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 .
Claims 1-27 are pending in this application.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 6/29/2026 has been entered.
Claim Rejections - 35 USC § 102
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.
Claim(s) 1-7, 9-27 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Baluch et al., US 2020/0042735 (hereinafter Baluch).
For claims 1, 14, 21, Baluch teaches a computer-implemented method comprising:
obtaining sequence data produced by a sequencer device, the sequence data comprising genomic data of interest and metadata (see Baluch, [0117], [0559], [0615], obtaining “raw genomic sequence data” that includes “metadata…and annotation data”);
processing the sequence data, the processing comprising:
separating the genomic data of interest from the metadata (see Baluch, Fig. 49, [0615] “separates metadata (e.g. quality values) and annotation data from the genomic sequences”); and
compressing the separated genomic data of interest based on comparing the separated genomic data of interest to a reference sequence that is different from the separated genomic data of interest to produce compressed genomic data (see Baluch, [0117], [0221], [0302], [0492], [0615], “sequencing data is compressed” includes “encoding” or “aligning a DNA sequence of nucleotides with respect to a reference sequence” and where reference sequence is “known a-priori”); and
storing the compressed genomic data and the metadata (see Baluch, [0117], [0549] – [0550], [0615], multiplexed coded sequence data and coded metadata into “container of information”).
For claims 2, 15, 22, Baluch teaches wherein the separating uses a configuration file that indicates indexes, and the separating separates the genomic data of interest from the metadata based on the indexes indicated by the configuration file (see Baluch, [0185], [0380], [0455], separating and indexing sequencing data via “Master Index Table (MIT)” that “contains one section per each class of data…and per each reference sequence,”).
For claim 3, Baluch teaches the method of claim 1, wherein the metadata comprises index data for a plurality of reads (see Baluch, [0191], [0380], [0455], [0549], metadata comprising “Master Index Table” used to access and/or “read” containers of compressed sequence data for decompression).
For claims 4, 16, 23, Baluch teaches wherein the separating comprises using the index data to demultiplex at least a portion of the sequence data to provide the separated genomic data of interest as per-sample genomic data (see Baluch, Fig. 50, [0118], [0416] – [0418], [0569], “genomic demultiplexer” accesses “Genomic Dataset Mapping Table” associated with multiplexed data to identify and separate “Genomic Data Streams” that includes “classification and labelling” of sequenced “organic samples”), wherein the compressing provides compressed per-sample genomic data as the compressed genomic data, and wherein the storing stores the index data (see Baluch, [0117], [0416] – [0418], encoding/compressing “Access Units” that are classified and labeled for specific “organic samples”).
For claim 5, Baluch teaches the method of claim 1, wherein the processing trims at least some of the metadata from other data of the sequence data (see Baluch, [0615], where separated “metadata…and annotation data from the genomic sequences” represents trimmed metadata).
For claims 6, 17, 24, Baluch teaches wherein the trimmed metadata comprises adapter data, Unique Molecular Identifiers (UMI) data, and/or data selected to be ignored, and wherein the storing stores each of the adapter data, Unique Molecular Identifiers (UMI) data, and/or data selected to be ignored (see Baluch, [0117], [0165], [0549] – [0550], [0615], metadata comprising an “identifier” for associated data represents UMI, and multiplexed coded sequence data and coded metadata into “container of information”).
For claim 7, Baluch teaches the method of claim 1, wherein the processing further comprises compressing the metadata to provide compressed metadata, wherein the storing stores the compressed metadata (see Baluch, [0117], [0549] – [0550], [0615], multiplexed coded sequence data and coded metadata into “container of information”).
For claim 9, Baluch teaches the method of claim 1, wherein the storing stores the compressed genomic data in one or more data files that also store the metadata (see Baluch, [0117], [0549] – [0550], [0615], multiplexed coded sequence data and coded metadata into “container of information”).
For claims 10, 18, 25, Baluch teaches further comprising, based on a request, recovering the sequence data from the stored compressed genomic data and metadata (see Baluch, Fig. 50, [0118], “demultiplex” represents recovery operation), the recovering comprising:
decompressing the compressed genomic data to provide decompressed genomic data of interest as the separated genomic data of interest (see Baluch, [0118], [0190] – [0191], “decode” or “decompressing” AU containing compressed genomic sequence data); and
combining the decompressed genomic data of interest with the metadata to provide combined genomic data and metadata (see Baluch, Fig. 50, [0053], [0118], decoded and decompressed into FASTQ or BAM output that comprises combined genomic data and associated metadata).
For claims 11, 19, 26, Baluch teaches wherein the metadata comprises index data for a plurality of reads (see Baluch, [0191], [0380], [0455], [0549], metadata comprising “Master Index Table” used to access and/or “read” containers of compressed sequence data for decompression), wherein the separating comprises using the index data to demultiplex at least a portion of the sequence data to provide the separated genomic data of interest as per-sample genomic data (see Baluch, Fig. 50, [0118], [0191], [0380], [0416] – [0418], [0455], [0569], “genomic demultiplexer” accesses “Genomic Dataset Mapping Table” associated with multiplexed data to identify and separate “Genomic Data Streams” that includes “classification and labelling” of sequenced “organic samples”), wherein the compressing provides compressed per-sample genomic data as the compressed genomic data, wherein the storing stores the index data (see Baluch, [0117], [0416] – [0418], encoding/compressing “Access Units” that are classified and labeled for specific “organic samples”), and wherein the combining comprises remultiplexing the decompressed genomic data of interest with the metadata to provide the combined genomic data and metadata (see Baluch, [0535], “re-encoding (decompressing and compressing) the data of AUs”).
For claims 12, 20, 27, Baluch teaches wherein the processing further comprises compressing the metadata to provide compressed metadata, wherein the storing stores the compressed metadata (see Baluch, [0117], [0549] – [0550], [0615], multiplexed coded sequence data and coded metadata into “container of information”), and wherein the recovering further comprises decompressing the compressed metadata to provide decompressed metadata as the metadata that is combined with the decompressed genomic data of interest (see Baluch, Fig. 50, [0053], [0118], decoded and decompressed into FASTQ or BAM output that comprises combined genomic data and associated metadata).
For claim 13, Baluch teaches the method of claim 1, further comprising sequencing, by the sequencer device, genomic material to produce and obtain the sequence data, wherein the sequencer device performs the obtaining, the processing, and the storing, and wherein the storing stores the compressed genomic data and the metadata to a storage device of the sequencer device (see Baluch, [0117], [0164] [0184], [0207], [0549] – [0550], [0615] “sequencing devices” for “sequencing runs” to produce “genomic datasets”, and multiplexed coded sequence data and coded metadata into “container of information”).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 8 is/are rejected under 35 U.S.C. 103 as being unpatentable over Baluch et al., US 2020/0042735 (hereinafter Baluch) in view of Alberti et al., US 2023/0274800 (hereinafter Alberti).
For claim 8, Alberti teaches wherein the storing stores the compressed genomic data in a first one or more data files and stores the metadata in a second one or more data files different from the first one or more data files (see Alberti, [0048], [0051], [0169] – [0174] “storing or transmitting the encoded genome sequencing data on or to a computer-readable storage medium,” [0190], “Said sequencing reads and the associated annotations can as well be decoupled and encapsulated in separate files”). It would have been obvious to one skilled in the art at the time of the invention to modify the teachings of Baluch with the teachings of Alberti to reduce the storage space for compressed representations of genomic sequencing data (see Alberti, [0011] – [0017] “compressing separately non-indexed descriptors from indexed textual descriptors is that these 2 classes of data, once separately grouped, show a lower entropy than when they are coded together, therefore higher compression ratio can be achieved”).
Response to Amendments & Arguments
Applicant’s arguments with respect to claim(s) rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 103 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Renzi et al., US 2020/0058378.
Alberti et al., US 2019/0214111.
Semenyuk US 2021/0050074.
Kennedy et al., US 2017/0116216. [0008]
Sheinin et al., US 2015/0227686. [0036]
Rizk US 2022/0415441.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JENSEN HU whose telephone number is (571)270-3803. The examiner can normally be reached Monday - Friday 9-5 PT.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sherief Badawi can be reached at 571-272-9782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JENSEN HU/Primary Examiner, Art Unit 2169
Prosecution Insights