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 .
Claim Status
Claims 1-20 are currently pending and under exam herein.
Priority
No priority is claimed. The Effective Filing Date (EFD) of the claimed invention is the filing date of 22 March 2023.
Information Disclosure Statement
The Information Disclosure Statement filed 22 March 2023 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS is included with this Office Action.
Drawings
The Drawings filed 22 March 2023 have been accepted.
Specification
Note: All references to the Specification herein pertain to the PG publication: US20240321395A1.
Claim Interpretation
In the interest of compact prosecution, the instant claims are examined to consider all claim limitations but the claims herein contain recitations of intended use, as recited below. The courts have stated that claims must be given their broadest reasonable interpretation consistent with the specification In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997); In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541,550-551 (CCPA 1969); and In re Zletz, 893 F.2d 319, 321-22, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989) (see MPEP § 2111). Thus the claims herein are given the broadest reasonable interpretation consistent with the indefinite claim language and specification wherein specific structures for the intended uses as recited in the claims are undefined. It is suggested that the claims be amended to recite active, positive limitations to avoid recitation of intended use in the claims.
Claims 1 (2-17) and those dependent therefrom recite the limitations “and if the endogenous control is apparent in the genetic data, determining whether the biological sample is contaminated based on calculating a composite alternative allele fraction of the sequences for the mitochondrial genetic material” wherein the claims recite contingent claim language.
With respect to contingent claiming, said contingencies as claimed require that the claims are interpreted as provided for in the MPEP at 2111.04 (II), wherein: “the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met). For example, assume a method claim requires step A, if a first condition happens and step B if a second condition happens. If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim. If the claimed invention requires the first condition to occur, then the broadest reasonable interpretation of the claim requires step A. If the claimed invention requires both the first and second conditions to occur, then the broadest reasonable interpretation of the claim requires both steps A and B”.
In the instant claims, the following are “contingent” recitations: Claim 1: “and if the endogenous control is apparent in the genetic data, determining whether the biological sample is contaminated” wherein the interpretation is as follows: “if ” the endogenous control is apparent” is equivalent to A in the above example and the alternative (due to the use of the word “if” [or not]) The BRI of the claim, as currently recited, requires only the scenario wherein A occurs, i.e. if control is apparent. However, in the alternative (if not) then the claim step is not required to be performed. The claim further includes that if this scenario occurs (if control is apparent) then determination is made of whether (or not) the sample is contaminated. Again, if this does not occur, then the determination step is not required. As such, claims 2-3 of calculating also are not required in the scenario wherein the endogenous control is not apparent.
With respect to the interpretations above, it is suggested that the claims be amended recite alternative language so as to avoid interpretation of contingent claiming, such as active, positive steps requiring determining contamination of the biological sample, wherein endogenous control is apparent based on calculation of a composite alternative allele fraction of the sequences for the mitochondrial genetic material or the like.
Claim Rejections - 35 USC § 112(b)-Indefiniteness
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.
Claims 1-20 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 11 recites, “wherein the using of the one or more mitochondrial probes is performed during enrichment of genetic material of the biological sample and prior to amplification of genetic material of the biological sample”, wherein there is insufficient antecedent basis in the claim for “during enrichment of the genetic material” as no “enrichment” step is performed in the claims prior to said recitation. Further, there is insufficient antecedent basis in the claim for “prior to amplification” as claim 10, from which claim 11 depends recites only the use of probes to collect genetic material and enable amplification, without positive active steps of actually amplifying mitochondrial genetic material. Clarification is requested.
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.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1 Analysis: Are claims directed to process, machine, manufacture/composition of matter
With respect to step (1): yes, the claims are directed to a method for performing quality control for a biological sample and a system for quality control for a biological sample.
Step 2A, Prong 1 Analysis: Do claims recite abstract idea
With respect to step (2A)(1), the claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the (2A)(1) evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and in conjunction with mathematical concepts (in particular mathematical relationships and formulas).
