DETAILED ACTION
Claim Status
Claims 1-20 are rejected.
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 .
Priority
This application does not make any claims of priority. Therefore, its effective filing date of claims 1-20 is 06/02/2023.
Information Disclosure Statement
The Information Disclosure Statement filed on 04/19/2023 is in compliance with the provisions of 37 CFR 1.97 and has been considered in full. A signed copy of list of references cited from the IDS is included with this Office Action.
Drawings
The drawings filed on 04/19/2023 are accepted.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea 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:
1, 9, 16. determining, by the one or more processors of the machine, that a second analysis is to be performed by a second version of the first analytical tool upon the sequenced data of the genetic sample, a third analytical tool into which second results of the second analytical tool are to be inputted specifying a minimum version of the first analytical tool, the determining that the second analysis is to be performed being based on the first version failing to satisfy the minimum version in conjunction with the second version satisfying the minimum version;
1, 9, 16. and causing, by one or more processors of the machine, the second analysis to be performed by the second version of the first analytical tool on the sequenced data of the genetic sample.
2, 10, 17. the second results of the second analysis by the first analytical tool include an improvement absent from the first results of the first analysis by the first analytical tool, the improvement including at least one of a correction to an error, an additional datum, a datum with increased precision, or a datum with increased accuracy.
3, 11, 18. the second analysis by the first analytical tool includes an improvement absent from the first analysis by the first analytical tool, the improvement including at least one of analyzing an additional portion of a gene, analyzing an additional gene, omitting analysis of a portion of a gene, omitting analysis of a gene, analyzing more total portions of genes, analyzing more total genes, analyzing fewer total portions of genes, or analyzing fewer total genes.
4, 12, 19. the second results of the second analysis by the first analytical tool include an improvement absent from the first results of the first analysis by the first analytical tool, the improvement including at least one of a data format supported by the third analytical tool, a file format supported by the third analytical tool, a metadata type supported by the third analytical tool, or a metadata value supported by the third analytical tool.
5, 13, 20. the first analytical tool is a primary analysis tool configured to perform alignment of the sequenced data of the genetic sample.
6, 14, 20. the second analytical tool is a secondary analysis tool configured to perform variant calling on the first results of the first analytical tool.
7, 15, 20. The third analytical tool is a tertiary analysis tool configured to process secondary results outputted by the second analytical tool based on processing the first results of the first analytical tool.
8. the tertiary analysis tool is configured to process the secondary results by performing at least one of ancestry analysis, traits analysis, or medical diagnosis.
The limitations for “determining” and “causing” are verbal equivalents for transformations made to genetic sequence data that are recited so broadly that they could be performed by a human being using a pen and paper. Therefore, these limitations fall under the “Mental process” grouping of abstract ideas. While claims 1-20 recite performing some aspects of the analysis with a “processor”, there are no additional limitations that indicate that this processor requires anything other than carrying out the recited mental process or mathematical concept in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claims 1-20 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 or applies or uses the recited judicial exception to effect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment. Specifically, the claims recite the following additional elements:
1. accessing, by one or more processors of a machine, first results of a first analysis performed by a first version of a first analytical tool on sequenced data of a genetic sample, a second analytical tool being available to process results of the first analytical tool
9. A non-transitory machine-readable storage medium comprising instructions that, when executed by one or more processors of a machine, cause the machine to perform operations comprising: accessing first results of a first analysis performed by a first version of a first analytical tool on sequenced data of a genetic sample, a second analytical tool being available to process results of the first analytical tool
16. A system comprising: one or more processors; and
16. a memory storing instructions that, when executed by at least one processor among the one or more processors, cause the system to perform operations comprising:
16. accessing first results of a first analysis performed by a first version of a first analytical tool on sequenced data of a genetic sample, a second analytical tool being available to process results of the first analytical tool;
The limitation for accessing data is a form of mere data gathering, similar to presenting offers to potential customers and gathering statistics generated based on the testing about how potential customers responded to the offers; the statistics are then used to calculate an optimized price, OIP Technologies, 788 F.3d at 1363, 115 USPQ2d at 1092-93. There are no limitations that indicate that the claimed processor or the formats of the provided data require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-20 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). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment. The instant claims recite additional elements enumerated above, in the section on step 2A.
The limitation for accessing data is well understood, routine and conventional, similar to Storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93. As discussed above, there are no additional limitations to indicate that the claimed processor requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-20 are not patent eligible.
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.
