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 .
Status of the Application
Claim(s) 1-20 are pending and under examination
The following Office Action is in response to Applicant's communication dated 08/19/2026.
Applicant amended independent claims 1, 17, and 19 to require “preparing a library of genetic material by: extracting the genetic material from cells included in a sample; and performing adaptor ligation and indexing of the genetic material”, thus overcame the previous rejection base on Brookman-Amissah, Roche, Invitrogen, and Parla. The amendments require Examiner to conduct a new search and apply new prior art. Accordingly, rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
New Claim Rejections - 35 USC § 103
Necessitated by amendments
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.
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.
Teer et al. and Samorodnitsky et al.
Claim(s) 1, 3, 4, 8, 10-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Teer et al. (Genome research 20.10 (2010): 1420-1431) in view of Samorodnitsky et al. (Hum Mutat. 2015;36(9):903-914).
Regarding claim 1, Teer discloses method comprising:
preparing a library of genetic material by: performing adaptor ligation and indexing of the genetic material; (e.g. ligating adapters containing six-base indexes to genomic DNA fragments [“Illumina library construction” section])
accessing the library of genetic material sourced from a sample; adding human Cot-1 DNA to the library at a ratio of between 100: 1 and 20: 1 of the human Cot-1 DNA to the genetic material to produce an enrichment pool; enriching the genetic material in the enrichment pool to produce enriched genetic material; (e.g. Hybrid capture of the library pool on the MGS array was performed as per the Sequence Capture protocol (Roche NimbleGen Inc.), but with minor modifications. Briefly, a 4.8-μL solution containing 100 μg of Cot-1 DNA, 4 μg of amplified library pool DNA. The disclosed Cot to genomic library mass ratio is 100:4 (i.e. 25 Cot: 1 genomic library), which is within the claimed ratio. DNA ultimately captured on MGS array, recovered, and amplified [“Hybrid capture and post-capture processing” and “MGS and pooled bar-coded samples” sections])
sequencing the enriched genetic material to produce sequencing data. (e.g. Sequencing was performed as described by the manufacturer's protocols (Illumina Inc.) [“Sequencing” section])
However, Teer does not disclose the step of extracting the genetic material from cells included in a sample.
Samorodnitsky discloses extracting the genetic material from cells (e.g. DNA was extracted from log phase growing cell lines using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) [“Cell Lines” section]
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to obtain genomic DNA extraction kits disclosed by Samorodnitsky prior to Teer’s genetic library preparation step because the DNeasy Blood & Tissue Kits eliminates the need for mechanical disruption, reduces hands-on time, and ensures consistent extraction of high-quality DNA [Qiagen’s “Product Details” section, attached as NPL].
Regarding claim 3, Teer further discloses the library of genetic material comprises receiving the -input-library with a mass of between 1 and 5 μg. (e.g. 4 μg of amplified library pool DNA [“Hybrid capture and post-capture processing” section])
Regarding claim 4, Teer further discloses adding human Cot-1 DNA at a concentration of more than 8 mg/mL. (e.g. add 4.8-μL solution containing 100 μg of Cot-1 DNA (i.e. 20.83 mg/mL Cot-1 DNA) [“Hybrid capture and post-capture processing” section])
Regarding claim 8, Teer further discloses sequencing of the enriched genetic material comprises applying the enriched genetic material to one or more flow cells of a sequencing device. (e.g. samples were sequenced using Illumina Version 2 cluster kits and Version 3 sequencing kits [“Sequencing” section]. A skilled artisan would have known that both Illumina Version 2 (v2) cluster/reagent kits and Version 3 (v3) sequencing kits use a flow cell)
Regarding claims 10 and 11, Teer further discloses genomic enrichment of a set of 12 pooled samples via the MGS method [abstract]. It would have been obvious to a POSITA to form that pool by first preparing two or more intermediate pools and then combining them, for example, combining two pools of 6 to acquire pool of 12. This arrangement would still preserves the libraries’ identities and relative representation. This modification represents "Obvious to try" – choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (see MPEP § 2143, (E)).
