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 .
Applicants Amendment
Applicants’ preliminary amendment filed 12/30/2021 has been received and entered. The substitute specification ahs been entered. Claims 21-44 were cancelled.
Applicants’ preliminary amendment filed 5/4/2022 has been received and entered. The drawings have been entered. The abstract has been entered. The title has been changed and the specification has been entered. Claims 1-44 has been cancelled, claims 45-64 have been added.
Claims 45-64 are pending.
Priority
This application filed 8/25/2021 is a continuation of 15/801868 filed 11/2/2017, now US Patent 11,133084, which is a continuation of 14/752773, now US Patent 10839939 which claims benefit to US Provisional application 62/017589 filed 6/26/2014; and is related to PCT/US15/38175 filed 6/26/2015.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 5/5/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Examiner note: The 61 page IDS filed appears to be a compilation of IDS forms, which were previously filed in the parent application during prosecution. None of the NPL nor foreign patent documents are provided in the filing, but in review of the parent appear to be present.
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).
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Claims 45-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 11,133084 (application 15/801868). In review of the newly filed claim amendments, the instant claims provide for the same steps as set forth in ‘084. A copy of the allowed independent claim is provided for the record.
A method of determining a sequence of a nucleic acid comprising, at a computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors:
obtaining, in electronic form, a plurality of sequence reads of the nucleic acid, wherein
the plurality of sequence reads comprises a plurality of sets of sequence reads,
the nucleic acid is greater than 100,000 base pairs in length,
each sequence read in the plurality of sequence reads has a length of less than 1000 bases,
the plurality of sets of sequence reads comprises more than 100,000 sets of sequence reads,
each respective sequence read in each respective set of sequence reads includes (i) a first portion that corresponds to a subset of the nucleic acid and (ii) a common second portion that forms an identifier that is independent of the sequence of the nucleic acid and that identifies a reaction partition, in a plurality of reaction partitions, in which the respective sequence read was formed, and
each respective set of sequence reads in the plurality of sets of sequence reads is formed in a corresponding reaction partition in the plurality of reaction partitions and each reaction partition includes one or more fragments of the nucleic acid that is used as a template for respective sequence reads in the reaction partition;
(B) creating a respective set of k-mers for each sequence read in the plurality of sequence reads, wherein the sets of k-mers collectively comprise a plurality of k-mers and the identifiers of the source sequence reads for each k-mer in the plurality of k-mers are retained,
(C) tracking, for each respective k-mer in the plurality of k-mers, an identity of each sequence read in the plurality of sequence reads that contains the respective k-mer and the identifier of the set of sequence reads that contains the sequence read;
(D) determining, using the plurality of k-mers, whether to derive a contig sequence that is more likely to be representative of a portion of the nucleic acid, wherein the contig sequence comprises (i) an origin node comprising a first uninterrupted set of overlapping k-mers within the plurality of k-mers and (ii) one of a first destination node comprising a second uninterrupted set of overlapping k-mers within the plurality of k-mers and a second destination node comprising a third uninterrupted set of overlapping k-mers within the plurality of k-mers, wherein the determining uses at least the identifiers of the sequence reads for k-mers in the first, second, and third uninterrupted set of overlapping k-mers; and
(E) assembling the sequence of the nucleic acid from the plurality of k-mers using at least the contig sequence.
Claims 45-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 10,839939 (application 14/752773).
In review of the newly filed claim amendments, the instant claims provide for the same steps as set forth in ‘939. A copy of the allowed independent claim is provided for the record.
