DETAILED ACTION
Claims 16-21, 23-26, 29-31 and 34-55. Cancelled.
Claim Objections
Claim 27 is objected to because of the following informalities: Claim 27 is incorrectly shown as cancelled (as part of group cancelling, shown as 23-27). Appropriate correction is required.
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.
3. Claims 1-15, 22, 27-28 and 32-33 rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without being integrated into a practical application and do not include additional elements that amount to significantly more than the judicial exception.
Utilizing the two step process adopted by the Supreme Court (Alice Corp vs CLS Bank Int'l, US Supreme Court, 110 USPQ2d 1976 (2014) and the recent 101 guideline, Federal Register Vol. 84, No., Jan 2019)), determination of the subject matter eligibility under the 35 USC 101 is as follows: Specifically, the Step 1 requires claim belongs to one of the four statutory categories (process, machine, manufacture, or composition of matter). If Step 1 is satisfied, then in the first part of Step 2A (Prong one), identification of any judicial recognized exceptions in the claim is made. If any limitation in the claim is identified as judicial recognized exception, then proceeding to the second part of Step 2A (Prong two), determination is made whether the identified judicial exception is being integrated into practical application. If the identified judicial exception is not integrated into a practical application, then in Step 2B, the claim is further evaluated to see if the additional elements, individually and in combination, provide “inventive concept” that would amount to significantly more than the judicial exception. If the element and combination of elements do not amount to significantly more than the judicial recognized exception itself, then the claim is ineligible under the 35 USC 101.
Looking at the claims, the claims satisfy the first part of the test 1A, namely the claims are directed to two of the four statutory classes, apparatus and method. In Step 2A Prong one, we next identify any judicial exceptions in the claims. In Claim 1 (as a representative example), we recognize that the limitations “determining, using the data, values of the at least one quality metric for each of at least some of the plurality of biological samples, identifying one or more sources of error for the data generated by processing the plurality of biological samples, the identifying performed using the values of the at least one quality metric and a statistical model representing causal relationships among the one or more physical components and/or the one or more workflow processes used to perform the sample processing workflow,” are abstract ideas, as they recite steps that can be performed by mental process. Similar rejections are made for other independent and dependent claims. With the identification of abstract ideas, we proceed to Step 2A, Prong two, where with additional elements and taken as a whole, we evaluate whether the identified abstract idea is being integrated into a practical application.
In Step 2A, Prong two, the claims additionally recite “processing of biological samples in a laboratory environment in accordance with a sample processing workflow, the sample processing workflow being performed using one or more physical components and/or one or more workflow processes,” “using at least one computer hardware processor to perform obtaining data about a plurality of biological samples, the data generated by processing the plurality of biological samples in accordance with the sample processing workflow,” and “hardware processor,” but said limitations, recited at high level of generality, are merely directed to insignificant data collection activity, and recitation of general-purpose computer for implementing the abstract idea. In the dependent claims 22-24, the claims additionally recite statistical graphical modeling using nodes and edges, but said limitations are insignificant post-solution of displaying data. The claims do not improve the functioning of any machines and do not improve other technology. At most, the claims are an improvement in the abstract idea of identifying sources of error occurring during processing of biological samples. However, improved or new abstract ideas are still abstract ideas, and not eligible under the 101. In short, the claims do not provide sufficient evidence to show that they are more than a drafting effort to monopolize the abstract idea. As such, the abstract idea is not integrated into a practical application. Consequently, with the identified abstract idea not being integrated into a practical application, we proceed to Step 2B and evaluate whether the additional elements provide “inventive concept” that would amount to significantly more than the abstract idea.
In Step 2B, the claims additionally recite “processing of biological samples in a laboratory environment in accordance with a sample processing workflow, the sample processing workflow being performed using one or more physical components and/or one or more workflow processes,” “using at least one computer hardware processor to perform obtaining data about a plurality of biological samples, the data generated by processing the plurality of biological samples in accordance with the sample processing workflow,” and “hardware processor,” but said limitations, recited at high level of generality, are merely directed to insignificant data collection activity, and recitation of general-purpose computer for implementing the abstract idea, that are well-understood, routine and conventional. In the dependent claims 22-24, the claims additionally recite graphical modeling using nodes and edges, but said limitations are insignificant post-solution of displaying data, that are well-understood, routine and conventional. As such, the claims do not provide additional elements that would amount to significantly more than the abstract idea.
In Summary, the claims recite abstract idea without being integrated into a practical application, and do not provide additional elements that would amount to significantly more than the abstract idea. As such, taken as a whole, the claims are ineligible under the 35 USC 101.
