nucleotide sequence identical to a first portion of the first strand to generate a first amplification product (paragraph 78, where a universal tag is included; see also paragraph 154 where universal priming sites are described).
With regard to claim 5, May teaches a method of claim 4, wherein the second amplifying step comprises using a second target-specific primer that specifically anneals to the first amplification product and a second adaptor primer having a nucleotide sequence identical to a second portion of the first strand to generate the final amplification product (paragraph 119-123, where nested pre-amplification is described).
With regard to claim 6, May teaches a method of claim 5, wherein the second adaptor primer is nested relative to the first adaptor primer (paragraph 119-123, where nested pre-amplification is described).
With regard to claim 12, May teaches a method of claim 1, wherein the one or more universal tail adaptors comprise a first universal tail adaptor and a second universal tail adaptor (paragraph 78, where a universal tag is included; see also paragraph 154 where universal priming sites are described).
With regard to claim 13, May teaches a method of claim 12, wherein tagging the cell free DNA comprises amplifying the cell free DNA with a first primer comprising the first universal tail adaptor and a second primer comprising the second universal tail adaptor (paragraph 78, where a universal tag is included; see also paragraph 154 where universal priming sites are described).
With regard to claim 14, May teaches a method of claim 12, wherein amplifying the tagged products comprises a single amplifying step (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification).
With regard to claim 15, May teaches a method of claim 14, wherein amplifying the tagged products comprises using a third primer and a fourth primer, wherein the third primer comprises a first sequencing tag and wherein the fourth primer comprises a second sequencing tag (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification).
With regard to claim 17, May teaches a method of claim 1, further comprising determining the presence or absence of aneuploidy in the fetus using sequence reads of the plurality of SNP loci generated from the massively parallel sequencing (Example 1, looks to enriched samples to analyze for fetal aneuploidy; see also paragraph 210 and 212 to 214).
With regard to claim 20, May teaches a method of claim 1, further comprising determining the presence or absence of a copy number variation in at least a portion of a chromosome (paragraph 69 to 76, where detection of copy number variations or differences are detected).
With regard to claim 21, May teaches a method of claim 16, further comprising determining the presence or absence of a copy number variation in at least a portion of a chromosome (paragraph 69 to 76, where detection of copy number variations or differences are detected).
Regarding claims 1 and 10, while May teaches the steps of the method as recited above, May does not teach wherein one of the amplifications introduces a barcode and one or more sequencing tags.
With regard to claim 1, McCloskey teaches wherein one of the amplifications introduces a barcode and one or more sequencing tags and wherein the final amplification product products comprise at least 50 different barcodes (paragraph 21, where "random barcode" refers to an arbitrary sequence that can uniquely identify a target nucleic acid in an experiment, and whose sequence is unknown at the start of the experiment; later in the same paragraph, McCloskey notes "a second sequence of 7 random nucleotides N selected from A, G, C, and Twill provide a maximum of 47 or 16,384 unique barcodes. In some embodiments, the length of the second sequence is between 3 and 30 nucleotides, such as between 5 and 25 nucleotides or between 7 and 13 nucleotides"; see Example 1, p 6, paragraph 53, where barcodes are useful in identifying unique sequences; see also Example 2, p 7, paragraph 63, where barcodes are again useful in identification of unique sequences; see also Table 1, for example; see also paragraph 5-6 and 106, for example, where sequencing tags are added).