Claims 1-4, 7, 9-12, 15-19 are rejected under 35 U.S.C. 103 as being unpatentable over Byeong-Su (KR20190015898A, newly cited) in view of Duncavage et al. (The Journal of Molecular Diagnostics, Vol. 25, No. 1, January 2023).
Regarding claims 1, 9 and 16, accessing the first results of a first analytical tool to process a genetic sample is taught by Byeong-Su (¶ 6). A second analytical tool or “sub-optimization workflow” is available to process the results of the first analytical tool (¶ 34). Byeong-su teaches implementation on a computer (¶ 53).
The generated sub-optimization workflow is variable based on the size of the genetic data and the attribute information (¶ 34). In the case of an error, the analysis is performed again using the log and processing data from the failed analysis (¶ 47). The results of a secondary analysis can be sent to a third analytical tool (fig. 3).
However, Byeong-Su is silent as to a second version of the first analytical tool.
Duncavage teaches using second versions of software tools within bioinformatics pipelines for reanalysis, in order to take advantage of changes made to modules within a bioinformatics pipeline (pg 2 right col ¶ 1, fig. 1E).
Regarding claims 2, 10, and 17, the second results of the second analysis by the first analytical tool in Byeong-Su contain a correction to an error (¶ 45-47).
Regarding claims 3, 11, and 18, the genetic analysis results of the second analysis by the first analytical tool in Byeong-Su contain more analyzed genes or portions of genes than those of the first analysis that stopped part-way due to error (¶ 45-47).
Regarding claims 4, 12, and 19, Byeong-Su states that their invention addresses that it is “difficult to understand the complicated dependency of various programs because the workflow is designed and analyzed by using various programs” (¶ 4). The sub-optimization workflow is based on the results of the upper standard workflow (¶ 35). Byeong-Su writes: “Each of the plurality of execution modules can be sequentially connected to the input / output of data.” The analysis results management unit stores the analysis results of every execution module, because each is required for the processing of the next step if there is an error (¶ 46). The sequentially connected programs with complicated dependency with optimization based on each of the other’s metadata that are required for each other means that data and metadata types are being updated for supporting the next tool (¶ 52).
Regarding claims 7 and 15, the third analytical tool process secondary results that are based on the first results (fig. 3).
Regarding claims 1-4, 7, 9-12, 15-19, An invention would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the invention if some teaching, suggestion, or motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. There is a teaching to use a second version of a software tool in the text of Duncavage, in order to use the advantages of a new software version (fig. 1E and description). There would be a reasonable expectation of success in making this combination to a person of ordinary skill in the art, as Byeong-Su’s method reanalyzes data with the same version of the tool, which would be simple to change. . Therefore, it would have been prima facie obvious to one of ordinary skill in the art at the time to modify the method of Byeong-Su by incorporating the differential versioning of Duncavage, in order to use the advantages of a new software version in error reanalysis(fig. 1E and description).
Claim(s) 5-6, 8, 13-14, and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Byeong-Su and Duncavage as applied to claims 1-4, 7, 9-12, 15-19 above, and further in view of Hu et al. (Agriculture 2018, 8(6), 75).
Regarding claims 5-6, 13-14, and 20, Hu states that “sequence alignment and variant calling are standard bioinformatics tasks when analysing sequencing data” (Hu introduction ¶ 2).
Regarding claim 20, the third analytical tool process secondary results that are based on the first results (Byeong-Su fig. 3).
Regarding claim 8, Hu states that “the detection of robust gene-trait associations” is a major goal in bioinformatics (Hu conclusion ¶ 1).
Regarding claims 5-6, 8, 13-14, and 20, An invention would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the invention if some teaching, suggestion, or motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. There is a teaching to use variant calling, alignment, and trait analysis in the text of Hu, in order to integrate bioinformatics into applications (abstract). There would be a
reasonable expectation of success in making this combination to a person of ordinary skill in the art, as Byeong-Su’s method is a bioinformatics genetic analysis workflow method with modules for different programs. Therefore, it would have been prima facie obvious to one of ordinary skill in the art at the time to modify the method of Byeong-Su and Duncavage by integrating alignment, variant calling, and trait analysis into the workflow as in Hu, in order to use bioinformatics in applications (abstract).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GRACELYN M HILL whose telephone number is (571)272-9871. The examiner can normally be reached Monday-Friday 8:30-5pm.
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, Olivia M Wise can be reached at 571-272-2249. 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.
/G.M.H./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
