DETAILED ACTION
Applicant's response, filed 16 March 2026, has been fully considered. The following rejections
and/or objections are either reiterated or newly applied. They constitute the complete set presently
being applied to the instant application.
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 .
Claim Status
Claims 1, 3-10, 12-13, 16-17, 20-21, 36-37, and 44-46 are pending.
Claims 1, 3-10, 12-13, 16-17, 20-21, 36-37, and 44-46 are rejected.
Specification
Response to Amendment
In view of applicant’s amendments to the specification previous objections to the specification regarding trade names and a lack of color drawings when referenced are withdrawn.
Claim Rejections - 35 USC § 112
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C. 112 (b) for antecedent basis have been withdrawn.
Claim Rejections - 35 USC § 101
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C. 101 have been reviewed, updated, and provided below.
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, 3-10, 12-13, 16-17, 20-21, 36-37, and 44-46 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more. The claims recite a method for detecting genetic variation in a subject’s genome. The judicial exception is not integrated into a practical application because while claims 1, 3-10, 12-13, 16-17, 20-21, 36-37, and 44-46 attempt to integrated the exception into a practical application, said application is either generically recited computer elements that do not add a meaningful limitation to the abstract idea or it is insignificant extra solution activity and merely implementing the abstract idea on a computer. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the computer elements only store and retrieve information in memory as well as perform basic calculations that are known to be well-understood, routine and conventional computer functions as recognized by the decisions listed in MPEP § 2106.05(d).
Framework with which to Analyze Subject Matter Eligibility:
Step 1: Are the claims directed to a category of stator subject matter (a process, machine, manufacture, or composition of matter)? [see MPEP § 2106.03]
Claims are directed to statutory subject matter, specifically a method (Claims 1, 3-10, 12-13, 16-17, 20-21, 36-37, and 44-46).
Step 2A Prong One: Do the claims recite a judicially recognized exception, i.e., an abstract idea, a law of nature, or a natural phenomenon? [see MPEP § 2106.04(a)]
The claims herein recite abstract ideas, specifically mental processes and mathematical concepts.
With respect to the Step 2A Prong One evaluation, the instant claims are found herein to recite abstract ideas that fall into the grouping of mental processes and mathematical concepts.
Claim 1: Processing sequence reads, sequentially aligning, aligning in parallel), and detecting genetic variation in the top paired alignment, are processes of selecting, comparing/contrasting, and analyzing that can be done via pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes.
Claim 3: Only the paired-end reads associated with a top alignment score to the first or second regions are aligned separately is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 8: The reads being aligned by using the BWA algorithm is a process of comparing/contrasting, and analyzing that can be done via pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process.
Claim 9: The aligner only emitting alignments that meet a minimum alignment score is a process of comparing/contrasting that can be done via pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process.
Claim 10: Pairing a first and second read based on a distance of less than about 1000 bases is a process of comparing/contrasting that can be done via pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process.
Claim 12: Generating multiple paired alignments, calculating an alignment score, and identifying the top paired alignment are processes of selecting, comparing/contrasting, and analyzing that can be done via pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes.
Claim 13: The top paired alignment is selected as having the smallest template length are processes of selecting, and comparing/contrasting that can be done via pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process.
Claim 16: Using an HMM caller to determine a copy number is a verbal articulation of a mathematical process and is therefore an abstract idea, specifically a mathematical concept.
Claim 17: The expected ploidy being 2 is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 36: The second region of interest comprising a gene and the first region comprising a functional homolog of the gene is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 37: The gene being HBA1 and the functional homolog being HBA2 is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 44: The multiple sites of interest are within an exon of HBA and an exon in another region of the genome is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 45: The multiple sites of interest are within an exon of HBA1 and an exon of HBA2 is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 46: The multiple sites of interest are within exons 1, 2, and/or 3 of HBA1 and exons 1, 2, and/or 3 of HBA2 is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Step 2A Prong Two: If the claims recite a judicial exception under prong one, then is the judicial exception integrated into a practical application? [see MPEP § 2106.04(d) and MPEP § 2106.05(a)-(c) & (e)-(h)]
Because the claims do recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application.
The following claims recite the following additional elements in the form of non-abstract elements:
Claim 1: Obtaining sequence reads by paired-end sequencing, aligning the first and second reads to a reference genome, and aligning sequence reads to a reference are insignificant extra solution activities, specifically necessary data gathering (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 3: Aligning the first and second reads to a reference genome is an insignificant extra solution activity, specifically mere data gathering (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 4: The sequence reads are obtained by direct targeted sequencing, and the first read comprises a genomic sequence read and the second read comprises a probe sequence is an insignificant extra solution activity, specifically mere data gathering (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 5: Sequence reads being obtained by solution DTS of multiple sites, the first read comprises a genomic sequence read and the second read comprises a combination of genomic sequence reads and a probe sequence read is an insignificant extra solution activity, specifically mere data gathering (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 6: The sequence reads are obtained by paired-end non-DTS targeted sequencing and they comprise genetic sequence reads is an insignificant extra solution activity, specifically mere data gathering (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 7: The reads are obtained by paired-end whole genome sequencing and the reads comprise genomic sequence reads is an insignificant extra solution activity, specifically mere data gathering (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 20: Using long-range PCR to amplify a portion of the genome and multiplex ligation-dependent probe amplification to assay are mere instructions to apply an exception, specifically the additional elements amount to nothing more than a recitation of the words "apply it" (See Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S. 208, 223, 110 USPQ2d 1976, 1983 (2014); Gottschalk v. Benson, 409 U.S. 63, 64, 175 USPQ 673, 674 (1972); Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)) [See MPEP § 2106.05(f)].
Claim 21: A portion of the first region is amplified by long-range PCR and sequenced by Sanger or NGS, genomic DNA is assayed by multiplex ligation-dependent probe amplification, or the genomic DNA is assayed by long-read sequencing are mere instructions to apply an exception, specifically the additional elements amount to nothing more than a recitation of the words "apply it" (See Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S. 208, 223, 110 USPQ2d 1976, 1983 (2014); Gottschalk v. Benson, 409 U.S. 63, 64, 175 USPQ 673, 674 (1972); Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)) [See MPEP § 2106.05(f)].
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? [see MPEP § 2106.05]
Because the additional claim elements do not integrate the abstract idea into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept.
The claims do not recite additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are generic, conventional or nonspecific. These additional elements include:
The additional elements of obtaining sequence reads by paired-end sequencing (Conventional: Specification [0153]-[0157]), aligning the reads to a reference genome (Conventional: Specification Paragraph [0037]), the sequence reads are obtained by direct targeted sequencing, and the first read comprises a genomic sequence read and the second read comprises a probe sequence (Conventional: Specification [0055]), sequence reads being obtained by solution DTS of multiple sites (Conventional: Specification [0055]), the sequence reads are obtained by paired-end non-DTS targeted sequencing (Conventional: Specification [0055]), the reads are obtained by paired-end whole genome sequencing (Conventional: Specification [0055]), using long-range PCR to amplify a portion of the genome (Conventional: Specification [0137]), multiplex ligation-dependent probe amplification to assay (Conventional: Specification [0150]), a portion of the first region is amplified by long-range PCR and sequenced by Sanger or NGS (Conventional: Specification [0137]), genomic DNA is assayed by multiplex ligation-dependent probe amplification (Conventional: Specification [0150]), or the genomic DNA is assayed by long-read sequencing (Conventional: Specification [0137]), are insignificant extra solution activities, specifically necessary data gathering that are conventional within the art (See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering), Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)]. Therefore, taken both individually and as whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept.
Therefore, claims 1, 3-10, 12-13, 16-17, 20-21, 36-37, and 44-46, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 3/16/2026 have been fully considered but they are not persuasive.
Applicant asserts on page 8 of the Remarks filed 3/16/2026 that the claimed method cannot be practically performed in the human mind as a human mind is not capable of performing the detection of genetic variation in a top aired alignment, specifically citing Id. (emphasis added) citing SRIInt'l, Inc. v. Cisco Systems, Inc., 930 F.3d 1295, 1304 (Fed. Cir. 2019) and the detection of suspicious activity using network monitors and network packets. However, examiner reminds applicant that according to MPEP 2106.04(a)(III)(C) - Claims can recite a mental process even if they are claimed as being performed on a computer (See Voter Verified, Inc. v. Election Systems & Software, LLC, 887 F.3d 1376, 1385, 126 USPQ2d 1498, 1504 (Fed. Cir. 2018), Symantec Corp., 838 F.3d at 1316-18, 120 USPQ2d at 1360, and Mortgage Grader, 811 F.3d. at 1324, 117 USPQ2d at 1699). In other words, the mere recitation of the use of a computer does not disqualify the claim as being directed to a mental process as is the case with claim 1, as all that is recited is the generic use of a generic computer.
Additionally, in the case of SRIInt'l, Inc. v. Cisco Systems, Inc., 930 F.3d 1295, 1304 (Fed. Cir. 2019) there is a fundamental difference between the instant application and the recited case in that the human mind is not capable of understanding the data within a network data packet, as compared to the detection of genetic variation in a top paired alignment, something that can and has been done by hand using BWA and a simple comparison in the number of mutations, which is completely understandable information within the human mind.
Claim Rejections - 35 USC § 102
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C. 102 for anticipation under the prior art is withdrawn.
Response to Arguments
Applicant’s arguments, see pages 9-10 of the Remarks, filed 3/16/2026, with respect to claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 have been fully considered and are persuasive. The rejection of claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 has been withdrawn as Kvitek et al. does not teach the reference genome not comprising a masked or modified portion of the region of interest.
Claim Rejections - 35 USC § 103
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C 103 have been reviewed, updated, and provided below.
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.
Claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Kvitek et al. (WO 2016168371 A1) and Li et al. (bioinformatics (2009) 1754-1760).
Claim 1 is directed to a method for detecting genetic variation in a genome of subject by aligning multiple sequence reads to a reference genome pairing a first and second read to generate a top paired alignment and detecting genetic variation in the top paired alignments.
Kvitek et al. teaches in claim 1 “A computer-implemented method for determining a likelihood of a presence or absence of a genetic variation in a gene of interest for a subject where the subject's genome also contains at least one counterpart gene to the gene of interest such that the counterpart genes have a high degree of homology to the gene of interest”, reading on a method for detecting genetic variation in a genome of a subject, the genome comprising highly homologous first and second regions of interest. Kvitek et al. teaches in claim 20 “wherein the sequence reads are obtained by a method comprising paired-end sequencing”, reading on obtaining sequence reads by paired-end sequencing from multiple sites of interest in the first and second regions of interest, wherein the sequence reads comprise a first read and a second read obtained at each site of interest. It would additionally be inherent that the use of paired end sequencing would select sequence reads that represent the first and second regions of interest equally as the method uses this to more accurately map reads and identify genetic variation in between the mapped sections. Kvitek et al. teaches in claim 1 “mapping sequence reads to the modified reference genome”, and on page 31, lines 13 -30 “As used herein, the terms "aligned", "alignment", or "aligning" refer to two or more nucleic acid sequences that can be identified as a match (e.g. , 100% identity) or partial match…Alignment of a sequence read can be a 100% sequence match (e.g., 100% identity). In some cases, an alignment is less than a 100% identity (e.g. , non-perfect match, partial match, partial alignment). In some embodiments an acceptable alignment of two nucleic acids comprises at least a 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91 %, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81 %, 80%, 79%, 78%, 77%, 76% or 75% identity… In some embodiments, an alignment comprises a mismatch (non-identical aligned nucleotides). In some embodiments, an alignment comprises 1, 2, 3, 4, 5 or more mismatches. Two or more sequences can be aligned using either strand”, reading on aligning sequence reads that represent the first and second regions of interest equally to a reference genome using an aligner, wherein first reads and second reads are aligned to the reference genome separately and the aligner emits multiple possible alignments for each of the first and second reads. Kvitek et al. teaches on page 49, line 25 “More than one machine in one location or multiple locations may be accessed by a user, and data may be mapped and/or processed in series and/or in parallel”, reading on processing sequence reads, using a computer, to generate a top paired that alignment that includes first reads and second reads that either: (i) align to the first region of interest;(ii) align to the second region of interest; (iii) sequentially align to the first and the second regions of interest; or (iv) align to the first and the second regions of interest in parallel. Kvitek et al. teaches in claim 1 “determining the likelihood of a presence or absence of a genetic variation in the gene of interest of the subject according to the sequence reads mapped to the gene of interest”, reading on detecting the genetic variation in the top paired alignment generated in step (e).
Kvitek et al. does not teach that the reference genome does not comprise a masked or modified portion of the first and second region of interest.
Li et al. teaches in the abstract “We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps”, reading on wherein the reference genome does not comprise a masked or modified portion of the first and second region of interest.
It would have been obvious at the time of first filing to have modified the teachings of Kvitek et al. for the method of claim 1, with the teachings of Li et al. for the use of their BWA method that aligns reads to a non-modified/masked reference such as the human reference genome as the latter teaches on page 1759, column 1, paragraph 4 “For short read alignment against the human reference genome, BWA is an order of magnitude faster than MAQ while achieving similar alignment accuracy. It supports gapped alignment for single-end reads, which is increasingly important when reads get longer and tend to contain indels. BWA outputs alignment in the SAM format to take the advantage of the downstream analyses implemented in SAMtools. BWA plus SAMtools provides most of functionality of the MAQ package with additional features”. One would have had a reasonable expectation of success given that this is merely limiting the reference to which you are aligning and the BWA method and alignment to the human reference genome is standard within the field. Therefore, it would have been obvious at the time of first filing to have modified the teachings of each and to be successful.
Claim 3 is directed to the method of claim 1 but further specifies aligning the first and second reads to a reference genome and aligning only the paired end reads associated with a top alignment score to the first or second regions.
Kvitek et al. teaches in claim 1 “A computer-implemented method for determining a likelihood of a presence or absence of a genetic variation in a gene of interest for a subject where the subject's genome also contains at least one counterpart gene to the gene of interest such that the counterpart genes have a high degree of homology to the gene of interest”, in claim 20 “wherein the sequence reads are obtained by a method comprising paired-end sequencing”, Kvitek et al. teaches on page 31, line 22 “In some embodiments an acceptable alignment of two nucleic acids comprises at least a 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91 %, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81 %, 80%, 79%, 78%, 77%, 76% or 75% identity. Parameters and thresholds (e.g., a percent identity thresholds) for an acceptable alignment or match can be predetermined by a user, module or program”, reading on comprising, before step (c), aligning first reads and second reads to a reference genome, wherein the aligner emits the best possible paired-end alignment to the first or second region of interest for each pair of first and second reads, and wherein only paired-end reads associated with a top alignment score to the first or second regions of interest are aligned separately in step (c).
Claim 6 is directed to the method of claim 1 but further specifies that the sequence reads are obtained by paired end non-DTS targeted sequencing and the reads comprise genomic sequence reads.
Kvitek et al. teaches in claim 20 “wherein the sequence reads are obtained by a method comprising paired-end sequencing”, reading on wherein the sequence reads are obtained by paired- end non-DTS targeted sequencing, and wherein both the first and second reads comprise genomic sequence reads.
Claim 8 is directed is directed to the method of claim 1 but further specifies that the reads are aligned using the Burrows-Wheeler Aligner algorithm.
Kvitek et al. teaches on page 31, line 36 “Sequence reads and/or paired-end reads are often mapped to a reference genome by use of a suitable mapping and/or alignment program non- limiting examples of which include BWA…”, reading on wherein in step (c) the sequence reads are aligned using the Burrows-Wheeler Aligner (BWA) algorithm.
Claim 9 is directed to the method of claim 1 but further specifies that the aligner only emits alignments that meet a minimum alignment score.
Kvitek et al. teaches on page 31, line 22 “In some embodiments an acceptable alignment of two nucleic acids comprises at least a 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91 %, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81 %, 80%, 79%, 78%, 77%, 76% or 75% identity. Parameters and thresholds (e.g., a percent identity thresholds) for an acceptable alignment or match can be predetermined by a user, module or program”, reading on wherein in step (c) the aligner only emits alignments that meet a minimum alignment score for the first and second regions of interest.
Claim 10 is directed to the method of claim 1 but further specifies that the reads are paired only if the alignments of the reads are within about 1000 bases of each other.
Kvitek et al. teaches on page 29, line 3 “In some embodiments, sequence reads are of a mean, median, average or absolute length of about 15 bp to about 900 bp long. In certain embodiments sequence reads are of a mean, median, average or absolute length about 1000 bp or more”, reading on wherein a first read and a second read are paired in step (e) only if the alignments of the first read and the second read to the first region of interest are within about 1000 bases of each other.
Claim 12 is directed to the method of claim 1 but further specifies generating multiple alignments, calculating an alignment score for each, and identifying the top alignment as that with the highest score.
Kvitek et al. teaches on page 31, line 22 “In some embodiments an acceptable alignment of two nucleic acids comprises at least a 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91 %, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81 %, 80%, 79%, 78%, 77%, 76% or 75% identity. Parameters and thresholds (e.g., a percent identity thresholds) for an acceptable alignment or match can be predetermined by a user, module or program”, reading on comprising generating multiple paired alignments in step (d), calculating an alignment score for each of the multiple paired alignments, and identifying the top paired alignment as having the highest alignment score.
Claim 17 is directed to the method of claim 1 but further specifies that the detecting is based on an expected ploidy of 2.
Kvitek et al. teaches on page 36, line 15 “Any suitable reference genome can be modified and used for a method, process, system or program herein. Human genomes, human genome assemblies and/or genomes from any other organisms can be used as a reference genome”, humans have ploidy of 2 thereby reading on wherein the detecting in step (e) is based on an expected ploidy of 2.
Claim 20 is directed to the method of claim 1 but further specifies amplification by long-range PCR and assaying via MLPA.
Kvitek et al. teaches on page 65, line 35 “The objective of this Example was to validate an assay for calling copy number variants (CNVs)…A method that uses multiplex ligation-dependent probe amplification (MLPA) and long-range PCR (LR-PCR) to disambiguate CNVs in exons 12-15 of PMS2…”, and page 66, line 14 “LR-PCR/Sanger disambiguation - Confirmed variants were still ambiguously located in either PMS2 or PMS2CL due to the possibility of gene conversion. LR-PCR and Sanger sequencing of the fixed differences between PMS2 and PMS2CL was used to disambiguate the location of the variant” reading on wherein if a genetic variation is detected in step [[(e)]](f), a portion of the subject's genome is amplified by long-range PCR and assayed by multiplex ligation-dependent probe amplification (MLPA).
Claim 21 is directed to the method of claim 1 but further specifies using NGS or Sanger to sequence genomic DNA from long-range PC, amplifying using MLPA and assaying by long-read sequencing.
Kvitek et al. teaches on page 29, line 3 “In some embodiments, sequence reads are of a mean, median, average or absolute length of about 15 bp to about 900 bp long. In certain embodiments sequence reads are of a mean, median, average or absolute length about 1000 bp or more”, which are long reads, on page 65, line 1 “To identify the presence or absence of known genetic variations in exons 12-15 of the human PMS2 gene that are associated with Lynch syndrome, blood samples will be obtained from the blood of human subjects, genomic DNA will be isolated from the samples and the genomic DNA of the samples will be sequenced using an NGS method”, and on page 65, line 35 “The objective of this Example was to validate an assay for calling copy number variants (CNVs)…A method that uses multiplex ligation-dependent probe amplification (MLPA) and long-range PCR (LR-PCR) to disambiguate CNVs in exons 12-15 of PMS2…”, and page 66, line 14 “LR-PCR/Sanger disambiguation - Confirmed variants were still ambiguously located in either PMS2 or PMS2CL due to the possibility of gene conversion. LR-PCR and Sanger sequencing of the fixed differences between PMS2 and PMS2CL was used to disambiguate the location of the variant” reading on wherein if a genetic variation is detected in step (f), a portion of the first region of interest is amplified by long-range PCR and the product or a portion thereof is sequenced by Sanger sequencing or NGS; or the subject's genomic DNA is assayed by multiplex ligation-dependent probe amplification (MLPA); or the subject's genomic DNA is assayed by long-read sequencing.
Claim 36 is directed to the method of claim 1 but further specifies that the regions of interest comprise a gene and its homolog.
Kvitek et al. teaches on page 3, line 13 “In some aspects provided herein is a computer-implemented method for determining a likelihood of a presence or absence of a genetic variation in a gene of interest for a subject where the subject's genome also contains one or more counterpart genes to the gene of interest such that the counterpart genes have a high degree of homology to the gene of interest”, reading on wherein the second region of interest comprises a gene and the first region of interest comprises a functional homolog of the gene.
Claims 4 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Kvitek et al. (WO 2016168371 A1) and Li et al. (bioinformatics (2009) 1754-1760) as applied to claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 above, and further in view of Vasson et al. (European Journal of Human Genetics (2013) 977-987).
Claim 4 is directed to the method of claim 1 but further specifies the use of direct targeted sequencing.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach the use of direct targeted sequencing.
Vasson et al. teaches in the abstract “To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints”, reading on wherein the sequence reads are obtained by direct targeted sequencing (DTS) of the multiple sites of interest, and wherein the first read comprises a genomic sequence read and the second read comprises a probe sequence read associated with a site of interest.
It would have been obvious at the time of the effective filing date to a person skilled in the art to modify the teachings of Kvitek et al. and Li et al. for the method of claim 1, with the teachings of Vasson et al. for the use of DTS and probe data as Vasson et al. teaches in the abstract “it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints”. One would have had a reasonable expectation of success given that it is merely using sequencing data that the method is already generating merely modifying the collection process requiring it to direct targeting paired-end sequencing. Therefore, it would have obvious at the time of effective filing to a person skilled in the art to modify the teachings of each and to be successful.
Claim 5 is directed to the method of claim 1 but further specifies the use of direct target sequencing.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach the use of direct targeted sequencing.
Vasson et al. teaches in the abstract “To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints”, reading on wherein the sequence reads are obtained by solution DTS of the multiple sites of interest, and wherein the first read comprises a genomic sequence read and the second read comprises a combination of a genomic sequence read and a probe sequence read associated with a site of interest.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Kvitek et al. (WO 2016168371 A1) and Li et al. (bioinformatics (2009) 1754-1760) as applied to claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 above, and further in view of Zhou et al. (Journal of medical genetics (2018) 735-743).
Claim 7 is directed to the method of claim 1 but further specifies that the sequences be obtained through paired-end sequencing using whole genome sequencing.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach that the sequences be obtained through paired-end sequencing using whole genome sequencing.
Zhou et al. teaches in the abstract “Copy number variation (CNV) analysis is an integral component of the study of human genomes in both research and clinical settings. Array-based CNV analysis is the current first-tier approach in clinical cytogenetics. Decreasing costs in high-throughput sequencing and cloud computing have opened doors for the development of sequencing-based CNV analysis pipelines with fast turnaround times. We carry out a systematic and quantitative comparative analysis for several low-coverage whole-genome sequencing (WGS) strategies to detect CNV in the human genome”, reading on wherein the sequence reads are obtained by paired- end whole genome sequencing, and wherein both the first and second reads comprise genomic sequence reads.
It would have been obvious at the time of the effective filing date to a person skilled in the art to modify the teachings of Kvitek et al. and Li et al. for the method of claim 1, with the teachings of Zhou et al. for the use of whole genome sequencing reads as Zhou et al. teaches in the abstract “Overall, low-coverage WGS strategies detect drastically more GS CNVs compared with arrays and are accompanied with smaller percentages of CNV calls without validation. Furthermore, we show that WGS (at ≥1× coverage) is able to detect all seven GS deletion CNVs >100 kb in NA12878, whereas only one is detected by most arrays. Lastly, we show that the much larger 15 Mbp Cri du chat deletion can be readily detected with short-insert paired-end WGS at even just 1× coverage”. One would have had a reasonable expectation of success given that the use of WGS methods does not change the overall method, it is completely compatible with paired-end sequencing and Zhou et al. is directed to CNV detection. Therefore, it would have obvious at the time of effective filing to a person skilled in the art to modify the teachings of each and to be successful.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Kvitek et al. (WO 2016168371 A1) and Li et al. (bioinformatics (2009) 1754-1760) as applied to claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 above, and further in view of Wu et al. (BMC Genomics (2018) 1-14).
Claim 13 is directed to the method of claim 1 but further specifies that the top paired alignment is selected as having the smallest template length.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach that the top paired alignment is selected as having the smallest template length.
Wu et al. teaches on page 11, column 1, paragraph 2 “Multiply-mapped reads from the two genome mapping steps were grouped and a pair of best alignment was chosen by the following ordered criteria: the alignment pair (A) had the smallest insert size”, reading on wherein the top paired alignment in step (e) is selected as having the smallest template length.
It would have been obvious at the time of the effective filing date to a person skilled in the art to modify the teachings of Kvitek et al. and Li et al. for the method of claim 1, with the teachings of Wu et al. for using the smallest template length as both are focused on alignment of reads and Wu et al.’s use of the described criteria increased accuracy of the alignment. One would have had a reasonable expectation of success given that Wu et al. explicitly shows the code for performing said method. Therefore, it would have obvious at the time of effective filing to a person skilled in the art to modify the teachings of each and to be successful.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Kvitek et al. (WO 2016168371 A1) and Li et al. (bioinformatics (2009) 1754-1760) as applied to claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 above, and further in view of Malekpour et al. (BMC Bioinformatics (2017) 1-11).
Claim 16 is directed to the method of claim 1 but further specifies the use of an HMM to determine copy number from sequencing reads.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach the use of an HMM to determine copy number from sequencing reads.
Malekpour et al. teaches in the abstract “In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM)”, reading on wherein the detecting in step (f) comprises using a hidden Markov model (HMM) caller to determine a copy number.
It would have been obvious at the time of the effective filing date to a person skilled in the art to modify the teachings of Kvitek et al. and Li et al. for the method of claim 1, with the teachings of Malekpour et al. for the use of mate pair NGS data and a Hidden Markov Model for CNV detection as Malekpour et al. teaches in the abstract “PSE-HMM is effective in taking observation dependencies into account and reaches a high accuracy in detecting genome-wide CNVs”. One would have had a reasonable expectation of success given that the mate pair NGS data is similar to paired-end sequencing reads. Therefore, it would have obvious at the time of effective filing to a person skilled in the art to modify the teachings of each and to be successful.
Claims 37 and 44-46 are rejected under 35 U.S.C. 103 as being unpatentable over Kvitek et al. (WO 2016168371 A1) as applied to claims 1, 3, 6, 8-10, 12, 17, 20-21, and 36 above, and further in view of Law et al. (Haematologica (2006) 297-302).
Claim 37 is directed to the method of claim 36 and thus claim 1, but further specifies that the genes be HBA1 and HBA2.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach the genes be HBA1 and HBA2.
Law et al. teaches on page 297, column 1, paragraph 2 “Despite their ancient origin, the HBA1 and HBA2 genes have remained very similar, comprising three segments of homology (the X, Y, and Z boxes) that are punctuated with non-homologous regions (I, II, and III)”, reading on wherein the gene is HBAI, and wherein the functional homolog is HBA2.
It would have been obvious at the time of the effective filing date to a person skilled in the art to modify the teachings of Kvitek et al. and Li et al. for the method of claim 1, with the teachings of Law et al. for the examination of the HBA1 and HBA2 genes as the method is directed to homologous sequences and according to Law et al. “The cluster was thought to result from duplication events that occurred more than 300 million years ago…Despite their ancient origin, the HBA1 and HBA2 genes have remained very similar…”. One would have had a reasonable expectation of success given that Law et al. is not altering the method but merely directing it towards a particular highly homologous region of the genome. Therefore, it would have obvious at the time of effective filing to a person skilled in the art to modify the teachings of each and to be successful.
Claim 44 is directed to the method of claim 1 but further specifies that the sites of interest be within exons of HBA and other parts of the subject’s genome.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described. Kvitek et al. teaches on page 88, line 19 “wherein the gene of interest of the subject is selected from PMS2, HBA1, HBG1, HBB, SBSD, and VWF”, and on page 65, line 35 “The objective of this Example was to validate an assay for calling copy number variants (CNVs)…A method that uses multiplex ligation-dependent probe amplification (MLPA) and long-range PCR (LR-PCR) to disambiguate CNVs in exons 12-15 of PMS2…”.
Kvitek et al. and Li et al. do not teach the sites of interest be within exons of HBA and other parts of the subject’s genome.
Law et al. teaches on page 297, column 1, paragraph 2 “Despite their ancient origin, the HBA1 and HBA2 genes have remained very similar, comprising three segments of homology (the X, Y, and Z boxes) that are punctuated with non-homologous regions (I, II, and III)”, which in view of Kvitek et al. reads on wherein the multiple sites of interest are within an exon of HBA and an exon in another part of the subject's genome.
Claim 45 is directed to the method of claim 1 but further specifies that the multiple sites of interest be within exons of HBA1 and HBA2.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described. Kvitek et al. teaches on page 88, line 19 “wherein the gene of interest of the subject is selected from PMS2, HBA1, HBG1, HBB, SBSD, and VWF”, page 88, line 23 “wherein the gene of interest of the subject is HBA1 and the at least one counterpart gene is HBA2”, and on page 65, line 35 “The objective of this Example was to validate an assay for calling copy number variants (CNVs)…A method that uses multiplex ligation-dependent probe amplification (MLPA) and long-range PCR (LR-PCR) to disambiguate CNVs in exons 12-15 of PMS2…”.
Kvitek et al. and Li et al. do not teach the multiple sites of interest be within exons of HBA1 and HBA2.
Law et al. teaches on page 297, column 1, paragraph 2 “Despite their ancient origin, the HBA1 and HBA2 genes have remained very similar, comprising three segments of homology (the X, Y, and Z boxes) that are punctuated with non-homologous regions (I, II, and III)”, which in view of Kvitek et al. reads on wherein the multiple sites of interest are within an exon of HBA1 and an exon of HBA2.
Claim 46 is directed to the method of claim 1 but further specifies that the multiple sites of interest be within exons 1, 2, and 3 of HBA1 and HBA 2. Kvitek et al. teaches on page 88, line 19 “wherein the gene of interest of the subject is selected from PMS2, HBA1, HBG1, HBB, SBSD, and VWF”, page 88, line 23 “wherein the gene of interest of the subject is HBA1 and the at least one counterpart gene is HBA2”, and on page 65, line 35 “The objective of this Example was to validate an assay for calling copy number variants (CNVs)…A method that uses multiplex ligation-dependent probe amplification (MLPA) and long-range PCR (LR-PCR) to disambiguate CNVs in exons 12-15 of PMS2…”.
Kvitek et al. and Li et al. teach the method of claim 1 as previously described.
Kvitek et al. and Li et al. do not teach the multiple sites of interest be within exons 1, 2, and 3 of HBA1 and HBA 2.
Law et al. teaches on page 297, column 1, paragraph 2 “Despite their ancient origin, the HBA1 and HBA2 genes have remained very similar, comprising three segments of homology (the X, Y, and Z boxes) that are punctuated with non-homologous regions (I, II, and III)”, which in view of Kvitek et al. would render obvious exons 1, 2, and 3 of HBA1/2 as Kvitek et al. is focusing on exons in HBA1 and HB2 and Law et al. focuses on the specific regions, thereby reading on wherein the multiple sites of interest are within exons 1, 2, and/or 3 of HBAI and exons 1, 2, and/or 3 of HBA2.
Response to Arguments
Applicant's arguments filed 3/16/2026 have been fully considered but they are not persuasive.
Applicant asserts on pages 10-11 of the Remarks filed 3/16/2026 that due to the amendments of claim 1, the basis for the rejection under 35 U.S.C. 102 is no longer anticipated and as such the dependent claims are no longer taught by the combination of references. Examiner agrees with applicant but has provided a new reference, Li et al., which teaches the newly amended limitations of claim 1.
Double Patenting
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under double patenting have been reviewed, updated, and provided below.
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 3-5, 9-10, 12-13, and 20-21, are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5-9, and 15 of copending Application No. 17/158,978 in view of Kvitek et al. (WO 2016168371 A1) and Li et al. (bioinformatics (2009) 1754-1760). Although the claims at issue are not identical, they are not patentably distinct from each other because while the claims are not exact matches for each other they are version of each other. For example, claim 14 of U.S. Patent Application No. 17/158,978 recites a ploidy of 4 however in U.S. Patent Application No. 17/630,385 it recites a ploidy of 2. While these might be different, they are directed to the same concept in limiting the abstract idea itself and do not change the function of the invention itself. Further examples of claims which read upon each other are provided below in table format for ease of reference. It would have been obvious at the time of filing to modify the teachings of Application No. 17/158,978 for a method for detecting genetic variation in a genome of a subject, with the teachings of Kvitek et al. for homologous regions, as it is merely adapting one known technique for another more specific technique for a more specified target. Furthermore, it would have been obvious to modify the teachings of the other two with the teachings of Li et al. for the use of their BWA method that aligns reads to a non-modified/masked reference such as the human reference genome as the latter teaches on page 1759, column 1, paragraph 4 “For short read alignment against the human reference genome, BWA is an order of magnitude faster than MAQ while achieving similar alignment accuracy. It supports gapped alignment for single-end reads, which is increasingly important when reads get longer and tend to contain indels. BWA outputs alignment in the SAM format to take the advantage of the downstream analyses implemented in SAMtools. BWA plus SAMtools provides most of functionality of the MAQ package with additional features”. One would have had a reasonable expectation of success given that Kvitek et al. teaches, on a general level the method of Application No. 17/158,978, but merely adapts it for highly homologous regions and that Li et al. is merely limiting the reference to which you are aligning and the BWA method and alignment to the human reference genome is standard within the field. As such any similarities between the two applications are then obvious where said scope is found between either the instant application or the reference.
This is a provisional nonstatutory double patenting rejection.
Application: 17/630,385
Application: 17/158,978
Claim 1: A method for detecting genetic variation in a genome of a subject, the genome comprising highly homologous first and second regions of interest, the method comprising: (a) obtaining sequence reads by paired-end sequencing from multiple sites of interest in the first and second regions of interest, wherein the sequence reads comprise a first read and a second read obtained at each site of interest; (b) selecting sequence reads that represent the first and second regions of interest equally;[[(b)]]c) aligning sequence reads to a reference genome, wherein first reads and second reads are aligned to the reference genome separately and the aligner emits multiple possible alignments for each of the first and second reads; [[(c)]](d) identifying first reads and second reads that either: (i) align to the first region of interest;(ii) align to the second region of interest; (iii) sequentially align to the first and the second regions of interest; or (iv) align to the first and the second regions of interest in parallel;[[(d)]](e} pairing a first read and a second read from the reads identified in step [[(c)]](d), thereby generating a top paired alignment; and [[(e)]]f detecting the genetic variation in the top paired alignment generated in step [[(d)]]e).
Claim 1: A method for detecting genetic variation in a genome of a subject, the genome comprising highly homologous first and second regions of interest, the method comprising:(a) obtaining sequence reads by paired-end sequencing from multiple sites of interest in the first and second regions of interest, wherein the sequence reads comprise a first read and a second read obtained at each site of interest;(b) aligning sequencing reads to a reference genome using an aligner, wherein first reads and second reads are aligned to the reference genome separately and the aligner emits multiple possible alignments for each of the first and second reads, wherein the reference genome does not comprise a masked or modified portion of the first and second region of interest; and(c) detecting, using a computer, a genetic variation in a top paired alignment comprising a paired first read and second read that align to the first region of interest.
Claim 39: A method comprising:sequencing genomic DNA extracted from a sample from the subject by pair-end sequencing, thereby obtaining sequence reads from multiple sites of interest in a first region of interest and a second region of interest, wherein the sequencing reads at each region of interest comprise a first read and a second read, andaligning the first read and the second read separately to a reference genome with an aligner that emits multiple possible alignments, thereby obtaining a top paired alignment wherein the first read and the second read aligns to the first region of interest, wherein the reference genome does not comprise a masked or modified portion of the first and second region of interest, and wherein the top paired alignment comprises a genetic variation.
Kvitek et al. teaches in claim 1 “A computer-implemented method for determining a likelihood of a presence or absence of a genetic variation in a gene of interest for a subject where the subject's genome also contains at least one counterpart gene to the gene of interest such that the counterpart genes have a high degree of homology to the gene of interest”, in claim 20 “wherein the sequence reads are obtained by a method comprising paired-end sequencing”, in claim 1 “mapping sequence reads to the modified reference genome”, and on page 31, lines 13 -30 “As used herein, the terms "aligned", "alignment", or "aligning" refer to two or more nucleic acid sequences that can be identified as a match (e.g. , 100% identity) or partial match…Alignment of a sequence read can be a 100% sequence match (e.g., 100% identity). In some cases, an alignment is less than a 100% identity (e.g. , non-perfect match, partial match, partial alignment). In some embodiments an acceptable alignment of two nucleic acids comprises at least a 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91 %, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81 %, 80%, 79%, 78%, 77%, 76% or 75% identity… In some embodiments, an alignment comprises a mismatch (non-identical aligned nucleotides). In some embodiments, an alignment comprises 1, 2, 3, 4, 5 or more mismatches. Two or more sequences can be aligned using either strand”, on page 49, line 25 “More than one machine in one location or multiple locations may be accessed by a user, and data may be mapped and/or processed in series and/or in parallel”, and in claim 1 “determining the likelihood of a presence or absence of a genetic variation in the gene of interest of the subject according to the sequence reads mapped to the gene of interest”.
Li et al. teaches in the abstract “We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps”
Claim 3: The method of claim 1, comprising, before step [[(b)]](c), aligning first reads and second reads to a reference genome, wherein the aligner emits the best possible paired-end alignment to the first or second region of interest for each pair of first and second reads, and wherein only paired-end reads associated with a top alignment score to the first or second regions of interest are aligned separately in step [[(b)]](c).
Claim 2: The method of claim 1, comprising, before (b), aligning first reads and second reads to a reference genome, wherein the aligner emits the best possible paired-end alignment to the first or second region of interest for each pair of first and second reads based on the highest alignment score, and wherein only paired-end reads associated with a top alignment score to the first or second region of interest are aligned separately in (b).
Claim 4: The method of claim 1, wherein the sequence reads are obtained by direct targeted sequencing (DTS) of the multiple sites of interest, and wherein the first read comprises a genomic sequence read and the second read comprises a probe sequence read associated with a site of interest.
Claim 3: The method of claim 1, wherein the sequence reads are obtained by direct targeted sequencing (DTS) of the multiple sites of interest, and wherein the first read comprises a genomic sequence read and the second read comprises a probe sequence read associated with a site of interest.
Claim 5: The method of claim 1, wherein the sequence reads are obtained by solution DTS of the multiple sites of interest, and wherein the first read comprises a genomic sequence read and the second read comprises a combination of a genomic sequence read and a probe sequence read associated with a site of interest.
Claim 3: The method of claim 1, wherein the sequence reads are obtained by direct targeted sequencing (DTS) of the multiple sites of interest, and wherein the first read comprises a genomic sequence read and the second read comprises a probe sequence read associated with a site of interest.
Claim 9: The method of claim 1, wherein in step [[(b)]](c) the aligner only emits alignments that meet a minimum alignment score for the first and second regions of interest.
Claim 5: The method of claim 1, wherein in (b) the aligner only emits alignments that meet a minimum alignment score for the first and second regions of interest.
Claim 10: The method of claim 1, wherein a first read and a second read are paired in step [[(d)]](e) only if the alignments of the first read and the second read to the first region of interest are within about 1000 bases of each other.
Claim 6: The method of claim 1, wherein a first read and a second read are paired only if the alignments of the first read and the second read to the first region of interest are within a certain number of bases of each other.
Claim 7: The method of claim 1, wherein a first read and a second read are paired in step (d) only if the alignments of the first read and the second read to the first region of interest are within about 100bp, about 200bp, about 300bp, about 400bp, about SOObp, about 600bp, about 700bp, about 800bp, about 900bp, about 1000bp, about 1l00bp, about 1200bp, about 1300bp, about 1400bp, about 1500bpm or more than 1500bp.
Claim 12: The method of claim 1, comprising generating multiple paired alignments in step (d), calculating an alignment score for each of the multiple paired alignments, and identifying the top paired alignment as having the highest alignment score.
Claim 8: The method of claim 1, comprising generating multiple paired alignments, calculating an alignment score for each of the multiple paired alignments, and identifying the top paired alignment as having the highest alignment score.
Claim 13: The method of claim 1, wherein the top paired alignment in step [[(d)]]() is selected as having the smallest template length.
Claim 9: The method of claim 1, wherein the top paired alignment is selected as having the smallest template length.
Claim 20: The method of claim 1, wherein if a genetic variation is detected in step [[(e)]](f), a portion of the subject's genome is amplified by long-range PCR and assayed by multiplex ligation-dependent probe amplification (MLPA).
Claim 15: The method of claim 1, wherein if a genetic variation is detected, a portion of the subject's genome is amplified by long-range PCR and assayed by multiplex ligation-dependent probe amplification (MLPA).
Claim 21: The method of claim 1, wherein if a genetic variation is detected in step [[(e)]](_f, a portion of the first region of interest is amplified by long-range PCR and the product or a portion thereof is sequenced by Sanger sequencing or NGS; orthe subject's genomic DNA is assayed by multiplex ligation-dependent probe amplification (MLPA); orthe subject's genomic DNA is assayed by long-read sequencing.
Claim 17: The method of claim 1, wherein if a genetic variation is detected, the subject's genomic DNA is assayed by multiplex ligation-dependent probe amplification (MLPA).
Response to Arguments
Applicant's arguments filed 3/16/2026 have been fully considered but they are not persuasive.
Applicant asserts on pages 10-11 of the Remarks filed 3/16/2026 that due to the amendments of claim 1, the basis for the rejection under 35 U.S.C. 102 is no longer anticipated and as such the dependent claims are no longer taught by the combination of references. Examiner agrees with applicant but has provided a new reference, Li et al., which teaches the newly amended limitations of claim 1.
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.
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/K.N.A./Examiner, Art Unit 1687
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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