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 previously canceled claims 1-99, 103, 116 and 118. Claims 100-102, 104-115, 117 and 119-122 are currently pending. Claim 119 remains withdrawn as being drawn to a nonelected invention. Claims 100-102, 104-115, 117 and 120-122 are currently under examination.
Any objection or rejection of record in the previous Office Action, which is not addressed in this action has been withdrawn in light of Applicant’s amendments and/or arguments. This action is Final.
Information Disclosure Statement
The information Disclosure Statement filed March 9, 2026 has been considered.
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 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 100, 104-105, 109-114, and 117 are rejected under 35 U.S.C. 103 as being unpatentable over Hindson et al. (United States Patent Application Publication US 2015/0376609 A1, published December 31, 2015), cited on the IDS filed September 08, 2021 in view of Duitama et al. (“Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data”, BMC Genomics.13 Suppl 2:S6, published April 12, 2012). This is a new rejected as necessitated by amendments.
Regarding claim 100, Hindson teaches a method comprising providing a heterogenous cell sample comprising a plurality of cells (Pages 4-5, [0050]). Hindson teaches a first cell comprising a first set of RNA transcripts and a second cell comprising a second set of RNA transcript (Page 14, [0111], Page 17, [0122], Pages 17-18, [0124], Pages 23-24, [0163] and Fig. 4). Hindson teaches partitioning the plurality of cells into a plurality of droplets (Page 1, [0007]-[0008] and Page 3, [0019]). Hindson teaches, upon partitioning, a first droplet of the plurality of droplets comprises the first cell comprising the first set of RNA transcripts and a first plurality of oligonucleotide barcodes each comprising a first barcode sequence (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 14, [0111], Page 17, [0122]—Pages 18, [0124], Pages 23-24, [0163] and Fig. 4). Hindson teaches a second droplet of the plurality of droplets comprises the second cell comprising the second set of RNA transcripts and a second plurality of oligonucleotide barcodes each comprising a second barcode sequence (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 14, [0111], Page 17, [0122]—Pages 18, [0124], Pages 18-19, [0128], Pages 23-24, [0163] and Fig. 4). Hindson teaches generating a first set of barcoded polynucleotides using the first set of RNA transcripts of the first cell and the first plurality of oligonucleotide barcodes and a given barcoded polynucleotide of the first set of barcoded polynucleotide comprises a sequence of a first RNA transcript of the first set of RNA transcripts and the first barcode sequence (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 14, [0111], Page 17, [0122]—Pages 18, [0124], Pages 18-19, [0128], Pages 23-24, [0163] and Fig. 4). Hindson teaches generating a second set of barcoded polynucleotides using the second set of RNA transcripts of the second cell and the second plurality of oligonucleotide barcodes and a given barcoded polynucleotide of the second set of barcoded polynucleotide comprises a sequence of a second RNA transcript of the second set of RNA transcripts and the second barcode sequence (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 14, [0111], Page 17, [0122]—Pages 18, [0124], Pages 18-19, [0128], Pages 23-24, [0163] and Fig. 4). Hindson teaches sequencing the first set of barcoded polynucleotides to yield first sequencing reads associated with the first cell (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 12, [0097]-[0102], Page 14, [0111], Page 17, [0122]—Pages 18, [0124], Pages 18-19, [0128], Pages 23-24, [0163] and Fig. 4). Hindson teaches the second set of barcoded polynucleotides yield second sequencing reads associated with the second cell (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 12, [0097]-[0102], Page 14, [0111], Page 17, [0122]—Pages 18, [0124], Pages 18-19, [0128], Pages 23-24, [0163] and Fig. 4). Hindson teaches the single cell analysis processes described allows for obtained phased sequence information from each cell allowing clearer characterization of variants within a cancer cell and analyzing cells to profile different mutations across cell populations as well as comparing cell populations to identify variations (Page 13, [0107], Page 20, [0134] and Page 21, [0143]). Hindson teaches using single cell analysis such as RNA-seq (Page 4, [0045]).
Regarding claim 104, Hindson teaches prior to (c), releasing the first set of RNA transcripts from the first cell into the first droplet (Page 1, [0007]-[0010]).
Regarding claim 105, Hindson teaches the first plurality of oligonucleotide barcodes are coupled to a first bead in the first droplet (Page 1, [0006]-[0008, Page 9, [0079], Page 14, [0112]).
Regarding claim 109, Hindson teaches the plurality of cells comprise first cells comprising the first cell and second cells comprising the second cell as well as the second cells comprise at least two cell types (Page 2, [0018], Page 4, [0047], Pages 4-5, [0050], Page 13, [0106]).
Regarding claim 110, Hindson teaches the first cells represent less than 50% of total cells in the heterogeneous cell sample (Pages 4-5, [0050]).