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)(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 1-15 and 32-33 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Nuzhdina et al., US-PGPUB 2021/0005284 (hereinafter Nuzhdina)
Regarding Claims 1 and 32-33. Nuzhdina discloses identifying sources of error occurring during processing of biological samples in a laboratory environment in accordance with a sample processing workflow, the sample processing workflow being performed using one or more physical components and/or one or more workflow processes, the sample processing workflow being associated with at least one quality metric (Abstract, evaluating quality of nucleic acid sequence; Paragraph [0083], detection of errors in sequence data; Paragraphs [0079]-[0083], sources of error in all stages of the workflow), comprising:
using at least one computer hardware processor to perform (Paragraph [0005], processor):
obtaining data about a plurality of biological samples (Paragraph [0004], obtain nucleic acid data), the data generated by processing the plurality of biological samples in accordance with the sample processing workflow (Paragraph [0080], conventional workflow; Paragraphs [0083]-[0084], preparing and processing of biological samples);
determining, using the data, values of the at least one quality metric for each of at
least some of the plurality of biological samples (Paragraph [0322], major histocompatibility complex, MHCs, as one example);
identifying one or more sources of error for the data generated by processing the
plurality of biological samples, the identifying performed using the values of the at least one quality metric and a statistical model representing causal relationships among the one or more physical components and/or the one or more workflow processes used to perform the sample processing workflow (Paragraph [0297], Paragraph [0320], sequencing platforms: Paragraph [0322], determining whether the MHCs match to statistically significant threshold. If don’t match, bad quality (e.g. source or integrity), and identifying the source of bad quality, etc.,); Fig. 6B, identifying genes that introduced bias in data, etc., Paragraph [0284], assessing the quality of sequence information, etc., [0288], where sequence information is obtained from sequencing platforms; Paragraph [0608]); and outputting information indicative of the identified one or more sources of error (Paragraph [0322], result reported to the user; Paragraph [0603], the results displayed to a user)
Regarding Claim 2. Nuzhdina discloses the information indicative of the identified one or more sources of error indicates a physical component, from among the one or more physical components used to perform the sample processing workflow, as a source of error for the data generated by processing the plurality of biological samples in accordance with the sample processing workflow (Paragraphs [0079]-[0085], errors at all stages, and [0087], identifying errors; [0211]-[0217]; [0284], assessing the quality of sequence information, etc., [0288], where sequencing information is obtained from sequencing platforms or instruments or equipments; [0294]-[0295], identifying the source, etc.)
Regarding Claim 3. Nuzhdina discloses the physical component is a piece of equipment used to perform at least one workflow process of the sample processing workflow, and outputting information further comprises outputting information identifying the piece of equipment (Paragraph [0320], sequencing platform, and Paragraph [0322], and quality of sequencing information, identifying the source, etc., and the quality result reported to the user; Paragraph [0603], the results displayed to a user)
Regarding Claim 4. Nuzhdina disclose the physical component is a reagent from a lot used to perform at least one workflow process of the sample processing workflow (Paragraphs [0235]-[0239], reagents.), and outputting information further comprises outputting information identifying the lot as a source of error for the data generated by processing the plurality of biological samples in accordance with the sample processing workflow (Paragraph [0076], Fig. 15; Paragraph [0608], batch; [0605], presented to the user)
Regarding Claim 5. Nuzhdina discloses the information indicative of the identified one or more sources of error indicates a workflow process, from among the one or more workflow processes used to perform the sample processing workflow, as a source of error for the data generated by processing the plurality of biological samples in accordance with the sample processing workflow (Paragraphs [0079]-[0085], errors at all stages, and [0087], identifying errors; [0211]-[0217]; [0284], assessing the quality of sequence information, etc., [0288], sequencing information obtained from sequencing platforms; [0294]-[0295], identifying the source, etc.)
Regarding Claim 6. Nuzhdina discloses the information indicative of the identified one or more sources of error indicates one or more of the pluralities of biological samples as a source of error for the data generated by processing the plurality of biological samples in accordance with the sample processing workflow Paragraph [0297], Paragraph [0322], determining whether the MHCs match to statistically significant threshold. If don’t match, bad quality or error; Fig. 6B, identifying genes that introduced bias in data)
Regarding Claim 7. Nuzhdina discloses processing the plurality of biological samples in accordance with the sample processing workflow Paragraph [0080], conventional workflow; Paragraphs [0083]-[0084])
Regarding Claim 8. Nudhdina discloses the one or more physical components include one or more reagents used in the sample processing workflow and/or one or more pieces of equipment used in the sample processing workflow (Paragraphs [0211]-[0217], etc; [0235]-[0239], reagents)
Regarding Claim 9. Nudhdina discloses the one or more physical components include at least one physical component selected from the group consisting of: an extraction machine, an extraction automation system, a library preparation automation system, a thermocycler, an automation system, a sequencing machine, a hybridization machine, a centrifugation machine, a liquid handling system, and a qPCR machine (Paragraph [0217], extraction; Paragraph [0577], library preparation; Paragraphs [0004]-[0008], [0177]-[0178], [0196], [0205], [0211]-[0217], sequencing, Paragraphs [0235]-[0239], reagents, buffers, etc.)
Regarding Claim 10. Nudhdina discloses the one or more physical components include at least one reagent selected from the group consisting of: a buffer, a binding buffer, a wash buffer, an organic reagent, an inorganic reagent, an acidic solution, and a basic solution (Paragraphs [0147], [0156], [0206], [0235]-[0239], reagents, buffers, etc.)