With regard to claim 10, McCloskey teaches a method of claim 1, wherein the one or more universal tail adaptors comprise a second barcode (paragraph 21, where "random barcode" refers to an arbitrary sequence that can uniquely identify a target nucleic acid in an experiment, and whose sequence is unknown at the start of the experiment; later in the same paragraph, McCloskey notes "a second sequence of 7 random nucleotides N selected from A, G, C, and Twill provide a maximum of 47 or 16,384 unique barcodes. In some embodiments, the length of the second sequence is between 3 and 30 nucleotides, such as between 5 and 25 nucleotides or between 7 and 13 nucleotides"; see Example 1, p 6, paragraph 53, where barcodes are useful in identifying unique sequences; see also Example 2, p 7, paragraph 63, where barcodes are again useful in identification of unique sequences; see also Table 1, for example; see also paragraph 5-6 and 106, for example, where sequencing tags are added).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the method of May to include multiple individual barcodes of McCloskey to arrive at the claimed invention with a reasonable expectation for success. Both May and McCloskey teach methods that include steps of primers, amplification and sequencing. May and McCloskey use the barcodes within the method in different ways. McCloskey teaches "the present invention provides methods for authenticating a nucleic acid molecule and its sequence with a molecular barcode and batch-stamp. In another aspect, the present invention provides methods for authenticating a nucleic acid amplification product" (Abstract). As an example, McCloskey also teaches "There were 22 sequences with a barcode that was identical to a sequence already obtained (i.e., redundant sequences). The remaining 110 sequences had distinct barcode regions that were 5 nucleotides long, indicating that those sequences originated from separate cells, or separate genomic target molecules" (paragraph 53). Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the method of May to include random and different, individual barcodes of McCloskey to arrive at the claimed invention with a reasonable expectation for success.
Claim(s) 11, 16, 18-19 and 22 is/are rejected under 35 U.S.C. 103 as being unpatentable over May et al. (US PGPub 20140227691; August 2014) in view of McCloskey et al. (PgPub 20070020640; January 2007) as applied over claims 1-6, 10, 12-15, 17, 20-21 and further in view of Rava et al. (US 2012/0010085; January 2012).
With regard to claim 18 and 19, May teaches a method for preparing a non-naturally occurring composition of amplified DNA from a sample, comprising:
tagging isolated cell free DNA with one or more universal tail adaptors to generate tagged products, wherein the isolated cell-free DNA is isolated from a blood sample collected from a pregnant woman, and wherein the isolated cell-free DNA comprises a mixture of fetal cell-free DNA and maternal cell-free DNA (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification);
amplifying the tagged products one or more times to generate final amplification products, wherein one of the amplifications comprises targeted amplification of a plurality of single nucleotide polymorphism (SNP) loci in a single reaction volume (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification);
and sequencing the plurality of SNP loci on the cell free DNA by conducting massively parallel sequencing on the final amplification products, wherein the plurality of SNP loci comprises 50-2,000 SNP loci (paragraph 199 where up to 1000 loci are amplified via multiplex; paragraph 71, 198, 110 where the method of amplification includes pre-amplification steps before multiplex amplification; see paragraph 76, where cell free nucleic acid is amplified using steps of pre-amplification and multiplex amplification), wherein the method further comprises determining the likelihood of the presence or absence of a single gene disease in the fetus using sequence reads of the plurality of SNP loci generated from the massively parallel sequencing (abstract; paragraph 202, where the method can be employed in genotyping and diagnosis of disease).
With regard to claim 11, Rava teaches a method of claim 1, wherein the one or more universal tail adaptors comprise a second sequencing tag (paragraph 123 and 171, where the method can be used for disease diagnosis; see also paragraph 143, where next generation or massively parallel sequencing is described).
With regard to claim 16, Rava teaches a method of claim 1, further comprising determining fetal fraction of the isolated cell-free DNA using sequence reads of the plurality of SNP loci generated from the massively parallel sequencing (paragraph 123 and 171, where the method can be used for disease diagnosis; see also paragraph 143, where next generation or massively parallel sequencing is described).
With regard to claim 18, Rava teaches a method of claim 1, further comprising co-amplifying a known quantity of a plurality of reference standards that amplify with essentially the same efficiency as a plurality of SNP loci in the targeted amplification, and using the reference standards correct for amplification bias that may occur between different SNP loci (paragraph 123 and 171, where the method can be used for disease diagnosis; see also paragraph 143, where next generation or massively parallel sequencing is described).