Regarding claim 111, Hindson teaches the first cells represent greater than or equal to about 1% of the total cells in the heterogeneous cell sample (Pages 4-5, [0050]).
Regarding claim 112, Hindson teaches determining a percentage of total cells in the heterogeneous cell sample represented by the second cells (Pages 4-5, [0050]).
Regarding claim 113, Hindson teaches the second cells represent greater than about 50% of the total cells in the heterogeneous cell sample (Pages 4-5, [0050]).
Regarding claim 114, Hindson teaches determining a percentage of total cells in the heterogeneous cell sample represented by the first cells (Pages 4-5, [0050] and Fig. 4).
Regarding claim 117, Hindson teaches subjecting the first set of RNA transcripts to a nucleic acid reaction in presence of a template switching oligonucleotide (Pages 16-17, [0119]-[0121], Page 18, [0127] and Page 23, [0159]-[0160]).
Regarding claim 120, Hindson teaches subjecting the first set of RNA transcripts to a reverse transcription reaction (Page 1, [0010] and Page 2, [0014]).
Regarding claim 121, Hindson teaches an oligonucleotide barcode of the first plurality of oligonucleotide barcodes further comprises a unique molecular identifier (UMI) and the second plurality of oligonucleotide barcodes comprise additional UMIs (Page 18-19, [0128] and Page 14, [0113]-[0114]).
Regarding claim 122, Hindson teaches detecting variations (Page 13, [0107], Page 20, [0134] and Page 21, [0143]). Hindson teaches the UMI of the oligonucleotide barcode and the additional UMIs of the second plurality of oligonucleotide barcodes (Page 1, [0006]-[0008], Pages 2-3, [0017]-[0019], Page 14, [0111]-[0114], Page 17, [0122]—Pages 18, [0124], Pages 18-19, [0128], Pages 23-24, [0163] and Fig. 4).
Hindson does not explicitly teach or suggest identifying a first genotype of the first cell using the first sequencing reads associated with the first cell and a second genotype of the second cell using the second sequencing reads. Hindson does not teach or suggest the first genotype of the first cell and the second genotype of the second cell are different genotypes. Hindson does not teach or suggest the first genotype comprises a first set of genetic variations comprising one or more single nucleotide variants (SNVs) and the second genotype comprises a second set of genetic variations comprising one or more single nucleotide variants (SNVs). Hindson does not teach or suggest generating reference allele counts and alternate allele counts.
Duitama teaches using RNA-seq data generated from blood cell tissues from three individuals (i.e., three different cell sets from a heterogenous sample using RNA transcripts; Abstract, Page 2, Right Column, Second Paragraph and Page 9, Right Column, Second Paragraph). Duitama teaches identifying a first genotype of the first cell using the first sequencing reads associated with the first cell and a second genotype of the second cell using the second sequencing reads (Abstract, Page 2, Left Column, Second Paragraph, Page 3, Left Column First Paragraph—Right Column, Second Paragraph, Page 4, Left Column, First Paragraph and Figs. 1-3, 5-6 and 8-9). Duitama teaches the methods discloses allows for improved genotype calling accuracy over existing methods, and retains its power to detect variants with a high specificity even from heterogeneous RNA-Seq samples (Pages 8, Right Column, First Paragraph). Duitama teaches the first genotype of the first cell and the second genotype of the second cell are different genotypes (Page 5, Left Column, First Paragraph and Figs. 2-3 and 5-9). Duitama teaches the first genotype comprises a first set of genetic variations comprising one or more single nucleotide variants (SNVs) and the second genotype comprises a second set of genetic variations comprising one or more single nucleotide variants (SNVs) (Abstract, Page 2, Left Column, Second Paragraph, Page 3, Left Column First Paragraph—Right Column, Second Paragraph, Page 4, Left Column, First Paragraph and Figs. 1-3, 5-6 and 8-9). Duitama teaches generating reference allele counts and alternate allele counts ( Page 2, Left Column, Second-Third Paragraph, Page 3, Left Column, First Paragraph, Page 4, Left Column, Second Paragraph and Right Column, Last Paragraph, Page 5, Left Column Last Paragraph, Page 7, Left Column, Second Paragraph and Fig. 7).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified Hindson with the teachings of Duitama, identifying a first genotype of the first cell using the first sequencing reads associated with the first cell with SNVs and a second genotype of the second cells with SNVs using the second sequencing reads. This would allow for improved genotype calling accuracy over existing methods, and retains its power to detect variants with a high specificity even from heterogeneous RNA-Seq samples as taught by Duitama (Pages 8, Right Column, First Paragraph).