Regarding Claim 11. Nudhdina discloses the one or more physical components include at least one selected from the group consisting of: a bait mix, a hybridization mix, a sequencing mix, a PCR master mix, and a primer mix (Paragraph [0178], primers, mixtures; Paragraph [0502], [0532]-[0533, PCR; ).
Regarding Claim 12. Nudhdina discloses the one or more physical components include at least one selected from the group consisting of: an enzyme, a labeled nucleotide, a sample plate, enrichment beads, a flow cell, a cartridge, a pipette, a pipette tip, and a sample tube (Paragraphs [0235]-[0240], enzymes, pipettes, tubes, etc.)
Regarding Claim 13. Nudhdina discloses the one or more workflow processes include at least one workflow process selected from the group consisting of: an extraction process, a library preparation process, an enrichment process, a hybridization process, a sequencing process, a centrifugation process, an assay setup process, an amplification process, and a qPCR process (Paragraphs [0004]-[0008], sequencing, [0058], library construction; extraction, Paragraph [0158], centrifugation, Paragraph [0177]-[0184], library preparation for RNA sequencing, enrichment, etc.,)
Regarding Claim 14. Nudhdina discloses the one or more workflow processes include a sequencing process, the one or more physical components include at least one sequencing machine and at least one sequencing reagent, the data includes sequencing data for each of the at least some of the plurality of biological samples, and the at least one quality metric includes sequencing metrics for the sequencing data (Paragraphs [0004]-[0008], [0177]-[0178], [0196], [0205], sequencing, Paragraphs [0235]-[0239], reagents, buffers, etc.)
Regarding Claim 15. Nudhdina discloses the statistical model represents causal relationships among the at least one sequencing machine, the at least one sequencing reagent, the plurality of biological samples, and the sequencing data (Paragraph [0322])
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 22 and 27-28 are rejected under 35 U.S.C. 103 as being unpatentable over Nuzhdina et al., US-PGPUB 2021/0005284 in view of Kincaid et al., US-PGPUB 2004/0150644 (hereinafter Kincaid)
Regarding Claim 22. Nuzhdina does not disclose the statistical model comprises a graphical model comprising: nodes representing random variables corresponding to at least some of the one or more physical components and/or at least some of the one or more workflow processes; and directed edges representing causal relationships among the at least some of the one or more physical components and/or the at least some of the one or more workflow processes.
Kincaid discloses the statistical model comprises a graphical model comprising: nodes representing random variables corresponding to at least some of the one or more physical components and/or at least some of the one or more workflow processes (Fig. 1B in particular; Abstract; Claim 29, degree of sharpness with respect to error statistics; Paragraphs [0002]-[0007], node or network diagrams used in workflow process, including biological diagrams; Paragraph [0010], Paragraph [0042], Paragraph [0072], as an example, nodes having measurements with relatively high p-values or high standard of deviation shown more blurring, while those with relatively low error statistic display relatively sharp) and directed edges representing causal relationships among the at least some of the one or more physical components and/or the at least some of the one or more workflow processes (Figs. 1-8)
At the time of the invention filed, it would have been obvious to a person of ordinary skill in the art to use the teaching of Kincaid in Nuzhdina and use the statistical model comprises a graphical model comprising: nodes representing random variables corresponding to at least some of the one or more physical components and/or at least some of the one or more workflow processes; and directed edges representing causal relationships among the at least some of the one or more physical components and/or the at least some of the one or more workflow processes, so as to present data to a user in an easier graphical format for enhanced data interpretation.
Regarding Claim 27. Kincaid discloses a node corresponding to a physical component of the sample processing workflow represents a random variable whose value is indicative of a degree to which the physical component contributes to error in the data generated by processing biological samples in accordance with the sample processing workflow (Fig. 1B in particular; Abstract; Claim 29, degree of sharpness with respect to error statistics; Paragraphs [0002]-[0007], node or network diagrams used in workflow process, including biological diagrams; Paragraph [0010], Paragraph [0042], Paragraph [0072], as an example, nodes having measurements with relatively high p-values or high standard of deviation shown more blurring, while those with relatively low error statistic display relatively sharp)
Regarding Claim 28. Kincaid discloses a node corresponding to a workflow process of the sample processing workflow represents a random variable whose value is indicative of a degree to which the workflow process contributes to error in the data generated by processing biological samples in accordance with the sample processing workflow (Fig. 1B in particular; Abstract; Claim 29, degree of sharpness with respect to error statistics; Paragraphs [0002]-[0007], node or network diagrams used in workflow process, including biological diagrams; Paragraph [0010], Paragraph [0042], Paragraph [0072], as an example, nodes having measurements with relatively high p-values or high standard of deviation shown more blurring, while those with relatively low error statistic display relatively sharp)
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Vasileiadis et al., US-PGPUB 2021/0208953
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/HYUN D PARK/ Primary Examiner, Art Unit 2857
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