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 .
Applicant’s Amendment/Request for Reconsideration-After Non-Final Rejection, filed 6/10/2026, has been entered and fully considered
Status of Claims
Claims 11-12 are cancelled.
Claims 1-10 and 13-20 are pending and are examined on the merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/402,940 filed 09/30/2016 is acknowledged.
Claim Rejections - 35 USC § 103
This rejection is maintained from the previous Office Action, with additional modifications.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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 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.
Claims 1-7, 10, 17-18 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Paweletz ("Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients Targeted NGS of Cell-Free DNA from Advanced NSCLC." Clinical Cancer Research 22.4 (2016): 915-922. Previously cited).
Claim 1 is interpreted as a method to enrich, to capture and to sequence hotspot regions and backbone regions from cell-free nucleic acid molecules from a sample. Under a broadest reasonable interpretation (BRI), both the hotspot regions and the backbone regions cover SNVs/indels that have been reported in cancer marker genes but the backbone regions are larger compared to the hotspot regions (This BRI is supported by claims 3 and 4). The bait mixture preferentially enriches the hotspot regions over the backbone regions. According to par. [0090], the backbone regions can be sacrificed (hence not enriched due to budget reason). Therefore, a bait set targeting the hotspot regions will also pull down the backbone region less efficiently. Under a BRI the “backbone regions” is not enriched because of the past tense “compared to” in claims 1 step c). Practically a probe set does not need to target the “backbone regions”, because enriching the “hotspot regions” purposefully means enrich preferentially over any regions (including the “backbone regions”), other than the “hotspot regions”.
Regarding claim 1, Paweletz teaches (i) collecting samples comprising cfDNA (para 2-4, col 2, pg. 916) from samples.
Paweletz teaches (a) attaching adapters to cfDNA and (b) amplifying the adapter-tagged cfDNA (Fig. 1, page 917).
Paweletz teaches (c) “bias-corrected NGS uses small capture probes (~40 bp, “Capture probes” reads on “bait” in the claim limitation) that are designed to be adjacent to the region of interest” (Fig. 1 (line 6 in the legend), pg. 917) and uses a probe set covers portions of 11 genes to enrich the targets in cfDNA (last para, col 1, pg. 917). Here the probe set for target enrich reads on the bait mixture in claim 1. Since the 11 genes are frequently mutated cancer genes, and also because Paweletz’s 11 gene cover 6 out of 7 genes (except the BRCA gene) listed in the instant claim 5, one would have a reason to believe that Paweletz’s probe set capturing the regions reads on the “hotspot regions”. Since under a BRI the backbone regions encompass the hotspot regions but larger, Paweletz’s probe set also captures the regions reads on the “backbone regions”.
Paweletz provides (page 917, Fig. 1 and legend) “C. in standard hybridization cfDNA fragments are captured with large capture probes (up to 120 bp) that span the genetic region of interest and may result in off-target fragments being isolated (e.g., daisy-chaining off-target DNA). Bias-corrected NGS uses small capture probes (`40 bp) that are designed to be adjacent to the region of interest. Primer extension of fragments copies genomic and adaptor sequences. Finally, amplification with tailed PCR primers creates sequencing ready clones. D, although both approaches allow sequencing of gene rearrangements, large capture probes designed to target one gene will inefficiently target fragments containing a large amount of fusion partner gene sequence, resulting in poor sensitivity”, which teaches hybridize-capture both large and small genomic regions and the small regions are captured (and hence sequenced) more efficiently over the larger genomic regions.
Step (d) is the logical consequence of step (c). Since Paweletz taught (page 917, Fig. 1 and legend) that small capture probes (`40 bp) enrich target more efficiently than the large capture probes (up to 120 bp), wherein both the small probe and the large probe target the same gene fusion region, the small probe and the large probe fit the claim 1 description for “hotspot region” and “neckbone region”. It is obvious that after selectively enrich the hotspot regions over the backbone regions, the average reading depth for the hotspot regions will be higher over the backbone regions.
Regarding claim 2, Paweletz teaches using a probe set covers portions of 11 genes to detect genome-level rearrangements that create chimeric gene fusions in ALK, ROS1, and RET, as well as gene mutations (last para, col 1 through 1st para, col 2, pg. 917), which, under a BRI, covers both the hotspot and the backbone regions.
Regarding claim 3, Paweletz teaches the targeted genomic regions include SNV and/or indels (Fig 2, pg. 918).
Regarding claim 4, Paweletz teaches the hotspot/backbone regions comprise
portions of 11 NSCLC marker genes including chimeric gene fusions in ALK, ROS1, and RET, as well as gene mutations (last para, col 1 through 1st para, col 2, pg. 917).
Regarding claim 5, Paweletz teaches the NSCLC marker genes overlap 6 of the 7 genes listed in claim 5 (except the BRCA gene. last para, col 1 through 1st para, col 2, pg. 917).
