DETAILED ACTION
The present Office Action is responsive to the Amendment received on June 26, 2026.
Preliminary Remark
Claims 2-4, 6, 8, 11-18, 20-29, 31, 32, 34-36, 38-40, 42-107, 109, and 112 are canceled.
Claims 30, 33, and 37 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention without traverse.
Information disclosure statement
The IDS received on June 26, 2026 and July 10, 2026 are proper and are being considered by the Examiner. The requisite fee under 37 CFR 1.97(v)(3) was satisfied with said submission. Both IDS have been submitted with 37 CFR 1.17(p) as required and so charged.
Claim Rejections - 35 USC § 112
The rejection of Claims 1, 5, 7, 9, 10, 19, 41, 108, 110, 111, and 113-119 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter, made in the Office Action mailed on April 1, 2026 is withdrawn in view of the Amendment received on June 26, 2026.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The rejection of claims 1, 5, 7, 9, 19, 41, 108, 110, 111, and 113-119 under 35 U.S.C. 103 as being unpatentable over Kinde et al. (PLoS One, July 2012, vol. 7, issue 7, e41162, pages 1-8) in view of Douville et al. (PNAS, February 20, 2018, vol. 115, no. 8, pages 1871-1876), Boyle et al. (PNAS, 1990, vol. 87, pages 7757-7761), and Murata et al. (Scientific Reports, October 2017, vol. 7, pages 1-8), made in the Office Action mailed on April 1, 2026 is maintained for the reasons of record.
Applicants’ arguments presented in the Amendment received on June 26, 2026 have been carefully considered but they have not been found persuasive for the reasons discussed in the, “Response to Arguments” section.
The Rejection:
With regard to claims 1 and 119, Kinde et al. teach a method of detecting aneuploidy in a subject’s sample via use of a massively parallel sequencing means, wherein the method produces amplification products with the use of a single pair of primers for the purposes of karyotyping:
“commercially available tests for circulating fetal DNA aneuploidy involve the preparation of whole genome libraries and the analysis of sufficient number of sequences on the relevant chromosomes to reliably detect small differences in copy number. The preparation of whole genome libraries involves several sequential steps” (page 1, 2nd column, bottom paragraph to page 2, 1st column, 1st paragraph)
“We reasoned that this process could be simplified if a defined number of fragments from throughout the genome could be amplified using a single primer pair, obviating the need for end-repair, terminal 3’-dA addition, or ligation to adapters.” (page 2, 1st column, 2nd paragraph)
Therefore, Kinde et al. teach a method of testing for the presence of aneuploidy in a genome of a mammal (i.e., maternal fetal DNA is tested), comprising:
amplifying a plurality of chromosomal sequences in a DNA sample obtained from a mammal with a single pair of primers complementary to the chromosomal sequence to form a plurality of amplicons (see above), wherein the plurality of amplicons comprise sequences from a plurality of different chromosomes (“allowing amplification of well-dispersed, repeated elements”, page 2, 1st column, bottom paragraph; also “number of uniquely assigned tags per experiment spanned 12-fold range (1,343,382 to 16,015,347)”, page 6, 1st column, 3rd paragraph; 31,547,988 high quality tags per individual … could be uniquely mapped to one of an average of 23,681 unique chromosomal positions”, page 6, 2nd column, 3rd paragraph; see also Fig. 2);
determining at least a portion of the nucleic acid sequence of the plurality of amplicons to generate amplicon sequences (FAST-SeqS, see also page 6, 1st column 3rd paragraph);
mapping the amplicon to a reference genome (“[w]e recovered an average of 31,547,988 high quality tags per individual … could be uniquely mapped to one of an average of 23,681 unique chromosomal positions”, page 6, 2nd column, 3rd paragraph);
dividing the amplicon sequences into a plurality of genomic intervals;
quantifying read counts for amplicon sequences mapped to the genomic intervals (“organizing our data into a list of positions [i.e., intervals] … each associated with a tag count, we were able to apply standard quantile normalization to FAST-SeqS data”, page 4, 1st column, 1st paragraph; applies for steps (d) and (e)); and
comparing the read counts of the amplicon sequences in the genomic intervals on a chromosome arm to an expected distribution (from reference sample), thereby testing for the presence of aneuploidy in the genome of the mammal (see Fig. 3(A); also “one determines the mean and standard deviation of tag counts lying within a chromosome of interest in a group of reference samples (e.g., samples with known euploid content), and then creates a standardized score (i.e., z-score) for a chromosome of interest for each sample … outliers are easily detected because they have a z-score > 3.0 … indicates that the normalized tag count of the outlier exceeds the mean of the reference group by at least three standard deviations”, page 4, 1st column, bottom paragraph to page 5, 1st column, 1st paragraph).
With regard to claims 5, 9, 110, and 111 the DNA is a biological sample from a subject (“DNA was obtained from normal spleen, peripheral blood, white blood cells (WBCs, or plasma from patients”, page 2, 1st column, 3rd paragraph).
With regard to claim 7, the sample is from plasma (see above).