With regard to claim 19, Rava teaches a method of claim 1, further comprising co-amplifying a known quantity of a reference standard that amplifies with essentially the same efficiency as a SNP locus in the targeted amplification, and using the reference standards for absolute quantification of a mutation or minor allele at the SNP locus (paragraph 123 and 171, where the method can be used for disease diagnosis; see also paragraph 143, where next generation or massively parallel sequencing is described).
With regard to claim 22, Rava teaches a method of claim 21, further comprising co-amplifying a known quantity of a reference standard that amplifies with essentially the same efficiency as a SNP locus in the targeted amplification, and using the reference standards for absolute quantification of a mutation or minor allele at the SNP locus (paragraph 88 and example 13, where copy number is key to analysis).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the method of May and McCloskey to include sequencing tags and determination of fetal fraction as described by Rava to arrive at the claimed invention with a reasonable expectation for success. Each of Rava, May and McCloskey teach methods that include steps of primers, amplification and sequencing. May and McCloskey use the barcodes within the method in different ways. Rava teaches “there is a need for additional methods that would enable the determination of the fraction of fetal nucleic acid in both male and female pregnancies. The method of the invention fulfills the need in providing the means to determine fetal fraction that is independent of the gender of the fetus. The method can be applied for determining simultaneously the presence or absence of a chromosomal aneuploidy or other copy number variation, and may be used in conjunction with nay known methods that are used to determine aneuploidies in maternal sample” (paragraph 7 and 8 on p 1 of Rava). Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the method of May to include random and different, individual barcodes of McCloskey to arrive at the claimed invention with a reasonable expectation for success.
Response to Arguments
Applicant's arguments filed December 22, 2025 have been fully considered but they are not persuasive.
Applicant traverses the obviousness rejection over Pieprzyk in view of McCloskey, Gormally and Gnirke. Applicant argues regarding molecular barcodes, "The Office Action cites paragraphs [0098] and [0285] of Pieprzyk for allegedly disclosing molecular barcodes. (Office Action, p. 8, para. 1.) Applicant respectfully disagrees, at least because both paragraphs [0098] and [0285] of Pieprzyk refer to sample barcodes and not molecular barcodes, as the Office Action itself acknowledges later (Office Action, p. 8, para. 2)." (p 6-7 of remarks)
Applicant quotes specific passages of 98 and 285 and argues "clearly refer to sample barcodes for purpose of tagging DNA molecules derived from the same sample with the same barcode such that sample origin of the amplicons can be identified, as opposed to molecular barcodes of the presently claimed invention by which "sequence reads derived from the same original cell-free DNA molecule are identified". (p 7 of remarks)
Applicant quotes a paragraph in paragraph 407. Applicant concludes "a person having ordinary skill in the art would have understood that Pieprzyk refers to sample barcodes for sample multiplexing and sample origin determination, and not molecular barcodes. Pieprzyk at least fails to teach or suggest "wherein the extracted cell-free DNA from the biological sample is tagged with a plurality of different molecular barcodes" (p 7 of remarks).
Next, regarding the McCloskey reference, Applicant argues there was no motivation provided to combine the teachings - Applicant argues case law at length and argues "fails to provide a reason why one of skill in the art should adjust the sample barcodes of Pieprzyk to include the random and different, individual barcodes of McCloskey" (p 9 of remarks)
Regarding McCloskey, Applicant argues "Furthermore, McCloskey is primarily directed to methods for authenticating an amplification product by "contacting a target nucleic acid molecule in a sample with a bar-coded oligonucleotide under suitable conditions to anneal the bar-coded oligonucleotide to the target nucleic acid molecule, wherein the bar-coded oligonucleotide comprises a first sequence complementary to the target nucleic acid molecule" (p 9 of remarks).
Applicant also argues "McCloskey used a barcoded oligonucleotide to tag a single specific target nucleic acid to generate a genomic template covering a specific gene (ligated target molecule), which can be used to authenticate a PCR reaction, as shown in Examples 1- 4 of McCloskey" (p 9 of remarks).