Regarding claim 6, Paweletz teaches the cfDNA is isolated from blood (penultimate para., col 2, page 916).
Regarding claim 7, Paweletz provides “Rather than studying circulating cells, these technologies study the free floating DNA contained in the plasma; in advanced cancer patients, a portion of this cfDNA may be derived from the tumor” (2nd para., col 2, page 915), which teaches the cfDNA comprising ctDNA.
Regarding claim 10, Paweletz provides “bias-corrected NGS uses multifunctional adaptors that include sequences for single-primer amplification (red), tags for sample identification (green), and sequence identification tags (blue) that, in conjunction with the fragmentation site (blue dot) identify unique sequence clones”, which teaches molecular barcode because the tags for sample identification (green), and sequence identification tags (blue) are barcodes.
Regarding claim 17, Paweletz teaches the cfDNA comprising circulating tumor DNA (Title and Abstract, pg. 915), and the targeted genomic regions include SNV and/or indels (Fig 2, pg. 918).
Regarding claim 18, Paweletz provides (page 917, Fig. 1) “C. in standard hybridization cfDNA fragments are captured with large capture probes (up to 120 bp) that span the genetic region of interest and may result in off-target fragments being isolated (e.g., daisy-chaining off-target DNA). Bias-corrected NGS uses small capture probes (`40 bp) that are designed to be adjacent to the region of interest. Primer extension of fragments copies genomic and adaptor sequences. Finally, amplification with tailed PCR primers creates sequencing ready clones. D, although both approaches allow sequencing of gene rearrangements, large capture probes designed to target one gene will inefficiently target fragments containing a large amount of fusion partner gene sequence, resulting in poor sensitivity”, which teaches sensitivity for the genetic variant in the hot-spot region is higher than the bigger backbone region, because a “genomic region” here anticipate a “genetic variant”.
Regarding claim 20, Paweletz provides (page 918, col 1 last line to col 2 first two lines) “Mean reads per sample was 8.9 million, with a mean coverage per base of 983 unique reads”. It would be obvious that the sequence read depth will go over 1000 counts/base and hence anticipates the claim limitation of read depth between 1000 count/base and 50000 counts/base.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Paweletz as applied to claims 1-7, 10, 17-18 and 20 above, and further in view of Fumagalli ("Assessing the effect of sequencing depth and sample size in population genetics inferences." PloS one 8.11 (2013): e79667. Previously cited).
Regarding claim 13, Paweletz is silent on sequencing budget. Fumagalli teaches per sample budget for sequencing (3rd para, col 1, pg. e79667).
It would have been prima facie obvious to combine Paweletz’s cfDNA footprint method that correlate the NSCLC disease status in patient samples with target enriched cfDNA profiles, with Fumagalli teaches per sample budget for sequencing (3rd para, col 1, pg. e79667). Because it is important in population genetics research when sample size and sequencing depth need be balanced in order to control budget.
One would reasonably expect success as both Paweletz and Fumagalli are about next generation sequencing. Fumagalli’s teaching per sample budget for sequencing (3rd para, col 1, pg. e79667) does not interfere with Paweletz’s method of target enrichment and data analysis for individual samples, but only ensure a balanced sequencing wherein the sample size and sequencing depth are balanced.
Claims 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Paweletz and Fumagalli as applied to claim 13, and further in view of Buermans ("Next generation sequencing technology: advances and applications." Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1842.10 (2014): 1932-1941. Previously cited).
Regarding claim 14, Paweletz and Fumagalli are silent on the sequence reads count of the claimed range. Buermans teaches the “Shotgun” sequencing which generates >100 million reads per sample (Table 2, pg. 1938).
Regarding claim 15, Paweletz and Fumagalli are silent on the sequence reads count of the claimed range. Buermans teaches the “Methylation analysis Whole genome” sequencing which generates >400 million reads per sample (Table 2, pg. 1938).
Regarding claim 16, Paweletz and Fumagalli are silent on the sequence reads count of the claimed range. Buermans teaches the “Whole genome” sequencing which generates 1 billion reads per sample with a read length
≥
100bp (Table 2, pg. 1938).
It would have been prima facie obvious to combine Paweletz and Fumagalli who teach cfDNA footprint method that correlate the NSCLC disease status in patient samples with target enriched cfDNA profiles, and per sample budget for sequencing, with Buermans teaching of different embodiments of reading depth and reading sizes (Table 2, pg. 1938). Because it is important in population genetics research when sample size and sequencing depth need be balanced at specific reading depth and reading sizes in order to control budget.
One would reasonably expect success as Paweletz, Fumagalli and Buermans are all about next generation sequencing. Buermans’ teaching per sample budget of different embodiments of reading depth and reading sizes (Table 2, pg. 1938) does not interfere the combined method of Paweletz and Fumagalli, but only enhance the balanced sequencing at specific reading depth and reading sizes.
