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 .
Claim Status
Claims 1-25 are cancelled.
Claims 26-42 are newly added.
Claims 26-42 are currently pending and examined on the merits.
Claims 26-42 are rejected.
Priority
The instant application is a CON of U.S. Application No. 15/585,009 filed on 2 May 2017, which is a DIV of U.S. Application No. 14/169,056 filed on 30 January 2014. At this point in examination, the effective filing date of claims 1-25 is 30 January 2014.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 9 January 2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description:
"325" and "327" in Figure 3A.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Figures 3A, 4A, 4B, 4C, 6, and 7 are submitted in color. Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
The drawings, submitted 9/27/2022, require correction because several nucleic acid sequences do not meet the proper disclosure requirements, as detailed below.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Sequence disclosures appearing in Figure 7 in the drawings filed on 9/27/2022 do not have sequence identifiers.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities:
Title on pg. 30, above para. 4, "inersertions" should read "insertions".
Appropriate correction is required.
Pg. 42, para. 1, lines 15-18 in the instant specification contains hyperlinks. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
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 26-42 are patent eligible under 35 U.S.C. 101 because the claimed invention recites additional elements that are unconventional under Step 2B. In particular, the two pseudo-reference genomes employed in independent claim 26, steps (d)-(f) and claim 36, steps (iv)-(vi) are novel constructs that are rooted in computer technology and improve the functioning of a sequencer apparatus and/or computer configured to perform sequencing. Compared with conventional reference sequences and genomes, the pseudo-reference genomes provide a unique computer construct comprising two separate and different genome sequences that require the computer or sequencer to perform separate and different aligning, scoring, and comparing operations using a single set of reads. Furthermore, using two pseudo-reference genomes—one containing one known indel allele and the other containing a different indel allele—alleviates the computational challenges of ambiguous alignments of indel-containing reads to conventional reference sequences that contain a generic representation of the indel. This can significantly improve the speed at which a computer or sequencer aligns indel-containing reads and thereby improves the speed of the overall phasing process. Therefore, because the claims are rooted in computer technology and recite an improvement to the way a computer, particularly a computer configured to perform sequencing, aligning, and phasing, operates, they are not directed to an abstract idea and are patent eligible.
Statutory Double Patenting
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claims 26 and 36 are rejected under 35 U.S.C. 101 as claiming the same invention as that of claims 3 and 13 of prior U.S. Patent No. 11,492,656 B2, referred to as ‘656 B2. This is a statutory double patenting rejection.
Regarding claim 26:
Regarding the recited a method of determining a haplotype or partial haplotype of a DNA sample comprising segments of genomic DNA, wherein a first segment of the genomic DNA contains sites of a plurality of heterozygous polymorphisms including a site of a first heterozygous indel polymorphism having a first indel allele and a second indel allele, wherein the first segment comprises the first indel allele, but not the second indel allele, at the site of the first heterozygous indel polymorphism, claim 1 of ‘656 B2 discloses “A method of determining a haplotype or partial haplotype of a DNA sample comprising segments of genomic DNA, wherein a first segment of the genomic DNA contains sites of a plurality of heterozygous polymorphisms including a site of a first heterozygous indel polymorphism having a first indel allele and a second indel allele, wherein the first segment comprises the first indel allele, but not the second indel allele, at the site of the first heterozygous indel polymorphism”.
Regarding the recited (a) sequencing the DNA sample including the first segment, wherein the sequencing produces a plurality of sequence reads, including at least a first read containing the sequence of the first indel allele and a second read containing the sequence of the second indel allele, and wherein the first segment of genomic DNA has a length of at least 50kb, claim 1 of ‘656 B2 discloses “(a) sequencing the DNA sample including the first segment, wherein the sequencing produces a plurality of sequence reads, including at least a first read containing the sequence of the first indel allele and a second read containing the sequence of the second indel allele, and wherein the first segment of genomic DNA has a length of at least 50 kb”.