A method of determining a sequence of a larger contiguous nucleic acid comprising, at a computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors:
(A) obtaining a plurality of oligonucleotide sequence reads of the larger contiguous nucleic acid, wherein the plurality of oligonucleotide sequence reads comprises a plurality of sets of oligonucleotide sequence reads, the larger contiguous nucleic acid is greater than 1 million base pairs in length, each oligonucleotide sequence read in the plurality of oligonucleotide sequence reads has a sequence length of less than 1000 bases, the plurality of sets of oligonucleotide sequence reads comprises more than 1 x 106 sets of oligonucleotide sequence reads, each respective oligonucleotide sequence read in each respective set of oligonucleotide sequence reads includes (i) a first portion that corresponds to a subset of the larger contiguous nucleic acid and (ii) a common second portion that forms an identifier that is independent of the oligonucleotide sequence of the larger contiguous nucleic acid and that identifies a reaction vessel partition, in a plurality of reaction vessel partitions, in which the respective oligonucleotide sequence read was formed, and each respective set of oligonucleotide sequence reads in the plurality of sets of oligonucleotide sequence reads is formed in a reaction vessel partition in the plurality of reaction vessel partitions and each reaction vessel partition includes one or more fragments of the larger contiguous nucleic acid that is used as the template for each respective oligonucleotide sequence read in the reaction vessel partition; 4
DB2/ 38919241.1Response to Office ActionAttorney Docket No. 104371-5013-US(B) creating a respective set of k-mers for each oligonucleotide sequence read in the plurality of oligonucleotide sequence reads, wherein the sets of k-mers collectively comprise a plurality of k-mers, k is an integer between 5 and 100, the identifiers of the oligonucleotide sequence reads for each k-mer in the plurality of k-mers is retained, k is less than the average length of the oligonucleotide sequence reads in the plurality of oligonucleotide sequence reads, and each respective set of k-mers includes at least eighty percent of the possible k- mers of length k of the first portion of the corresponding oligonucleotide sequence read;
(C) tracking, for each respective k-mer in the plurality of k-mers, an identity of each oligonucleotide sequence read in the plurality of oligonucleotide sequence reads that contains the respective k-mer and the identifier of the set of oligonucleotide sequence reads that contains the oligonucleotide sequence read;
(D) graphing the plurality k-mers as a graph comprising a plurality of nodes connected by a plurality of directed arcs, wherein each node comprises an uninterrupted set of k-mers in the plurality of k-mers of length k with k-1 overlap, each arc connects an origin node to a destination node in the plurality of nodes, a final k-mer of an origin node has k-1 overlap with an initial k-mer of a destination node, and a first origin node has a first directed arc with both a first destination node and a second destination node in the plurality of nodes;
(E) merging the origin node with the first destination node or the second destination node in order to derive a contig oligonucleotide sequence that is more likely to be representative of a portion of the larger contiguous nucleic acid, wherein the contig oligonucleotide sequence comprises (i) the origin node and (ii) one of the first destination node and the second destination node, wherein the determining uses 5 DB2/ 38919241.1Response to Office ActionAttorney Docket No. 104371-5013-USat least the identifiers of the oligonucleotide sequence reads for k-mers in the first origin node, the first destination node, and the second destination node; and
(F) using the graph, after the determining (E), to assemble the sequence of the larger contiguous nucleic acid.
Conclusion
No claim is allowed.
At the time of filing several methods of aligning and assembling sequence reads where k-mers were used to compare and align sequences were well known (see guidance in Miller et al. (Genomics 2010-of record). Further, methods that use barcodes that provide information about the source of the read data were also known (see Rotem et al -of record). However methodology that incorporates a partitioning sequence for alignment of short read data for a context of longer aligned/reference/assembled sequences was not specifically taught in the art of record. Moreover, while claim 2 generally is directed to a method to obtain entities that contain sets of entities that corresponds to a source and has an identification sequence, and creates a set of pieces of the length k representing the corresponding entity, tracking the pieces, and providing a directed graph with nodes and directed arcs in order to determine if the entities/nodes should be merged, the claims require specific shared sequences and means to partition sequences which are not taught in the art of record (such as that previous set forth in Plattner et al provide teaching for a system for processing a plurality of string data values generated from a nucleic acid sequencing machine upon processing a nucleic acid sample).
For purposes of 35 U.S.C. 101 it is noted that claim 2 is directed generally to a method with steps to obtain entities that contain sets of entities that corresponds to a source and has an identification sequence, and creates a set of pieces of the length k representing the corresponding entity, tracking the pieces, and providing a directed graph with nodes and directed arcs in order to determine if the entities/nodes should be merged. In light of the guidance of the specification and as provided by the drawings, the claims appear to be directed providing read sequences with barcode tags for identification and assembling the sequences relative to their homologous overlapping sequences. One such means to practice the steps of the claim and for graphing appears to be in the use of de Bruijn graph (see [00145] for example). Under step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method performed with a computer system. Under step 2A of the 101 analysis, for evaluation of the possible judicial exception of the claims, it is found that steps A-E of the claims as they are directed to obtaining sequence read data that is information, and performing an evaluation of the sequence read data to assemble the short reads/k-mers into longer contiguous reads, and as instructional steps to analyze data and the relationship of sequence one to another are considered the judicial exception of the claim. However, the claims as amended now require that the ‘contiguous nucleic acid is greater than 1 million base pairs in length’ and that ‘the sequence reads comprises more than 1 x 106 sets of oligonucleotide sequence reads’ which cannot practically performed in one’s mind or on paper, and does not appear to fall into the category of a mental process as indicated previously for claim 1 and appear consistent with the claims of US Patent 10,839939.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached on Mon-Fri; 9:00-5:00.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
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