Claims 8 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Paweletz as applied to claims 1 and 17, and further in view of Snyder ("Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin." Cell 164.1-2 (2016): 57-68. Previously cited).
Regarding claim 8, Paweletz teaches “bias-corrected NGS uses small capture probes (~40 bp) that are designed to be adjacent to the region of interest” (Fig. 1 (line 6 in the legend), pg. 917) and uses a probe set covers portions of 11 genes to enrich the targets in cfDNA (last para, col 1, pg. 917). Here the probe set for target enrich reads on the bait mixture in claim 1. However, Paweletz is not explicit on “nucleosome-associated regions”.
Snyder teaches step (i) studying nucleosome-associated regions from cell-free nucleic acid molecules from a sample of a subject might correlated with tissue-or-origin (penultimate para, col 2, pg. 57 through 1st para, col 1, pg. 58). However, Snyder does not teach step (ii) correlating the nucleosome occupancy with variation in methylation status.
Regarding claim 19, Snyder teaches generating consensus sequences from sequence reads (last para, col 1, pg. 66).
It would have been prima facie obvious to combine Paweletz’s cfDNA footprint method that correlate the NSCLC disease status in patient samples with target enriched cfDNA profiles, with Snyder teaching of correlation between nucleosome occupancy and tissue origin. Because (Snyder: page 57, Section “Abstract”) “the cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin.”
One would reasonably expect success as both Paweletz and Snyder are about next generation sequencing. The combination uses similar experimental procedures and materials but will reveal more about tissue origin and disease status.
Response to Applicant’s Arguments
Applicant's arguments filed on 10 June 2026 have been fully considered but they are not persuasive. Particularly:
In the Remarks filed 6/10/2026, Applicant argues (pages 5-6, the connection paragraph) that ”The Examiner appears to take the view that Paweletz discloses that both small (~40 bp) probes and large (up to 120 bp) probes are used in a single assay to reject the present claims. However, Applicant respectfully submits that the interpretation by the Examiner is incorrect because Paweletz discusses the use of two different probe sizes as part of the comparison of two different, separate workflows, namely "standard hybridization" and "bias-corrected NGS", the latter of which is the focus of Paweletz. It is the larger, ~120bp probes which are described as being "inefficient" and leading to "poor sensitivity" compared to the smaller probes of the bias-corrected NGS method. The "Supplemental Methods" section of Paweletz discloses on page 1 that "[a]mplified genomic libraries are denatured and hybridized with 40 nt targeting probes", confirming that probes of only a single length were used in the "Bias-corrected NGS method" shown in Figure 1. Because Paweletz does not disclose a single bait set panel comprising probes configured to yield differential enrichment, it fails to disclose every limitation of claim 1. Therefore, Paweletz fails to anticipate the claims.”
In response, Applicant’s argument is not persuasive. claim 1 step c) does not require two probe sets. As discussed above over the 103 rejection, “a bait set panel which is configured to preferentially enrich for the hotspot regions compared to …” is interpreted as one bait set to enrich the hotspot regions. The region after the “compared to …” is not necessarily enriched by a bait set. Practically, any regions (including the backbone regions) not enriched by the bait set satisfy the claim requirement. Paweletz teaches one probe set covers portions of 11 genes to enrich the targets in cfDNA (last para, col 1, pg. 917). The 11 gene target the hot spot regions. As a logical consequence, any regions outside the hotspot regions are not enriched. So, Paweletz teaches one probe set to preferentially enrich the hotspot regions compared to the backbone regions.
In the Remarks, Applicant argued (page 6, 2nd para) “The present claims are also not obvious in view of the teachings of Paweletz. The claimed method provides a novel and non-obvious approach for the identification of both hotspot and backbone regions from cell-free nucleic acid molecules in a single workflow. A person of ordinary skill in the art reading Paweletz would be focused on optimizing the workflow for genetic variant detection and, in particular, the use of shorter probes with increased efficiency to maximize on-target reads and minimize artifacts. Paweletz neither discloses nor suggests configuring a single panel to purposely yield differential enrichment efficiencies between defined "hotspot" and "backbone" regions as recited by the present claims. Thus, Paweletz does not teach or suggest the combination of both types of probes within a single panel. Further, Paweletz does not teach or suggest the configuration of these probes to target distinct regions with differential efficiency.”
In response, Applicant’s argument is not persuasive. As discussed above, claim 1 step c) does not require two probe sets. Step (d) is the logical consequence of step (c), and “compared to the backbone regions” is the logical consequence of “preferentially enrich for the hotspot regions”.
The interpretation is also supported in step c) (of claim 1), the purpose of the operation is “to provide an enriched set of nucleic acids”, not “two enriched sets”.
All the other arguments are rooted in claims.
Hence the art rejection is maintained, and the claims are not ready for allowance.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GUOZHEN LIU whose telephone number is (571)272-0224. The examiner can normally be reached Monday-Friday 8-5.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571) 270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights