Prosecution Insights
Last updated: September 17, 2026
Application No. 18/780,961

METHODS FOR HUMAN LEUKOCYTE ANTIGEN TYPING AND PHASING

Non-Final OA §101§103
Filed
Jul 23, 2024
Priority
Jan 25, 2022 — provisional 63/302,812 +2 more
Examiner
POHNERT, STEVEN C
Art Unit
Tech Center
Assignee
Dovetail Genomics LLC
OA Round
1 (Non-Final)
12%
Grant Probability
At Risk
1-2
OA Rounds
2y 0m
Est. Remaining
31%
With Interview

Examiner Intelligence

Grants only 12% of cases
12%
Career Allowance Rate
107 granted / 870 resolved
-47.7% vs TC avg
Strong +18% interview lift
Without
With
+18.4%
Interview Lift
resolved cases with interview
Typical timeline
4y 2m
Avg Prosecution
84 currently pending
Career history
969
Total Applications
across all art units

Statute-Specific Performance

§101
14.4%
-25.6% vs TC avg
§103
31.6%
-8.4% vs TC avg
§102
9.5%
-30.5% vs TC avg
§112
35.3%
-4.7% vs TC avg
Black line = Tech Center average estimate • Based on career data from 870 resolved cases

Office Action

§101 §103
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 The instant application was filed 07/23/2024 and is a continuation of PCT/US23/11549 , filed 01/25/2023 and claims priority from provisional application 63302812 , filed 01/25/2022. Information Disclosure Statement The information disclosure statement (IDS) submitted on 9/20/2024 and 3/26/2026 are being considered by the examiner. Claim Rejections - 35 USC § 101 35 U.S.C. 101 reads as follows: Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title. Claims 1-4, 6, 9-10, 12, 14-15, 19, 24-28, 31-32, 46-47 are rejected under 35 U.S.C. 101 because the claimed invention is directed to mental step without significantly more. The claim(s) recite(s) the abstract idea or mental step of aligning, identifying, sorting, comparing and comparing; or aligning, identifying, sorting, comparing and comparing. This judicial exception is not integrated into a practical application because if there is no deletion or an amplification or unchanged expression or increased expression no treatment step is required. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because if there is no deletion or an amplification or unchanged expression or increased expression no treatment step is required. Claim analysis The instant claim 1 is directed towards method of obtaining a phased human leukocyte antigen (HLA) type of a sample comprising:(a) aligning a plurality of sequencing reads to a reference genome or a first variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus;(b) identifying a plurality of single nucleotide polymorphisms (SNPs) [[and/]]or indels in said plurality of sequencing reads;(c) sorting said plurality of SNPs [[and ]]or indels into phase blocks;(d) aligning said plurality of sequencing reads to [[said]] a second variation graph to identify a plurality of HLA types;(e) comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele; and(f) comparing said SNP signature of (e) to said phase blocks of (c) to obtain said phased HLA type.. The aligning, identifying, sorting, comparing and comparing steps are a mental steps or abstract ideas. Independent claim 24 is drawn to A method of obtaining a phased human leukocyte antigen (HLA) type of a sample comprising:(a) aligning a plurality of sequencing reads to a reference genome or a variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus;(b) identifying a plurality of single nucleotide polymorphisms (SNPs) [[and/]]or indels in said plurality of sequencing reads;(c) sorting said plurality of SNPs and indels into a plurality of phase blocks;(d) comparing said plurality of SNPs with a plurality of SNP signatures of known HLA types to identify a plurality of HLA types; and(e) comparing said plurality of SNP signatures of (d) to said phase blocks of (c) to obtain said phased HLA type. The aligning, identifying, sorting, comparing and comparing steps are a mental steps or abstract ideas. Dependent claims set forth further limitations to how the sequencings reads are obtained.. According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility. Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the both independent claims are directed towards a process. Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, abstract idea or mental step With regards to claim 1, the claim recites, “(a) aligning a plurality of sequencing reads to a reference genome or a first variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus;(b) identifying a plurality of single nucleotide polymorphisms (SNPs) [[and/]]or indels in said plurality of sequencing reads;(c) sorting said plurality of SNPs [[and ]]or indels into phase blocks;(d) aligning said plurality of sequencing reads to [[said]] a second variation graph to identify a plurality of HLA types;(e) comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele; and(f) comparing said SNP signature of (e) to said phase blocks of (c) to obtain said phased HLA type..” These can all be interpreted as a mental steps. Claim 24 is drawn to A method of obtaining a phased human leukocyte antigen (HLA) type of a sample comprising:(a) aligning a plurality of sequencing reads to a reference genome or a variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus;(b) identifying a plurality of single nucleotide polymorphisms (SNPs) [[and/]]or indels in said plurality of sequencing reads;(c) sorting said plurality of SNPs and indels into a plurality of phase blocks;(d) comparing said plurality of SNPs with a plurality of SNP signatures of known HLA types to identify a plurality of HLA types; and(e) comparing said plurality of SNP signatures of (d) to said phase blocks of (c) to obtain said phased HLA type. These can all be interpreted as a mental steps. Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as the claims provide no limitations which depend from or otherwise integrate the judicial exception.. Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, the independent claims provide no limitations which require an active step in which a sample is used. While dependent claims provide how the sequencing reads are obtained, the teachings of Ren ( US 2020/0199670 A1 )and Dilthey (Bioinformatics, 3 April 2019, Vol 35, No. 21, pg 4394-4396), Mundig (WO 2020/264185) demonstrate these are routine and conventional. Claim Rejections - 35 USC § 103 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. Claim(s) 1-4, 9-10, 14-15, 19, 24-28, 31-32, 46-47, 51 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ren ( US 2020/0199670 A1 )and Dilthey Bioinformatics, 3 April 2019, Vol 35, No. 21, pg 4394-4396 Regarding claim 1, Ren teaches a method of obtaining a phased human leukocyte antigen (HLA) type of a sample (para [0133] - "First, phasing information for GM12878 was obtained from previously published data ... Then, the HaploSeq and the local conditional phasing (LCP) protocols were utilized to generate a single haplotype structure over the HLA locus and phased -95% of alleles in GM12878."), comprising: (a) aligning a plurality of sequencing reads to a reference genome, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus (para [001 OJ - "sequencing the subset of proximally-ligated DNA fragments to obtain a plurality of sequence reads and assembling the plurality of sequence reads to construct a targeted haplotype."; para [0079] - "Hi-C reads were aligned to the mm9 (mouse) or the hg18 (human) genome."; para [0127] - "More specifically, after preparing the Capture Hi-C library, the resulting library was sequenced at-1 >< sequencing depth, using paired-end 100 bp read lengths. In theory, this sequencing depth would be enough to cover each base in the genome once. The coverage over the entire HLA locus (including all non-targeted sequences across the locus) was then computed and determined to be -32.1 ><. To compute the HLA locus enrichment, the HLA coverage was divided by the genomic coverage. All monoclonal mapped reads from the Capture-Hie sequencing data were binned into 100 kb bins genome wide. Here, the total number of reads falling into each bin at the HLA locus and the adjacent off-target region on chromosome 6 was plotted. It was found that the targeted HLA locus was approximately from 29 M to 33.4 M, which displays significant enrichment relative to nontargeted adjacent regions on chromosome 6."), (b) identifying a plurality of single nucleotide polymorphisms (SNPs) and/or indels in said plurality of sequencing reads (para [0119] - "For four different tissue donors, the inventors were able to generate haplotypes spanning entire chromosomes with 99.5% completeness (the coverage of haplotype resolved genomic regions) on average and with an average resolution (the coverage of phased heterozygous SNPs) ranging from 78% to 89% in each tissue donor. The accuracy of haplotype predictions was validated by comparing the concordance of predicted haplotypes with the SNPs residing in the same paired-end sequencing reads."); (c) sorting said plurality of SNPs and indels into phase blocks (para [0031] - "Heterozygous SNPs and indels can be used to distinguish the homologous chromosomes. Local haplotype blocks ("block 1" and "block 2") can be built from short insert sequencing reads."); (e) comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele (para [0105] -"To assess the accuracy of the heterozygous variants within the MVP block, the inventors compared the predicted haplotypes generated de novo by HaploSeq analysis with the known haplotypes of the CAST and J129 alleles. The inventors define accuracy as the fraction of phased heterozygous variants that are correctly phased in the MVP block (FIG. 7). Of the variants that were assigned to MVP haplotype block, the inventors observed >99.5% accuracy in distinguishing between the two known haplotypes (FIG. 3b)."); and (f) comparing said SNP signature of (c) to said phase blocks of (c) to obtain said phased HLA type (para [0134] - "As shown in the table, after HapCUT, the inventors generated a complete haplotype structure of the HLA locus and phase "46% of all heterozygous SNPs at -96% accuracy. After LCP, -95% of all heterozygous SNPs were phased at-98% accuracy. Of the final haplotypes structure, the accuracies of the SNPs phased by HapCUT and LCP were found to be -96% and 99%, respectively."; para [0105] - "To assess the accuracy of the heterozygous variants within the MVP block, the inventors compared the predicted haplotypes generated de novo by HaploSeq analysis with the known haplotypes of the CAST and J129 alleles. The inventors define accuracy as the fraction of phased heterozygous variants that are correctly phased in the MVP block (FIG. 7). Of the variants that were assigned to MVP haplotype block, the inventors observed >99.5% accuracy in distinguishing between the two known haplotypes (FIG. 3B )."), yet does not specifically teach (d) aligning said plurality of sequencing reads to said variation graph to identify a plurality of HLA types Dilthey teaches aligning sequencing reads to variation graph to identify HLA type (pg 4394, Abstract - "HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) lllumina data; from long-read Oxford Nano pore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data) and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample."; pg 4395, col1, para 4 - "For HLA type inference, we employ the likelihood model of HLA*PRG ... Briefly, at each locus, we maximize P (aligned reads a1, a2) over all pairs (a1, a2) of possible HLA alleles. For long reads, we increase INDEL rates in the underlying alignment likelihood (Supplementary Note S1)."). f) comparing said SNP signature of (c) to said phase blocks of (c) to obtain said phased HLA type (para [0134] - "As shown in the table, after HapCUT, the inventors generated a complete haplotype structure of the HLA locus and phase -46% of all heterozygous SNPs at -96% accuracy. After LCP, -95% of all heterozygous SNPs were phased at -98% accuracy. Of the final haplotypes structure, the accuracies of the SNPs phased by HapCUT and LCP were found to be-96% and 99%, respectively."; para [0105]- "To assess the accuracy of the heterozygous variants within the MVP block, the inventors compared the predicted haplotypes generated de novo by HaploSeq analysis with the known haplotypes of the CAST and J129 alleles. The inventors define accuracy as the fraction of phased heterozygous variants that are correctly phased in the MVP block (FIG. 7). Of the variants that were assigned to MVP haplotype block, the inventors observed >99.5% accuracy in distinguishing between the two known haplotypes (FIG. 3B)."), yet does not specifically teach (d) aligning said plurality of sequencing reads to said variation graph to identify a plurality of HLA types and a computer-implemented method of obtaining a phased human. Ren does not specifically teach aligning sequencing reads to variation graph to identify HLA type, and computational method of analyzing samples. However, Dilthey teaches aligning sequencing reads to variation graph to identify HLA type (pg 4394, Abstract - "HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) lllumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data) and from genome assemblies. Computational requirements for a typical sample vary between 7 and 14 CPU hours per sample."; pg 4395, col1, para 4 - "For HLA type inference, we employ the likelihood model of HLA*PRG (Dilthey et al., 2016). Briefly, at each locus, we maximize P (aligned reads a1, a2) over all pairs (a1, a2) of possible HLA alleles. For long reads, we increase INDEL rates in the underlying alignment likelihood (Supplementary Note S1)."). Dilthey teaches computational requirements for sample analysis (pg 4395, col 2, para 2 - "Computational requirements depend on sample type and coverage (0.65 CPU hours on average for exome samples; between 2.9 and 14 CPU hours for a typical WGS sample; Supplementary Table S3). Assembly typing was successfully applied to assess diploid MHC assembly quality and phasing accuracy in two recent de novo assembly projects (Jain et al., 2018; Koren et al., 2018)"). It would have been obvious prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to align a plurality of sequencing reads to a reference genome or variant graph to identify a SNP signature for each HLA allele. The artisan would be motivated as Ren teaches a method of obtaining a phased human leukocyte antigen (HLA) aligning a plurality of sequencing reads to a reference genome, identifying a plurality of single nucleotide polymorphisms (SNPs), comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele, comparing said SNP signature to said phase blocks of to obtain said phased HLA type, and Dilthey teaches aligning sequencing reads to variation graph to identify HLA type, and computational method of analyzing samples. The artisan would have a reasonable expectation of success as the artisan is merely combining known methods of analyzing HLA. With regards to claim 2, Ren teaches “[0010] The invention further provides a method for targeted haplotyping of an organism. The method includes providing a cell of the organism that contains a set of chromosomes having genomic DNA; incubating the cell or the nuclei thereof with a fixation agent for a period of time and restricting the fixated DNA with a restriction enzyme in order to allow proximity-ligation of the genomic DNA in situ and thereby to form ligated genomic DNA; fragmenting the ligated genomic DNA to form a proximally ligated complex having a first genomic DNA fragment and a second genomic DNA fragment; contacting the proximally-ligated DNA fragments with one or more oligonucleotides that hybridize to pre-selected regions of a subset of the proximally-ligated fragments to provide a subset of proximally-ligated fragments hybridized to the oligonucleotides, separating the subset of proximally-ligated fragments from the oligonucleotides; sequencing the subset of proximally-ligated DNA fragments to obtain a plurality of sequence reads and assembling the plurality of sequence reads to construct a targeted haplotype. In one embodiment, the oligonucleotides are immobilized.” Thus Ren at least renders obvious the steps of claim 2. With regards to claim 3, Ren teaches crosslinking with formaldehyde (0032) With regards to claim 4, Ren teaches fragmenting with a restriction enzyme (0032) With regards to claim 9, Ren teaches labeling (0012-0013) With regards to claim 10 Ren teaches labeling with biotin (0013) With regards to claim 15, Ren teaches HLA-DBQ1 (0049) With regards to claim 19, Dilthey teaches 14 CPU hours (abstract) Regarding claim 24, Ren teaches a method of obtaining a phased human leukocyte antigen (HLA) type of a sample comprising: (a) aligning a plurality of sequencing reads to a variation graph, wherein at least a portion of said plurality of sequencing reads correspond to an HLA gene locus (para [0133] - "First, phasing information for GM12878 was obtained from previously published data (Genomes Project, C. et al. Nature 467, 1061-1073, (2010)). Then, the HaploSeq and the local conditional phasing (LCP) protocols were utilized to generate a single haplotype structure over the HLA locus and phased -95% of alleles in GM12878."), comprising: (b) identifying a plurality of single nucleotide polymorphisms (SNPs) and/or indels in said plurality of sequencing reads (para [0119] - "For four different tissue donors, the inventors were able to generate haplotypes spanning entire chromosomes with 99.5% completeness (the coverage of haplotype resolved genomic regions) on average and with an average resolution (the coverage of phased heterozygous SNPs) ranging from 78% to 89% in each tissue donor. The accuracy of haplotype predictions was validated by comparing the concordance of predicted haplotypes with the SNPs residing in the same paired-end sequencing reads."); (c) sorting said plurality of SNPs and indels into phase blocks (para [0031] - "Heterozygous SNPs and indels can be used to distinguish the homologous chromosomes. Local haplotype blocks ("block 1" and "block 2") can be built from short insert sequencing reads."); (e) comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele (para 0105] -"To assess the accuracy of the heterozygous variants within the MVP block, the inventors compared the predicted haplotypes generated de nova by HaploSeq analysis with the known haplotypes of the CAST and J129 alleles. The inventors define accuracy as the fraction of phased heterozygous variants that are correctly phased in the MVP block (FIG. 7). Of the variants that were assigned to MVP haplotype block, the inventors observed >99.5% accuracy in distinguishing between the two known haplotypes (FIG. b)."); and (f) comparing said SNP signature of (c) to said phase blocks of (c) to obtain said phased HLA type (para [0134] - "As shown in the table, after HapCUT, the inventors generated a complete haplotype structure of the HLA locus and phase -46% of all heterozygous SNPs at -96% accuracy. After LCP, -95% of all heterozygous SNPs were phased at -98% accuracy. Of the final haplotypes structure, the accuracies of the SNPs phased by HapCUT and LCP were found to be -96% and 99%, respectively."; para [0105] - "To assess the accuracy of the heterozygous variants within the MVP block, the inventors compared the predicted haplotypes generated de nova by HaploSeq analysis with the known haplotypes of the CAST and J129 alleles. The inventors define accuracy as the fraction of phased heterozygous variants that are correctly phased in the MVP block (FIG. 7). Of the variants that were assigned to MVP haplotype block, the inventors observed >99.5% accuracy in distinguishing between the two known haplotypes (FIG. 3B)."), yet does not specifically teach (d) aligning said plurality of sequencing reads to said variation graph to identify a plurality of HLA types. However, Dilthey teaches aligning sequencing reads to variation graph to identify HLA type (pg 4394, Abstract - "HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) lllumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data) and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample."; pg 4395, col1, para 4 - "For HLA type inference, we employ the likelihood model of HLA*PRG (Dilthey et al., 2016). Briefly, at each locus, we maximize P (aligned reads a1, a2) over all pairs (a1, a2) of possible HLA alleles. For long reads, we increase INDEL rates in the underlying alignment likelihood (Supplementary Note S 1 )."). Therefore it would have been prima facie obvious to one of ordinary skill in the art to align a plurality of sequencing reads to a reference genome or variant graph to identify a SNP signature for each HLA allele. The artisan would be motivated as Ren teaches a method of obtaining a phased human leukocyte antigen (HLA) aligning a plurality of sequencing reads to a reference genome, identifying a