Claims 101-102 are rejected under 35 U.S.C. 103 as being unpatentable over Hindson et al. (United States Patent Application Publication US 2015/0376609 A1, published December 31, 2015), cited on the IDS filed September 08, 2021, and Duitama et al. (“Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data”, BMC Genomics.13 Suppl 2:S6, published April 12, 2012), as applied to claims 100, 104-105, 109-114, 117 and 120-122 above, and further in view of Chen et al. (U.S. Patent Application Publication US 2014/0315755 A1, published October 23, 2014), cited on the IDS Filed September 08, 2021. This rejection is maintained and modified as necessitated by amendments.
Regarding claims 101 and 102, Hindson teaches the RNA transcript as discussed above.
Hindson does not teach or suggest the one or more SNVs of the first set of genetic variations comprise an SNV located in an untranslated region (UTR) of the first RNA transcript. Hindson does not teach or suggest the UTR of the first RNA transcript is a 3' UTR of the first RNA transcript.
Chen teaches construction of RNA libraries and the sequencing of RNAs (Abstract and (Page 4, [0017]). Chen teaches SNPs may occur specifically in a 3’ untranslated region (UTR) of a RNA transcript (Page 7, [0025]-[0027]). Chen teaches that 3’-UTR suppresses the growth of human tumor cell lines, thus the 3’-UTR is a preferred targeting area (Page 4, [0017]). Chen teaches having the SNP occur in the 3’-UTR could provide a map of the SNPs which could provide a unique genotype marker or genetic signature for a specified population or individual, which would allow for SNP identification and screening (Page 7, [0027]).
As a common field of endeavor Hindson and Chen disclose methods for transcriptomics, and sequencing RNA.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified Hindson with the teachings of Chen where the SNPs may occur specifically in a 3’ untranslated region (UTR) of a RNA transcript. Since the 3’-UTR is a preferred targeting area due to the suppression of the growth of human tumor cell lines, having the SNP occur in the 3’-UTR could provide a map of the SNPs which could provide a unique genotype marker or genetic signature for a specified population or individual, which would allow for SNP identification and screening as taught by Chen (Page 4, [0017] and Page 7, [0027]).
Claims 106 and 115 are rejected under 35 U.S.C. 103 as being unpatentable over Hindson et al. (United States Patent Application Publication US 2015/0376609 A1, published December 31, 2015), cited on the IDS filed September 08, 2021, and Duitama et al. (“Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data”, BMC Genomics.13 Suppl 2:S6, published April 12, 2012), as applied to claims 100, 104-105, 109-114, 117 and 120-122 above, and further in view of Hindson et al. (U.S. Patent Application Publication US 2014/0378349 A1, published December 25, 2014), cited on the IDS Filed September 08, 2021, herein after Hindson ‘349. This rejection is maintained and modified as necessitated by amendments.
Regarding claim 106, Hindson teaches the first bead of the first droplet comprised oligonucleotide barcodes as discussed above.
Regarding claim 115, Hindson teaches a percentage of the heterogeneous sample represented by the first cell sample as discussed above.
Hindson does not teaches or suggest the first bead of the first droplet comprises at least 1,000,000 oligonucleotide barcodes. Hindson does not teach or suggest the percentage of the total cells in the heterogeneous cell sample represented by the first cells at a sensitivity of at least about 95%.
Hindson ‘349 teaches single cell sample processing for sequencing applications with diverse libraries of beads attached to oligonucleotides containing barcodes (Abstract and Page 1, [0006]). Hindson ‘349 teaches the bead specifically being a gel bead (Page 1, [0004]). Hindson ‘349 teaches distinguishing first cells in a heterogenous sample with a sensitivity of 95 % (Page 57, [0436]-[0438] and Page 58, [0443]). Hindson ‘349 teaches the given bead of the given droplet comprises at least 1,000,000 oligonucleotide barcodes (Page 1, [0004]). Hindson ‘349 teaches in the given droplet, applying a stimulus to the given droplet to degrade the given bead, thereby releasing the oligonucleotide barcodes from the given bead into the given droplet (Page 1, [0005], Page 2, [0011], Page 6, [0041 and Page 9 [0098]. Hindson ‘349 teaches that degrading the bead to release the barcode sequences from the bead allows the barcoded sequences to become available for further amplification, sequencing and applying an algorithm to perform analysis of barcodes to align sequencing reads and/or identify the sample from which a particular sequence read belongs (Page 9, [0098]-[0099]). Hindson ‘349 teaches counting barcodes (UMI) may aid in determining the expression level of a gene (Page 48, [0365]). Hindson ‘349 teaches the methods provided may also be used to prepare polynucleotides contained within cells in a manner that enables cell-specific information to be obtained as well as enable detection of genetic variations from very small samples (Page 56, [0429]) and Page 57, [0438]).
