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 .
Election/Restrictions
Applicant’s election without traverse of Group 1 drawn to a method for aligning sequence reads to a reference sequence with a Burrows-Wheeler transform using seed length (claim 1-12) in the reply filed on 07/30/2026 is acknowledged.
Claims 13-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 07/30/2026.
Claim Status
Claim 1-15 are pending.
Claim 13-15 are withdrawn, as discussed above.
Claims 1-13 are under examination herein.
Claims 1-13 are rejected.
Priority
The instant application is a continuation of PCT/EP2021/064094 , filed 05/26/202, which claims priority from US Provisional Application 63/030931, filed 05/28/2020. As such, the effective filing date assigned to each of claims 1-12 is 05/28/2020.
Information Disclosure Statement
The Information Disclosure Statements filed11/23/2022 and 11/07/2025 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. A signed copy of the IDS is included with this Office Action.
Drawings
The drawing filed 11/23/2026 are accepted.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 9-12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
With respect to claim 9, and claims dependent thereon, it is unclear whether the wherein clause is intended to require performing the sequencing within the metes and bounds of the claimed invention, or if it is only further limiting the type of data utilized in the invention such that performing the sequencing is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of sequencing, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the sequencing is not required to be performed. The rejection may be overcome by clarifying what steps are required to be performed.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 1 recites aligning a first set of sequence reads from an entire population of sequence reads to a reference sequence with a Burrows-Wheeler transform using a first seed length, wherein the first seed length is selected based on an error rate of the sequence reads; masking the first set of sequence reads such that the entire population of sequence reads comprises a subset of masked sequence reads and unmasked sequence reads; aligning a second set of sequence reads from the unmasked sequence reads to the reference sequence with the Burrow-Wheeler transform using a second seed length, wherein the second seed length is smaller than the first seed length; and determining an alignment of the sequence reads to the reference sequence based on the first set of sequence reads and the second set of sequence reads.
Claim 2 recites further comprising iteratively masking and aligning additional sets of sequence reads with each subsequent set of reads having a smaller seed length, and determining the alignment of the sequence reads with the additional sets of sequence reads.
Claim 12 recites further comprising calculating a frequency each loci is found in the sequence reads.
These recitations equate to steps of collecting information, analyzing data and making observations, evaluations and judgements that can be carried out in the human mind. Specifically, aligning sets of reads, masking the aligned reads and aligning further sets from the unmasked reads, determining an alignment of the sequence reads to a reference based on the sets of reads, and calculating a frequency each loci is found in the sequence reads can be practically performing the human mind as claimed, since the mind can read data and align sequence reads as recited and make mathematical estimations/comparisons as claimed and are similar to the concepts of collecting and comparing known information in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011) and collecting information, analyzing it, and reporting certain results of the collection and analysis in Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016) that the courts have identified as concepts that can be practically performed in the human mind. Therefore, each of the above recited limitations fall under the “Mental Processes” grouping of abstract ideas. Furthermore, the step of calculating a frequency each loci is found in the sequence reads equates to organizing information and manipulating information through mathematical correlations and reciting a mathematical equation, similar to the concepts of taking existing information, manipulating the data using mathematical functions, and organizing this information into a new form in Digitech Image Techs., LLC v. Electronics for Imaging, Inc., 758 F.3d 1344, 1350, 111 USPQ2d 1717, 1721 (Fed. Cir. 2014). Therefore, these limitations fall under the “mathematical concepts” grouping of abstract ideas. Claims 3-11 further qualify the judicial exceptions. As such, claims 1-12 recite an abstract idea (Step 2A, Prong 1: YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology, applies or uses the recited judicial exception to affect a particular treatment for a condition, implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, effects a transformation or reduction of a particular article to a different state or thing or applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, because the claims do not recite any additional elements. As such, claims 1-12 are directed to an abstract idea (Step 2A, Prong 2: NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). As discussed above, the instant claims do not provide additional elements that are sufficient to amount to significantly more than the judicial exceptions because the claims do not recite additional elements. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-12 are not patent eligible.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Van Rooyen et al. (WO2017123664A1; 11/23/2022 IDS, Foreign Patent Document #1; hereafter referred to as Van Rooyen), as evidenced by Rang et al. (Genome biology 2018, 19(1), p.90; hereafter referred to as Rang).
With respect to claims 1-2, Van Rooyen disclose a method and infrastructure comprising receiving a plurality of reads of genomic sequence data and one or more genetic reference sequences and processing the plurality of reads of genomic sequence data to map and align at least some of the plurality of reads of genomic sequence data according to the one or more genetic reference sequences using a Burrows-Wheeler transform, which supports a variable seed length, to map a selection of reads (i.e. a set) to a reference using a compression formula that compresses repeating sequences of data (claim 11; para 0129; para 0184).
Van Rooyen also discloses the longer the seed, however, the more likely it is that the seeds derived from the sequenced DNA may include an error and that the seed length may be chosen to maximize matches, while at the same time minimizing non-matches due to the incorporation of errors and/or variants, indicating that the seed length is based on the error rate of the sequences (para 00217-00218).
Van Rooyen further discloses after initial seed mapping, it is possible to refine seed mapping with anchored seeds of a shorter length, and that a key to make anchored seed mapping work is that mapper engine queries to the anchored-seed hash table are guided by the results of initial seed mapping. Initial matches may not successfully map all exon segments of a read, but they are very likely to map at least one exon segment of each read, or of its paired end mate read, and given at least one K-base match within at least one exon segment in an RNA read or its mate, any other exon segments in the read which were not successfully mapped by K-base seeds (i.e. initial set of sequences) are very likely to match relatively nearby in the reference genome and one or more reference bins within the search range of successfully-mapped K-base seeds can be queried in the anchored-seed hash table using L-base seeds (i.e. second set of sequences), and thus, K-base seed matches serve as anchors for local searches with shorter L-base seeds (para 00332-00335; para 00393-00396).
With respect to claim 3-5, Van Rooyen discloses any suitable seed length may be employed in a mapping function, and that seed size could be base-4 logarithm of bin/sequence read size, suggesting the based on the size of the sequence reads, the seed length could be 4 bases (para 0216; para 00332-00333).
With respect to claim 6-8, Van Rooyen discloses the sequencing can be nanopore sequencing (para 0028). The prior art to Rang discloses a major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15% (abstract).
With respect to claim 9-11, Van Rooyen discloses in order to compare the subject's DNA/RNA genome to that of the standard reference genome, it needs to be determined where each of these reads map to the reference genome, such as how each is aligned with respect to one another, and/or how each read can also be sorted by chromosome order so as to determine at what position and in which chromosome each read belongs, indicating the set of chromosomes would include and/or be limited to chromosomes 13, 18, 22, X and Y, and once it is determined where in the genome each read belongs, the full length genetic sequence may be determined, and then the differences between the subject's genetic code and that of the referent can be assessed, and further discloses reads could be concatenated (para 0063; para 00172; para 00126).
With respect to claim 12, Van Rooyen discloses sorting may involve one or more of sorting the reads that align to the relatively same position, such as the same chromosome position, so as to produce a pileup, such that all the reads that cover the same location are physically grouped together, and that all of the reads that overlap a given position in the genome maybe be adjacent to each other after sorting and they can be piled up and readily examined to determine if the majority of them agree with the reference value or not, suggesting a frequency for each position is calculated (para –176; para 00423-00424).
Conclusion
No claims allowed.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIDHI DHARITHREESAN whose telephone number is (571)272-5486. The examiner can normally be reached Monday - Friday 9:00 - 5:00.
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/N.D./Examiner, Art Unit 1686
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