Regarding the recited (b) examining at least 10,000 of the plurality of sequence reads, including the first read and the second read, to identify and characterize the plurality of heterozygous polymorphisms including the first heterozygous indel polymorphism, wherein each of the plurality of heterozygous polymorphisms is characterized by a genome location and sequences of each allele, claim 1 of ‘656 B2 discloses “(b) examining at least 10,000 of the plurality of sequence reads, including the first read and the second read, to identify and characterize the plurality of heterozygous polymorphisms including the first heterozygous indel polymorphism, wherein each of the plurality of heterozygous polymorphisms is characterized by a genome location and sequences of each allele”.
Regarding the recited (c) generating a VCF file comprising a list of heterozygous polymorphisms in the DNA sample, wherein the list of heterozygous polymorphisms includes the genome location and sequences of each allele of the heterozygous polymorphisms in the DNA sample, claim 2 of ‘656 B2 discloses “generating a file comprising a list of heterozygous polymorphisms in the DNA sample, wherein the list of heterozygous polymorphisms includes the genome location and sequences of each allele of the heterozygous polymorphisms in the DNA sample”. Claim 3 of ‘656 B2 further discloses “wherein the file is a VCF file”.
Regarding the recited (d) using the genome locations and allele sequences, including sequences of the first and second indel alleles, in the VCF file to prepare a first pseudo-reference genome and a second pseudo-reference genome to modify a reference genome having a length that is at least 1000 times the length of the reads to produce two pseudo-reference genomes, a first pseudo-reference genome representing the sequence of the first indel allele at the genome location of the first heterozygous indel polymorphism, and a second pseudo-reference genome representing the sequence of the second indel allele at the genome location of the first heterozygous indel polymorphism, wherein the first pseudo-reference genome and the second pseudo-reference genome are electronically formatted and configured to work with computational aligners to align sequence reads containing the first and second indel alleles, claim 1 of ‘656 B2 discloses “(c) modifying a reference genome having a length that is at least 1000 times the length of the reads to produce two pseudo-reference genomes, a first pseudo-reference genome representing the sequence of the first indel allele at the genome location of the first heterozygous indel polymorphism, and a second pseudo-reference genome representing the sequence of the second indel allele at the genome location of the first heterozygous indel polymorphism, wherein the first pseudo-reference genome and the second pseudo-reference genome are electronically formatted and configured to work with computational aligners to align sequence reads containing the first and second indel alleles”. Claim 2 of ‘656 B2 further discloses “using the genome location and allele sequences, including sequences of the first and second indel alleles, in the file to prepare the first and second pseudo-reference genomes”.
Regarding the recited (e) computationally aligning the at least 10,000 sequence reads to the first pseudo-reference genome and computationally generating a score of the alignment to the first pseudo-reference genome, claim 1 of ‘656 B2 discloses “(d) computationally aligning the at least 10,000 sequence reads to the first pseudo-reference genome and computationally generating a score of the alignment to the first pseudo-reference genome”.
Regarding the recited (f) computationally aligning the at least 10,000 sequence reads to the second pseudo-reference genome and computationally generating a score of the alignment to the second pseudo-reference genome, claim 1 of ‘656 B2 discloses “(e) computationally aligning the at least 10,000 sequence reads to the second pseudo-reference genome and computationally generating a score of the alignment to the second pseudo-reference genome”.
Regarding the recited (g) comparing the scores of the alignments to the first and second pseudo-reference genomes, claim 1 of ‘656 B2 discloses “(f) comparing the scores of the alignments to the first and second pseudo-reference genomes”.
Regarding the recited (h) selecting the first pseudo-reference genome for reads from the first segment based on a higher scoring alignment, claim 1 of ‘656 B2 discloses “(g) selecting the first pseudo-reference genome for reads from the first segment based on a higher scoring alignment”.
Regarding the recited (i) developing a partial or complete haplotype from alleles of the first segment, wherein one allele of the partial or complete haplotype is the first indel allele, claim 1 of ‘656 B2 discloses “(h) developing a partial or complete haplotype from alleles of the first segment, wherein one allele of the partial or complete haplotype is the first indel allele”.