With regard to claim 41, at least 300,000 amplicons are formed in the step of amplifying using said single primer pair (“[w]e recovered an average of 31,547,988 high quality tags per individual … could be uniquely mapped to one of an average of 23,681 unique chromosomal positions”, page 6, 2nd column, 3rd paragraph).
With regard to claim 113, the expected distribution is a normal distribution (i.e., distribution based on euploidy).
With regard to claims 114 and 115, z-score is generated and analyzed (see pages 4 and 5).
Kinde et al. explicitly teach that their method employs single pair of primers that target repetitive nucleotide element found within the human genome (“FAST-1 amplification primers … allowing amplification of well-dispersed, repeated elements”, page 2, 1st column, bottom paragraph), but do not explicitly teach the use of all types of such elements that can be utilized in their method.
Consequently, SINEs are not targeted by the single pair of primers, and therefore, the artisans are silent with respect to the genomic intervals being from about 100 to 125,000,000 nucleotides (claim 19).
As well, the amplicons generated in the method of Kinde et al. have an average amplicon length range of 124 to 142 bp, which is slightly beyond that of 10-110 bps (claim 108)
Kinde et al. do not explicitly teach that the amount of starting sample DNA is between 0.01 pg to 500 pg.
While Kinde et al. explicitly teach that the method is for determining aneuploidy, the artisans do not explicitly utilize machine learning for classification (claims 116), when making an aneuploidy call (claim 117), based on the z-score (claim 118).
Douville et al. teach a method of utilizing machine-learning to determine aneuploidy status from amplification products produced by single pair of primers directed to LINEs:
“single primer pair can be used to amplify 38,000 long interspersed nuclear elements (LINEs) by FAST-SeqS … even in single cells derived from preimplantation embryos … We describe here … WALDO … an algorithm for amplicon-based aneuploidy detection … WALDO can be applied to identify chromosome arm gains or losses with improved sensitivity and equivalent specificity compared to previous approaches. Furthermore, we incorporate machine learning to make genome-wide aneuploidy calls, in which samples are classified according to their aneuploidy status” (page 1872, 1st column, 2nd paragraph)
Boyle et al. teach a well-recognized means amplifying SINEs for karyotyping (“we present an analysis of the chromosomal distribution of LINE and SINE sequences …” (page 7757, 2nd column, 3rd paragraph).
Murata et al. teach that starting DNA amounts in the picogram amounts can be amplified and analyzed (“[n]inety-picogram, or two-hundred and ninety picograms of mixed DNA samples were used in PCR …”, page 6).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Kinde et al. with the teachings of Douville et al., Boyle et al. and Murata et al., thereby arriving at the invention as claimed for the following reasons.
Kinde et al. teach a method of detecting aneuploidy in a human sample, wherein the artisans teach the use of a single pair of primers that target well-dispersed, repeated elements, as well as mapping, dividing into genomic intervals and comparing the read counts in the genomic intervals. While the artisans did not explicitly teach that other types of dispersed elements could be utilized in their method, one of ordinary skill in the art would have recognized that other prior art known repeat elements that are well-dispersed would have also yielded a predictable outcome.
Indeed, in combination with Douville et al. teaching that another prior art known, well-dispersed repeat element, LINEs, a known retrotransposable element is used in a similar process as that of Kinde et al. with the addition of utilizing machine learning for calculating the Z-score taught by Kinde et al. for classifying the aneuploidy status, one of ordinary skill in the art would have also have expected another retrotransposable element, SINEs, which had already been known in the art to be used in ploidy determination (i.e., karyotype, as taught by Boyle et al.) would have also yielded same predictable outcome when assayed in combination with the method taught by Kinde et al. and Douville et al.
As to the amount of starting DNA that can be utilized in the picogram range, such would have been within the reasonable expectation of successful range of amplification in view of the sensitivity demonstrated by Murata et al., yielding no more than a predictable outcome.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
For these reasons, the invention as claimed is deemed prima facie obvious over the cited references.
Response to Arguments:
Applicants traverse the rejection.
Applicants provide a separate summary of the teachings provided the cited references (page 7, Response).
On page 8, bottom to page 9, Applicants then appear to argue that the teachings of Murata are directed toward a pyrosequencing-based methylation assay for analysis of LINE-1 family and does not teach detection of aneuploidy (page 8, bottom). Applicants argue that the teachings of Murata is therefore vastly different from the method recited in claim 1, does not use a single primer pair, nor amplifies SINE, and does not detect aneuploidy (page 9, Response).
These arguments are not found persuasive because Applicants’ arguments are simply picking out each reference individually when the rejection was based on a combination of references.