Regarding claims 12 and 13, Teer further discloses accessing the library comprises receiving ten to fifty pooled libraries that have been combined. (e.g. genomic enrichment of a set of 12 pooled samples via the MGS method [abstract])
Regarding claim 14, Teer further discloses adding one or more additional blockers to the enrichment pool. (e.g. using universal PCR primer PE 1.0 and 2.0 (used as blocking oligonucleotides to reduce nonspecific hybridization [“Hybrid capture and post-capture processing” section])
Regarding claim 15, Teer further discloses enriching the genetic material in the enrichment pool comprises amplifying the genetic material prior to sequencing. (e.g. Amplification was performed as described in the PE sequencing protocol (Illumina Inc.) before sequencing [“Hybrid capture and post-capture processing”section])
Regarding claim 16, Teer further discloses enriching the genetic material in the enrichment pool comprises controlling concentration of the genetic material. (e.g. Teer teaches controlling the concentration of the genetic material during enrichment by combining 4 μg of amplified library pool DNA with Cot-1 DNA, other blocking oligonucleotides, and hybridization buffers to produce a final volume of 16 μL [“Hybrid capture and post-capture processing” section]. Selecting such library mass and final reaction volume gives library DNA concentration of 250 ng/ μL in enrichment mixture)
Regarding claims 17 and 18, Teer discloses method comprising:
preparing a library of genetic material by: performing adaptor ligation and indexing of the genetic material; (e.g. ligating adapters containing six-base indexes to genomic DNA fragments [“Illumina library construction” section])
accessing the library of genetic material sourced from a sample; adding human Cot-1 DNA to the library to produce an enrichment pool, wherein the human Cot-1 DNA is at least 10 uL of human Cot-1 DNA at a concentration of at least 12 mg/mL; (e.g. Hybrid capture of the library pool on the MGS array was performed as per the Sequence Capture protocol (Roche NimbleGen Inc.), but with minor modifications. Briefly, a 4.8-μL solution containing 100 μg of Cot-1 DNA, 4 μg of amplified library pool DNA. The disclosed working concentration of Cot-DNA calculated as: 100 μg / 4.8 μL=20.83 mg/mL. [“Hybrid capture and post-capture processing” and “MGS and pooled bar-coded samples” sections])
sequencing the enriched genetic material to produce sequencing data. (e.g. Sequencing was performed as described by the manufacturer's protocols (Illumina Inc.) [“Sequencing” section])
However, Teer does not disclose the step of extracting the genetic material from cells included in a sample.
Samorodnitsky discloses extracting the genetic material from cells (e.g. DNA was extracted from log phase growing cell lines using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) [“Cell Lines” section]
The rationale for combining the Teer and Samorodnitsky references with respect to claim 17 is the same as set forth above for claim 1 and is incorporated herein by reference, as claim 17 does not introduce limitation that would alter the motivation to combine or the predictable resulted achieved by the combination.
Regarding claim 19, Teer discloses method comprising:
preparing a library of genetic material by: performing adaptor ligation and indexing of the genetic material; (e.g. ligating adapters containing six-base indexes to genomic DNA fragments [“Illumina library construction” section])
accessing the library of genetic material sourced from a sample; adding at least 100 μg human Cot-1 DNA to the library to produce an enrichment pool; enriching the genetic material in the enrichment pool to produce enriched genetic material; (e.g. Hybrid capture of the library pool on the MGS array was performed as per the Sequence Capture protocol (Roche NimbleGen Inc.), but with minor modifications. Briefly, a 4.8-μL solution containing 100 μg of Cot-1 DNA, 4 μg of amplified library pool DNA. [“Hybrid capture and post-capture processing” and “MGS and pooled bar-coded samples” sections])
sequencing the enriched genetic material to produce sequencing data. (e.g. Sequencing was performed as described by the manufacturer's protocols (Illumina Inc.) [“Sequencing” section])
However, Teer does not disclose the step of extracting the genetic material from cells included in a sample.