Regarding claim 36:
Regarding the recited a system for haplotyping genomic DNA samples comprising segments of genomic DNA, wherein a first segment of the genomic DNA contains sites of a plurality of heterozygous polymorphisms including a site of a first heterozygous indel polymorphism having a first indel allele and a second indel allele, wherein the first segment comprises the first indel allele, but not the second indel allele, at the site of the first heterozygous indel polymorphism, the system comprising: (a) a sequencer configured to receive nucleic acids samples and providing nucleic acid sequence information from the sample; (b) a processor; and (c) one or more computer-readable storage media having stored thereon instructions for execution on said processor to evaluate sequence reads from the sequencer, claim 13 of ‘656 B2 discloses “A system for haplotyping genomic DNA samples comprising segments of genomic DNA, wherein a first segment of the genomic DNA contains sites of a plurality of heterozygous polymorphisms including a site of a first heterozygous indel polymorphism having a first indel allele and a second indel allele, wherein the first segment comprises the first indel allele, but not the second indel allele, at the site of the first heterozygous indel polymorphism, the system comprising: (a) a sequencer configured to receive nucleic acids samples and providing nucleic acid sequence information from the sample; (b) a processor; and (c) one or more computer-readable storage media having stored thereon instructions for execution on said processor to evaluate sequence reads from the sequencer”.
Regarding the recited (i) sequencing the DNA sample including the first segment, wherein the sequencing produces a plurality of sequence reads, including at least a first read containing the sequence of the first indel allele and a second read containing the sequence of the second indel allele, and wherein the first segment of genomic DNA has a length of at least 50kb, claim 13 of ‘656 B2 discloses “(i) sequencing the DNA sample including the first segment, wherein the sequencing produces a plurality of sequence reads, including at least a first read containing the sequence of the first indel allele and a second read containing the sequence of the second indel allele, and wherein the first segment of genomic DNA has a length of at least 50 kb”.
Regarding the recited (ii) examining at least 10,000 of the plurality of sequence reads, including the first read and the second read, to identify and characterize the plurality of heterozygous polymorphisms including the first heterozygous indel polymorphism, wherein each of the plurality of heterozygous polymorphisms is characterized by a genome location and sequences of each allele, claim 13 of ‘656 B2 discloses “(ii) examining at least 10,000 of the plurality of sequence reads, including the first read and the second read, to identify and characterize the plurality of heterozygous polymorphisms including the first heterozygous indel polymorphism, wherein each of the plurality of heterozygous polymorphisms is characterized by a genome location and sequences of each allele”.
Regarding the recited (iii) generating a VCF file comprising a list of heterozygous polymorphisms in the DNA sample, wherein the list of heterozygous polymorphisms includes the genome location and sequences of each allele of the heterozygous polymorphisms in the DNA sample, claim 14 of ‘656 B2 discloses “generating a file comprising a list of heterozygous polymorphisms in the DNA sample, wherein the list of heterozygous polymorphisms includes the genome location and sequences of each allele of the heterozygous polymorphisms in the DNA sample”. Claim 15 of ‘656 B2 further discloses “wherein the file is a VCF file”.
Regarding the recited (iv) using the genome locations and allele sequences, including sequences of the first and second indel alleles, in the VCF file to prepare a first pseudo-reference genome and a second pseudo-reference genome to modify a reference genome having a length that is at least 1000 times the length of the reads to produce two pseudo-reference genomes, a first pseudo-reference genome representing the sequence of the first indel allele at the genome location of the first heterozygous indel polymorphism, and a second pseudo-reference genome representing the sequence of the second indel allele at the genome location of the first heterozygous indel polymorphism, wherein the first pseudo-reference genome and the second pseudo-reference genome are electronically formatted and configured to work with computational aligners to align sequence reads containing the first and second indel alleles, claim 13 of ‘656 B2 discloses “(iii) modifying a reference genome having a length that is at least 1000 times the length of the reads to produce two pseudo-reference genomes, a first pseudo-reference genome representing the sequence of the first indel allele at the genome location of the first heterozygous indel polymorphism, and a second pseudo-reference genome representing the sequence of the second indel allele at the genome location of the first heterozygous indel polymorphism, wherein the first pseudo-reference genome and the second pseudo-reference genome are electronically formatted and configured to work with computational aligners to align sequence reads containing the first and second indel alleles”. Claim 14 of ‘656 B2 further discloses “using the genome location and allele sequences, including sequences of the first and second indel alleles, in the file to prepare the first and second pseudo-reference genomes”.