plurality of single nucleotide polymorphisms (SNPs), comparing said plurality of HLA types to a plurality of known HLA alleles to obtain a SNP signature for each HLA allele, comparing said SNP signature to said phase blocks of to obtain said phased HLA type, and Dilthey teaches aligning sequencing reads to variation graph to identify HLA type. The artisan would have a reasonable expectation of success as the artisan is merely combining known method of analyzing HAL. With regards to claims 25-26, Ren teaches(para [0031] - "Heterozygous SNPs and indels can be used to distinguish the homologous chromosomes. Local haplotype blocks ("block 1" and "block 2") can be built from short insert sequencing reads."); With regards to claim 27, Dilthey teaches IMGT database which comprise HLA types With regards to claim 28, Dilthey teaches comparison to a reference genome (, 4395, 2nd paragraph). With regards to claims 31-32, Ren teaches “[0010] The invention further provides a method for targeted haplotyping of an organism. The method includes providing a cell of the organism that contains a set of chromosomes having genomic DNA; incubating the cell or the nuclei thereof with a fixation agent for a period of time and restricting the fixated DNA with a restriction enzyme in order to allow proximity-ligation of the genomic DNA in situ and thereby to form ligated genomic DNA; fragmenting the ligated genomic DNA to form a proximally ligated complex having a first genomic DNA fragment and a second genomic DNA fragment; contacting the proximally-ligated DNA fragments with one or more oligonucleotides that hybridize to pre-selected regions of a subset of the proximally-ligated fragments to provide a subset of proximally-ligated fragments hybridized to the oligonucleotides, separating the subset of proximally-ligated fragments from the oligonucleotides; sequencing the subset of proximally-ligated DNA fragments to obtain a plurality of sequence reads and assembling the plurality of sequence reads to construct a targeted haplotype. In one embodiment, the oligonucleotides are immobilized.” Thus Ren at least renders obvious the steps of claim 31-32. With regards to claims 46, Dilthey teaches, “Linear alignments are obtained by aligning input reads against a modified reference genome (GRCh38 plus the eight MHC haplotypes and IMGT genomic sequences) with BWA-MEM.” With regards to claim 47, Ren teaches HLA-DBQ1 (0049) With regards to claim 51, Dilthey teaches 14 CPU hours (abstract) Claim(s) 6 and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ren ( US 2020/0199670 A1 )and Dilthey (Bioinformatics, 3 April 2019, Vol 35, No. 21, pg 4394-4396) as applied to claims 1-4, 9-10, 14-15, 19, 24-28, 31-32, 46-47, 51 above, and further in view of Mundig (WO 2020/264185) The teachings of Ren and Dilthey render the independent claims obvious as set forth above including proximity ligation or sue of a barcode . While Ren teaches fragmenting DNA, Ren does not specifically teach fragmenting with a micrococcal nuclease. However, Mundig teaches a proximity ligation method. Mundig teaches the use a micrococcal nuclease (para [0042] - "Methods herein can utilize techniques including, but not limited to, DNase digestion, micrococcal nuclease (MNase) digestion, recombinase treatment, size selection."). Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date to use the micrococcal nuclease in a phased human leukocyte antigen (HLA) aligning methods of Dilthey and Ren. The artisan would be motivated to determine how MNase of Mundig perform relative to the methods of Ren and Dilthey. The artisan would have a reasonable expectation of success as the artisan is merely substituting one means of fragmenting for another means of fragmenting. Further Mending teaches, “Alternately, often subsequent to nucleic acid partitioning, partitions can be provided with adapters having distinct, specific or cell-distinguishing sequence (e.g., nucleic acid barcode) adjacent to integration sites or mosaic ends, or can be provided with distinct integration sites or mosaic ends, such that nucleic acids of a first partition receive integration segments or mosaic ends having a first identifying segment while nucleic acid segments of a second partition receive integration segments having a second identifying segment.”(0073) Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to barcode the oligonucleotides. The artisan would be motivated to barcode the oligonucleotides as Mundig teaches barcodes can be used to distinguish, partition or otherwise identify the source of the nucleic acid. The artisan would have a reasonable expectation of success as the artisan is using known methods to tag or barcode nucleic acids. Summary No claims are allowed. Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday 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, Anne Gussow can be reached at (571)272-6047. 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. /Steven Pohnert/ Primary Examiner, Art Unit 1683
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Prosecution Timeline

Jul 23, 2024
Application Filed
Aug 31, 2026
Non-Final Rejection mailed — §101, §103 (current)

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