Samorodnitsky discloses extracting the genetic material from cells (e.g. DNA was extracted from log phase growing cell lines using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) [“Cell Lines” section]
The rationale for combining the Teer and Samorodnitsky references with respect to claim 19 is the same as set forth above for claim 1 and is incorporated herein by reference, as claim 19 does not introduce limitation that would alter the motivation to combine or the predictable resulted achieved by the combination.
Regarding claim 20, Teer further discloses accessing the library of genetic material comprises receiving the library with a mass between 1 and 5 μg. (e.g. 4 μg of amplified library pool DNA. [“Hybrid capture and post-capture processing” and “MGS and pooled bar-coded samples” sections])
Teer et al., Samorodnitsky et al., Mercer et al., and Day et al.
Claim(s) 2 and 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Teer et al. (Genome research 20.10 (2010): 1420-1431) in view of Samorodnitsky et al. (Hum Mutat. 2015;36(9):903-914), Mercer et al. (Nat Biotechnol. 2011;30(1):99-104), and Day et al. (PLoS One 9.10 (2014): e111756).
Regarding claim 2, Teer does not disclose human Cot-1 DNA to the library is done at a ratio of 33:1.
Mercer discloses optimized DNA sequence capture array assay containing 3 μg of library material and 100 μg of human CoT-1 DNA (i.e. 1 library material :33 CoT-1 DNA ratio) [“Optimized cDNA sequence capture array processing” section]
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to increase the ratio between the library to human Cot-1 DNA from Teer’s 1:25 ratio to Mercer’s 1:33 ratio because Day reports that increasing amount of Cot-1 DNA improve the absolute yield of on-target reads while simultaneously reducing off-target yields. In Day’s experiment, the highest concentration evaluated yielded the optimal on-target read performance [page 8]. Thus, a skilled artisan would have been motivated to optimize the assay by applying Mercer’s library to human Cot-1 DNA ratio of 1:33 with reasonable expectation of success since Mercer successfully obtained effective repeat suppression during target capture. This improvement represents selection of a workable value of a known result effective variable as set forth in MPEP § 2144.05; use of known technique to improve similar devices (methods, or products) in the same way; applying a known technique to a known device (method, or product) ready for improvement to yield predictable results as set forth in; and some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention as set forth in KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (MPEP § 2143 C, D, and G)
Regarding claim 5, Teer further the library of genetic material comprises receiving the -input-library with a mass of between 1 and 5 μg. (e.g. 4 μg of amplified library pool DNA [“Hybrid capture and post-capture processing” section]); human Cot-1 DNA at a concentration of more than 8 mg/mL. (e.g. add 4.8-μL solution containing 100 μg of Cot-1 DNA (i.e. 20.83 mg/mL Cot-1 DNA) [“Hybrid capture and post-capture processing” section])
However, Teer does not disclose human Cot-1 DNA to the library is done at a ratio of 33:1.
Mercer discloses library of genetic material comprises receiving the -input-library with a mass of between 1 and 5 μg. (e.g. 3 μg of library material [“Optimized cDNA sequence capture array processing” section]); human Cot-1 DNA at a concentration of more than 8 mg/mL. (e.g. add 4.8-μL solution containing 100 μg of Cot-1 DNA (i.e. 20.83 mg/mL Cot-1 DNA [“Optimized cDNA sequence capture array processing” section]); and human Cot-1 DNA to the library is done at a ratio of 33:1 (e.g. optimized DNA sequence capture array assay containing 3 μg of library material and 100 μg of human CoT-1 DNA (i.e. Cot-1 DNA to the library at a ratio of 33:1) [“Optimized cDNA sequence capture array processing” section])
The rationale for combining Teer, Samorodnitsky, Qiagen, Mercer, and Day references with respect to claim 5 is the same as set forth above for claim 2 and is incorporated herein by reference, as claim 5 does not introduce a limitation that would alter the motivation to combine or the predictable resulted achieved by the combination.
Teer et al., Samorodnitsky et al., and Day et al.