Regarding the recited (v) computationally aligning the at least 10,000 sequence reads to the first pseudo-reference genome and computationally generating a score of the alignment to the first pseudo-reference genome, claim 13 of ‘656 B2 discloses “(iv) computationally aligning the at least 10,000 sequence reads to the first pseudo-reference genome and computationally generating a score of the alignment to the first pseudo-reference genome”.
Regarding the recited (vi) computationally aligning the at least 10,000 sequence reads to the second pseudo-reference genome and computationally generating a score of the alignment to the second pseudo-reference genome, claim 13 of ‘656 B2 discloses “(v) computationally aligning the at least 10,000 sequence reads to the second pseudo-reference genome and computationally generating a score of the alignment to the second pseudo-reference genome”.
Regarding the recited (vii) comparing the scores of the alignments to the first and second pseudo-reference genomes, claim 13 of ‘656 B2 discloses “(vi) comparing the scores of the alignments to the first and second pseudo-reference genomes”.
Regarding the recited (viii) selecting the first pseudo-reference genome for reads from the first segment based on a higher scoring alignment, claim 13 of ‘656 B2 discloses “(vii) selecting the first pseudo-reference genome for reads from the first segment based on a higher scoring alignment”.
Regarding the recited (ix) developing a partial or complete haplotype from alleles of the first segment, wherein one allele of the partial or complete haplotype is the first indel allele, claim 13 of ‘656 B2 discloses “(viii) developing a partial or complete haplotype from alleles of the first segment, wherein one allele of the partial or complete haplotype is the first indel allele”.
Non-Statutory Double Patenting
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 27-35 and 37-42 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 4-12 and 16-21 of U.S. Patent No. 11,492,656 B2, referred to as ‘656 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over the claims of U.S. Patent No. 11,492,656 B2.
Regarding claim 27:
Regarding the recited processing the DNA sample to produce an enriched DNA sample enriched for DNA from the first segment of the genomic DNA, wherein the first segment contains a plurality of alleles from a first haplotype including the first indel allele, claim 4 of ‘656 B2 discloses “processing the DNA sample to produce an enriched DNA sample enriched for DNA from the first segment of the genomic DNA, wherein the first segment contains a plurality of alleles from a first haplotype including the first indel allele”.
Regarding claim 28:
Regarding the recited wherein sequencing the DNA sample comprises sequencing the enriched DNA sample to produce the plurality of sequence reads, which are shorter in length than the first segment, wherein some of the sequence reads contain the first indel allele, claim 5 of ‘656 B2 discloses “wherein sequencing the DNA sample comprises sequencing the enriched DNA sample to produce the plurality of sequence reads, which are shorter in length than the first segment, wherein some of the sequence reads contain the first indel allele”.
Regarding claims 29 and 37:
Regarding the recited wherein the plurality of sequence reads aligned to the two pseudo-reference genomes cluster into islands on the two pseudo-reference genomes, claims 6 and 16 of ‘656 B2 discloses “wherein the plurality of sequence reads aligned to the two pseudo-reference genomes cluster into islands on the two pseudo-reference genomes”.
Regarding claim 30:
Regarding the recited selecting a group of the aligned reads that belong to a first island on the first pseudo-reference genome, claim 7 of ‘656 B2 discloses “selecting a group of the aligned reads that belong to a first island on the first pseudo-reference genome”.