As a common field of endeavor Hindson and Hindson ‘349 disclose methods for single cell transcriptomics using barcoded beads within a droplet.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified Hindson with the teachings of Hindson ‘394 to use the first bead of the first droplet comprising at least 1,000,000 oligonucleotide barcodes as well as the percentage of the heterogeneous cell sample represented by the first cells is determined at a sensitivity of at least about 95%. This would allow the barcoded sequences to become available for further amplification, sequencing and applying an algorithm to perform analysis of barcodes to align sequencing reads and/or identify the sample from which a particular sequence read belongs as taught by Hindson ‘349 (Page 9, [0098]-[0099]). Hindson ‘349 further teaches the methods provided may also be used to prepare polynucleotides contained within cells in a manner that enables cell-specific information to be obtained as well as enable detection of genetic variations from very small samples (Page 56, [0429]) and Page 57, [0438]).
Claims 107 and 108 are rejected under 35 U.S.C. 103 as being unpatentable over Hindson et al. (United States Patent Application Publication US 2015/0376609 A1, published December 31, 2015), cited on the IDS filed September 08, 2021, and Duitama et al. (“Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data”, BMC Genomics.13 Suppl 2:S6, published April 12, 2012), as applied to claims 100, 104-105, 109-114, 117 and 120-122 above, and further in view of Katsonis et al. ("Single Nucleotide Variations: Biological Impact and Theoretical Interpretation" Protein Science 23, Vol. 12, Pages 1650-1666, published December 23, 2014), cited on the IDS Filed September 08, 2021. This rejection is maintained and modified as necessitated by amendments.
Regarding claims 107 and 108, Hindson teaches the method of claim 100 as discussed above.
Hindson does not teach or suggest that each of the first and second set of variations comprises at least 30 SNVs. Hindson does not teach or suggest that the first set of genetic variations and the second set of genetic variations do not comprise genetic variations common to both the first and second set of genetic variations.
Katsonis teaches targeted sequencing and transcriptomics as well as identifying SNVs (Page 1650, Right Column, Last Paragraph, Page 1651, Right Column, First Paragraph and Page 1659, Right Column Second to Last Paragraph). Katsonis teaches a minor and major population of SNVs (Page 1652, Right Colum, Second Paragraph). Katsonis teaches the detection of non-synonymous single nucleotide variations (nsSNVs) in cells and their relationship to diseases, including cancer (Page 1658, Whole Left Column). Katsonis teaches thousands of such mutations in some cancers, where the mutations are specific to individual types of cancers, and so inherently do not share a common cancer types (Page 1658, Whole Left Column). Katsonis teaches developing computational methods to estimate the functional impact of SNVs is crucial to understanding the genotype–phenotype relationship, and their importance to research and clinical practice such as SNV impact prediction methods and applications to guided mutagenesis and to the identification of disease causing variants and genes (Page 1659, Left Column, Last Paragraph).
As a common field of endeavor Hindson, Hindson ‘349 and Katsonis all disclose methods for transcriptomics and sequencing.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified Hindson with the teachings of Katsonis to include use of up to thousands of SNVs corresponding to cancers as taught with the reasonable expectation of successfully expanding the ability to identify more cancer types. Developing computational methods to estimate the functional impact of SNVs is crucial to understanding the genotype–phenotype relationship, and their importance to research and clinical practice such as SNV impact prediction methods and applications to guided mutagenesis and to the identification of disease causing variants and genes as taught by Katsonis (Page 1659, Left Column, Last Paragraph).
Response to Arguments
Applicant’s arguments and amendments, filed March 03, 2026, regarding the rejections under 35 U.S.C. 103 have been fully considered and are persuasive.
Therefore, these rejections have been withdrawn.
However, upon further consideration, new grounds of rejection under 35 U.S.C. § 103 are made in view of Applicant’s amendments.
As discussed above newly cited Duitama discloses identifying a first genotype of the first cell using the first sequencing reads associated with the first cell with SNVs and a second genotype of the second cells with SNVs using the second sequencing reads. Duitama discloses that this would allow for improved genotype calling accuracy over existing methods, and retains its power to detect variants with a high specificity even from heterogeneous RNA-Seq samples (Pages 8, Right Column, First Paragraph).
Therefore, for those reasons and those listed above, Hindson in view of Duitama, Hindson and Duitama in view of Chen, Hindson and Duitama in view of Hindson ‘349, and Hindson and Duitama in view of Katsonis are deemed to render the instant invention obvious.
Conclusion
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 JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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, 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.
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.
/JESSICA D PARISI/ Examiner, Art Unit 1684
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684
Prosecution Insights