One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
As discussed in the above rejection, the primary reference, Kinde et al. teach a method which employs a method which amplifies from a repetitive nuclear element (LINE) utilizing a single pair of primers that generate a plurality of unique amplicons, sequence the amplicons to generate a read count, map the amplicons, count the number of read counts to genomic intervals, for the purposes of detecting aneuploidy:
“commercially available tests for circulating fetal DNA aneuploidy involve the preparation of whole genome libraries and the analysis of sufficient number of sequences on the relevant chromosomes to reliably detect small differences in copy number. The preparation of whole genome libraries involves several sequential steps” (page 1, 2nd column, bottom paragraph to page 2, 1st column, 1st paragraph)
“We reasoned that this process could be simplified if a defined number of fragments from throughout the genome could be amplified using a single primer pair, obviating the need for end-repair, terminal 3’-dA addition, or ligation to adapters.” (page 2, 1st column, 2nd paragraph)
“allowing amplification of well-dispersed, repeated elements” (page 2, 1st column, bottom paragraph)
“number of uniquely assigned tags per experiment spanned 12-fold range (1,343,382 to 16,015,347)” (page 6, 1st column, 3rd paragraph)
“31,547,988 high quality tags per individual … could be uniquely mapped to one of an average of 23,681 unique chromosomal positions” (page 6, 2nd column, 3rd paragraph; see also Fig. 2)
“[w]e recovered an average of 31,547,988 high quality tags per individual … could be uniquely mapped to one of an average of 23,681 unique chromosomal positions” (page 6, 2nd column, 3rd paragraph)
“organizing our data into a list of positions [i.e., intervals] … each associated with a tag count, we were able to apply standard quantile normalization to FAST-SeqS data” (page 4, 1st column, 1st paragraph; applies for steps (d) and (e))
“one determines the mean and standard deviation of tag counts lying within a chromosome of interest in a group of reference samples (e.g., samples with known euploid content), and then creates a standardized score (i.e., z-score) for a chromosome of interest for each sample … outliers are easily detected because they have a z-score > 3.0 … indicates that the normalized tag count of the outlier exceeds the mean of the reference group by at least three standard deviations”, page 4, 1st column, bottom paragraph to page 5, 1st column, 1st paragraph).
While Kinde et al. do not explicitly extend their findings to apply for other repetitive elements, such as SINEs, the copy number variation determination, Boyle et al. teach a well-recognized means utilizing SINEs for karyotyping, to which karyotypes have long been associated with determining chromosomal numerical abnormalities:
“we present an analysis of the chromosomal distribution of LINE and SINE sequences …” (page 7757, 2nd column, 3rd paragraph).
Therefore, the Office contends that one of ordinary skill in the art would have had a reasonable expectation of success at applying the method of Kinde et al. and utilize them with SINEs based on their similar usability in karyotyping.
Indeed, the amplification of Alu-repeats (SINEs) have been employed in method of karyotyping in various assays, as evidenced by Mosch et al.:
“we developed a novel strategy of single-cell DNA quantitation of identified neurons on brain slices, based on slide-based cytometry (SBC), PCR amplification of alu-repeats, and chromogenic in situ hybridization (CISH), three independent methods with high intermethod reliability, and applied this method to quantify the DNA amounts of identified neurons in AD and normal adults” (page 6860, 1st column)
“the PI integral1 showed a highly significant correlation with the DNA content determined by PCR amplification of alu repeats” (page 6861, 1st column, bottom paragraph)
The legal standard for “reasonable expectation of success” is provided by case law and is summarized in MPEP 2144.08, which notes “obviousness does not require absolute predictability, only a reasonable expectation of success; i.e., a reasonable expectation of obtaining similar properties. See, e.g., In re O'Farrell, 853 F.2d 894, 903, 7 USPQ2d 1673, 1681 (Fed. Cir. 1988).”
As to Applicants’ arguments regarding the amount of input DNA being utilized, the Office is not convinced as the amount of starting DNA has been routinely optimized with amounts ranging in the picoliters, with the advent of PCR, for which Kinde et al. employs, with amounts shown by Murata et al.
The utilization of 0.01 picogram to 500 picogram (which is a 0.5 nanogram) of stating DNA in a method that involves an amplification reaction, therefore, is deemed well-within the optimizable range and not a surprising discovery.
The rejection is maintained therefore.
Conclusion
No claims are allowed.
The Office reiterates that claim 10 is free of prior art.
The closest prior art if Kinde et al., wherein the pair of primers employed to amplify their dispersed repeat elements show the below homology to that of SEQ ID NO: 1:
SEQ ID NO: 1 cgacgtaaaa cgacggccag tnnnnnnnnn nnnnnnn ggt gaaaccccgt ctctaca
CGACGTAAAA CGACGGCCAG TNNNNNNNNN NNNNNNN ACA CAGGGAGGGG AACAT
Kinde et al. (R1-for a, see Table S2, supplemental, attached)
As seen the sequence from 5’ end of the primer to the last base, “N”, these regions are identical as they are directed to a universal primer binding sequence and identifier sequences typically used in a commercially available next-gen sequencing reaction. The region following thereafter to the 3’ end, however, are different as this region is the region that anneals to the SINEs as presently claimed. As no prior art teaches or suggests this primer or the region to be targeted, the primers of the SEQ ID number pair 1 and 10 are deemed free of prior art. As well, their 95% homolog is also deemed free of prior art as the sequence variance within the length of the SEQ ID number reasonably allows for inclusion of mutations and/or modifications for optimization.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 September 8, 2026
/YJK/
1 PI integral is discussed as representative of “relative DNA content of the cells” see page 6860, 2nd column
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