Regarding the recited using alleles from the group of aligned reads to define the first haplotype or a portion of the first haplotype, claim 7 of ‘656 B2 discloses “using alleles from the group of aligned reads to define the first haplotype or a portion of the first haplotype”.
Regarding claim 31:
Regarding the recited determining the complete haplotype containing the first indel allele, claim 10 of ‘656 B2 discloses “determining the complete haplotype containing the first indel allele”.
Regarding claims 32 and 41:
Regarding the recited wherein the first segment is at least about 100 kb in length, claims 11 and 20 of ‘656 B2 discloses “wherein the first segment is at least about 100 kb in length”.
Regarding claims 33 and 42:
Regarding the recited wherein at least one of the first and second indel alleles is an insertion allele, claims 12 and 21 of ‘656 B2 discloses “wherein at least one of the first and second indel alleles is an insertion allele”.
Regarding claim 34:
Regarding the recited tagging the first segment with an index or a partial index at multiple locations along the first segment's length, claim 8 of ‘656 B2 discloses “tagging the first segment with an index or a partial index at multiple locations along the first segment's length”.
Regarding claim 35:
Regarding the recited wherein selecting the group of the aligned reads that belong to a first island on the first pseudo-reference genome comprises determining distances separating adjacent ones of the aligned reads on the reference genome, wherein the separation distances between adjacent aligned reads fall into at least two groups distinguishable by the magnitude of their separation distances, claim 9 of ‘656 B2 discloses “wherein selecting the group of the aligned reads that belong to a first island on the first pseudo-reference genome comprises determining distances separating adjacent ones of the aligned reads on the reference genome, wherein the separation distances between adjacent aligned reads fall into at least two groups distinguishable by the magnitude of their separation distances”.
Regarding claim 38:
Regarding the recited wherein the instructions further comprise instructions for: selecting a group of the aligned reads that belong to a first island on the first pseudo-reference genome, claim 17 of ‘656 B2 discloses “wherein the instructions further comprise instructions for: selecting a group of the aligned reads that belong to a first island on the first pseudo-reference genome”.
Regarding the recited wherein the instructions further comprise instructions for: using alleles from the group of aligned reads to define the partial or complete haplotype, claim 17 of ‘656 B2 discloses “wherein the instructions further comprise instructions for: using alleles from the group of aligned reads to define the partial or complete haplotype”.
Regarding claim 39:
Regarding the recited wherein the instructions for selecting the group of the aligned reads that belong to a first island on the first pseudo-reference genome comprises instructions for determining distances separating adjacent ones of the aligned reads on the reference genome, wherein the separation distances between adjacent aligned reads fall into at least two groups distinguishable by the magnitude of their separation distances, claim 18 of ‘656 B2 discloses “wherein the instructions for selecting the group of the aligned reads that belong to a first island on the first pseudo-reference genome comprises instructions for determining distances separating adjacent ones of the aligned reads on the reference genome, wherein the separation distances between adjacent aligned reads fall into at least two groups distinguishable by the magnitude of their separation distances”.
Regarding claim 40:
Regarding the recited wherein the instructions further comprise instructions for: determining the complete haplotype containing the first indel allele, claim 19 of ‘656 B2 discloses “wherein the instructions further comprise instructions for: determining the complete haplotype containing the first indel allele”.
Therefore, the invention as recited in claims 27-35 and 37-42 is prima facie obvious over U.S. Patent No. 11,492,656 B2. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to use a method of determining a haplotype or partial haplotype of a DNA sample according to the limitations recited in claims 27-35 and 37-42 of the instant application based on claims 4-12 and 16-21 of U.S. Patent No. 11,492,656 B2.
Conclusion
No claims are allowed.
It is noted that the claims are free from the prior art and found to be patent eligible for the same reasons set forth in the parent application, now U.S. Patent No. 11,492,656 B2.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jammy Luo whose telephone number is (571)272-2358. The examiner can normally be reached Monday - Friday, 9:00 AM - 5:00 PM EST.
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/J.N.L./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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