Applicant further argues "McCloskey does not teach or suggest "the extracted cell-free DNA from the biological sample is tagged with a plurality of different molecular barcodes," as recited by the present claims" and "McCloskey fails to teach or suggest and that "sequence reads derived from the same original cell-free DNA molecule are identified using the molecular barcode," as recited by the present claims" (p 9 of remarks).
Finally, Applicant concludes "Pieprzyk is not concerned with identifying sequence reads that were derived from the same original cell-free DNA molecule. As explained above, Pieprzyk is only concerned with pooling samples, therefore one of skill in the art would not be motivated to add molecular barcodes to the methods of Pieprzyk" (p 9 of remarks).
Applicant argues Gnirke and Gormally do not cure the deficiencies of Gormally (epigenetic changes in cancer) or Gnirke (hybrid capture probes) -
In response, these arguments have been carefully considered, but they are not persuasive. Applicant's arguments are centered on the aspects of the method that are focused on identification and the usefulness of the molecular barcodes in steps of identification, as claimed, in the method. While Applicant argues there is no motivation to combine Pieprzyk and McCloskey, like Applicant's method, both of these references are focused on methods that include amplification, barcodes and identification of specific target sequences.
While Applicant argues that McCloskey uses their barcode in a way that is distinct from Applicant's method, and Applicant argues McCloskey "fails to teach or suggest and that "sequence reads derived from the same original cell-free DNA molecule are identified using the molecular barcode," as recited by the present claims, in fact, on this subject, McCloskey specifically teaches "'random barcode' refers to an arbitrary sequence that can uniquely identify a target nucleic acid in an experiment, and whose sequence is unknown at the start of the experiment. (paragraph 21). Further, regarding the issue of identification, McCloskey teaches "Each genomic fragment is marked prior to amplification, allowing us to identify contaminant and redundant sequences and to quantify accurately the proportion of cells carrying a particular sequence variant by counting only distinctly tagged sequences". Just like the instantly claimed method is focused on "obtaining an identity derived from the sequence reads of one or more genetic or epigenetic features ... wherein sequence reads derived from the same original cell-free DNA molecule are identified using the molecular barcode", McCloskey is focused on counting only uniquely tagged sequence variants.
Next, while Applicant argues Pieprzyk is not interested in identifying sequence reads and only focused on pooling, Pieprzyk teaches the method can be focused on identification in a variety of contexts. For example, Pieprzyk teaches "The methods of the invention are applicable to any technique aimed at detecting the presence or amount of one or more target nucleic acids in a nucleic acid sample. Thus, for example, these methods are applicable to identifying the presence of particular polymorphisms (such as SNPs), alleles, or haplotypes, or chromosomal abnormalities, such as amplifications, deletions, or aneuploidy. The methods may be employed in genotyping, which can be carried out in a number of contexts, including diagnosis of genetic diseases or disorders, pharmacogenomics (personalized medicine), quality control in agriculture (e.g., for seeds or livestock), the study and management of populations of plants or animals (e.g., in aquaculture or fisheries management or in the determination of population diversity), or paternity or forensic identifications. The methods of the invention can be applied in the identification of sequences indicative of particular conditions or organisms in biological or
environmental samples" (pp 298). Further, as established in the rejection of record, at Example 10, which describes a "method of fetal aneuploidy detection by next generation sequencers as published by both Quake and Lo", a "multiplex reaction is performed and then run on the sequencer. They both create reactions products that can be identified and counted to make the determination of aneuploidy" (pp 626-632). While Pieprzyk incorporates molecular barcodes in the method of aneuploidy determination, identification of specific sequences is a key part of the method as described by Pieprzyk.
For at least these reasons, while Applicant's arguments have been considered, they are not sufficient to place the claims in condition for allowance and the rejections are maintained.
Conclusion
No claims are allowed. All claims stand rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681