DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The IDS received on July 18, 2024; August 20, 2024; September 3, 2025; October 29, 2025; and December 15, 2025 are proper and are being considered by the Examiner.
Drawings
The drawings filed on May 18, 2024 are acceptable.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 7 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 7 is indefinite because the claim does not provide any further limitation to that of parent claim 2. Cancelation is suggested.
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.
Claims 1-11 are rejected under 35 U.S.C. 103 as being unpatentable over Vaisvila et al. (Genome Research, published June 17, 2021, vol. 31, no. 7, pages 1280-1289) in view of Samoila et al. (JALM, July 2020, pages 788-797) and Chiu et al. (Blood, 2017, vol. 130, suppl_1, pages 1-3).
With regard to claims 1, 2, and 7, Vaisvila et al. teach a method of whole-genome sequencing from human cfDNA sample (“cfDNA was extracted from 5 mL human plasma”, page 1286) and sequencing the cfDNA sample for methylation of CpG sites across the genome, wherein the method involves no more than 9 amplification cycles (“EM-seq libraries had higher library yields using fewer PCR cycles for all DNA inputs … increasing the effective genome coverage”, page 1281, 2nd column, 4th paragraph; also Fig. 3A, where 8 PCR cycles were used for 10 ng of DNA input, 6 cycles were used for 50 ng of input DNA and 4 cycles were used for 200 ng of input DNA; “1-ng and 10-ng low-input EM-seq libraries both covered 54 million CpGs … the same number identified using the standard EM-seq protocol”, producing 650 million reads, see Fig. 3B).
With regard to claims 3 and 8, the amplification cycles take place during library preparation for the high throughout sequencing procedure.
With regard to claims 4, 5, 9, and 10 (in-part), more than 2 million CpG sites are sequenced (“1-ng and 10-ng low-input EM-seq libraries both covered 54 million CpGs”, page 1283, 2nd column).
While Vaisvila et al. teach that the cell-free DNA was extracted from 5 mL of plasma (see above), the artisans do not explicitly teach that the sample was from < 10 ml of blood, or that the average sequence depth of > 600, > 625, > 650, > 675, > 700 or > 725 was reached (claims 6 and 11).
Samoila et al. teach that 10 mL of blood collected in a tube provides 6 mL of plasma from which cfDNA are extracted and the amount yielded (see also Table 1):
“cfDNA extraction for 3 frequently used plasma input volumes 2, 4, and 6 mL, was validated … cfDNA extraction yields were highly proportional to plasma volume input … [b]ased on the amount of plasma available from a single 10 mL blood collection tube, cfDNA extraction using an automated 6 mL extraction protocol is used routinely”, page 791, 1st column)
Chiu et al. teach a method of sequencing methylation in genome from cell-free DNA in plasma, wherein the artisans teach a read depth of 600x (“next-generation sequencing to profiling 5hmC in plasma cfDNA samples … profiled 5hmC with 1-2 ng of DNA extracted from 1 ml of plasma … obtained ~25 million reads per sample, providing a depth coverage ~600x …”, pages 1- and 2).
It would have been prima facie obvious to one of ordinary skill in the art before the effective fling date of the claimed invention to combine the teachings of Vaisvilla et al., Samoila et al. and Chiu et la., thereby arriving at the invention as claimed for the following reasons.
As discussed above, Vaisvila et al. teach a method of performing sequencing on cell-free DNA from plasma samples that involve less than 10 cycles of PCR amplification. While Vaisvila et al. do not teach how much blood was employed for the 5 mL of plasma employed, as evidenced by Samoila et al. a typical 10 ml of blood sample yields around 6 mL of plasma, with the amount of cfDNA yield shown in Table 1 which provides more than 10 ng/mL of cfDNA in the sample (see page 792, 1st column, bottom paragraph). Therefore, one of ordinary skill in the art would have recognized that given the 5 mL of plasma employed by Vaisvila et al. would have been provided by blood amount of 10 mL or less, and in the alternative blood sample of less than 10 ml would have provided more than enough cell-free DNA from which to perform the method of Vaisvila et al.1
As to the sequencing depth, sequencing depth is known in the art as a number of times a particular region is spanned by sequence reads from a sequencing reaction. In the context of the methylation determination, the sequence depth of 600 or greater would indicate greater than 600 assessments of the methylation status of that locus.
However, as evidenced by Chiu et al. achieving a sequencing read depth of 600 is not uncommon, as known in the art so as to increase the sequence veracity.
Therefore, based on the amount of amount of CpGs in the assay of Vaisvila et al. with the desire to provide more accurate sequence read with higher sequence read depth, one of ordinary skill in the art would have had a reasonable expectation of success that the method of Vaisvila et al. would have been fully able to employ a blood sample of less or equal to 10 ml of blood, that yield sufficient amount of plasma sample from which cell-free DNA are extracted for the purpose of sequencing the CpG sites in a high throughput sequencing reaction with read depths that are greater than equal to 600x.
The invention as claimed is deemed prima facie obvious over the teachings of the artisans of record therefore.
Conclusion
No claims are allowed.
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YOUNG J KIM/Primary Examiner
Art Unit 1637 July 23, 2026
/YJK/
1 Vaisvila et al. teach the use of 10 ng of cfDNA with PCR cycles for sequencing reaction.
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