Claim(s) 6, 7, and 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Teer et al. (Genome research 20.10 (2010): 1420-1431) in view of Samorodnitsky et al. (Hum Mutat. 2015;36(9):903-914) and Day et al. (PLoS One 9.10 (2014): e111756).
Regarding claim 6, Teer teaches using Cot-1 DNA as a blocking reagent for genomic enrichment, but does not report the result on target percentages.
Samorodnitsky disclosed the whole exome capture methods using SeqCap and SureSelect (both uses Cot-1 DNA as blockers). Table 2 reports 84.97% of mapped reads align to the target regions for SureSelect and 79.1% of mapped reads align to the target regions for SeqCap. Both values exceed 70%.
Day teaches that increasing amount of Cot-1 DNA improves the absolute yield of on-target reads while simultaneously reducing off-target yields. In Day’s experiment, the highest concentration evaluated yielded the optimal on-target read performance [page 8].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to implement Samorodnitsky’s exome solution hybridization capture in Teer workflow while retaining Teer’s Cot-1 DNA blocking strategy to concentrate sequencing on exonic regions while reducing repetitive and off target capture. Samorodnitsky already demonstrates that the commercially available kits can result greater than 70% on target reads. Teer indicates compatibility with solution base capture, and Day strengthen the teaching that optimizing Cot-1 DNA further improve capture performance. A skilled artisan would have had reasonable expectations of success achieving greater than 70% on target reads as demonstrated in Samorodnitsky’s findings.
Regarding claim 7, the same combination rejection of claim 6 applies here. The 84.97% and 79.1% of on target fractions corresponds to 15.03% and 20.29% outside target fractions respectively; wherein target correspond to exome, the non target corresponds to non-exome.
Regarding claim 9, Teer and Samorodnitsky do not expressly compare capture efficiency between assay with and without Cot-DNA blockers.
Day teaches that increasing amount of Cot-1 DNA improves the absolute yield of on-target reads while simultaneously reducing off-target yields. Day further teaches downstream Illumina, wherein majority of samples were run in 24-plex in a single HiSeq 2000 sequencing lane, thus employing the flow-cell sequencing limitation. Table 5 compares capture performance at different Cot-DNA levels, wherein 20 folds condition produce ~30 million on target reads in total (15 million non-repeats and 15 million repeats); 5 folds condition produce ~18 million on target reads in total (10 million non-repeats and 8 million repeats). These values can be used to calculate present improvement between the conditions: [(30 million/18 million)-1]x 100% gives 67% which falls within the claimed 50% to 70% improvement in enriched genetic material when applying the claimed Cot-1 DNA to the library at a ratio of between 100: 1 and 20: 1.
Since Teer and Day both uses Illumina base flow cell sequencing platforms, comparable Cot-1 DNA ratio, and similar general enrichment objective, a skilled artisan would have had reasonably expected Day’s increase in on-target yield statistics to also improve/applicable to Teer’s workflow and improve capture efficiency by 50% to 70% when using the disclosed Cot-1 DNA to the library at a ratio of between 100: 1 and 20: 1. This modification represents selection of a workable value of a known result effective variable as set forth in MPEP § 2144.05; use of known technique to improve similar devices (methods, or products) in the same way; applying a known technique to a known device (method, or product) ready for improvement to yield predictable results as set forth in; and some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention as set forth in KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007) (MPEP § 2143 C, D, and G).
Conclusion
No claims are allowed
Supporting References:
SeqCap EZ Library SR User’s Guide is included as NPL because step 5 recites “Add 5 μl of COT Human DNA” which confirms that SeqCap EZ uses Cot-DNA as referenced in rejection of claim 6 and 7.
2015 doctoral dissertation is included as NPL because section 3.6 page 53 recites “SureSelect block mixture was prepared from 2.5 µl SureSelect Block #1 (contains Human Cot-1DNA to block repetitive elements)” which confirms that SureSelect uses Cot-DNA as referenced in rejection of claim 6 and 7.
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 Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KHAI QUYNH TIEN PHAM/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