The claim steps to abstract ideas are as follows:
Claim 1:
determining whether an endogenous control is apparent in the genetic data based on whether at least a threshold amount of the genetic data includes sequences for mitochondrial genetic material; and if the endogenous control is apparent in the genetic data, determining whether the biological sample is contaminated based on calculating a composite alternative allele fraction of the sequences for the mitochondrial genetic material, wherein said operation of making a determination is a step that is directed to mental processes whereby one can assess given data and make a determination given said data. Further steps directed to “calculating” are those that are mental processes that can be performed using pen and paper and also mathematical processes by which the Specification discloses that said calculations include calculations with respect to an average, median, mean or weighted value, which are statistical calculations.
Claim 2:
calculating the composite alternative allele fraction based on the mitochondrial genetic material comprises calculating a median, average, or mean alternative allele fraction, based on calculated alternative allele fractions at loci for called mitochondrial genetic variants, wherein, as above, said operations are mathematical.
Claim 3:
calculating the composite alternative allele fraction based on the mitochondrial genetic material comprises determining whether the composite alternative allele fraction is over a predetermined threshold, wherein as above said operations are directed to mathematical processes of threshold determinations.
Claim 4:
wherein the predetermined threshold is 0.98, wherein said step further limits the threshold determination.
Claim 5:
determining that the biological sample is contaminated if the composite alternative allele fraction is below the predetermined threshold, wherein steps directed to determining are those that are mental operations as described above.
Claim 6:
determining whether the endogenous control is apparent comprises reviewing the genetic data to confirm that human genetic material is in the biological sample, wherein steps directed to determining are those that are mental operations as described above.
Claim 7:
wherein the threshold amount comprises at least twenty percent of a mitochondrial genome covered by at least ten reads, wherein said step further limits the threshold determination.
Claim 15:
wherein determining whether an endogenous control is apparent comprises determining whether at least 20% of the mitochondrial contig is present in the plurality of reads, wherein said step further limits the judicial exception recited above directed to “determining”, which is a mental process.
Claim 16:
wherein, if less than the threshold amount of the genetic data includes sequences for the mitochondrial genetic material is present in the sample, the endogenous control is not apparent, which further limits the step in claim 1 of determining endogenous control as described above.
Claim 17:
calculating an alternative allele fraction at each of multiple loci across the mitochondrial genome; for each of the loci, determining whether the alternative allele fraction is above a minimum threshold; and for each of the loci, if the alternative allele fraction is above the minimum threshold, calling a mitochondrial genetic variant at the loci, wherein the step directed to calculating is one that is a mathematical process as above and determining, as described above, is a mental operation of making assessments from provided data and further wherein steps directed to “calling’ are those that are akin to “naming” the loci as a genetic variant, as no limits on actual calling are recited.
Claim 18:
determine whether an endogenous control is apparent in the genetic data based on whether at least a threshold amount of the genetic data includes sequences for the mitochondrial genetic material; calculate a composite alternative allele fraction of the sequences for the mitochondrial genetic material; and determine whether the biological sample is contaminated based on the calculated composite alternative allele fraction, wherein said operation of making a determination is a step that is directed to mental processes whereby one can assess given data and make a determination given said data. Further steps directed to “calculating” are those that are mental processes that can be performed using pen and paper and also mathematical processes by which the Specification discloses that said calculations include calculations with respect to an average, median, mean or weighted value, which are statistical calculations.
Claim 19:
calculate the composite alternative allele fraction based on the mitochondrial genetic material comprises calculating a median, average, or mean alternative allele fraction, based calculated alternative allele fractions at loci for called mitochondrial genetic variants, wherein, as above, said operations are mathematical.
Claim 20:
calculate the composite alternative allele fraction based on the mitochondrial genetic material comprises determining whether the composite alternative allele fraction is over a predetermined threshold, wherein as above said operations are directed to mathematical processes of threshold determinations.
Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined herein to each cover performance either in the mind (calculations by hand or pen and paper) and performance by mathematical operation (calculation for assessment allele fraction). There are no specifics as to the methodology involved in “determining” or in “calculating” and thus, under the BRI, one could simply, for example, perform said operation with pen and paper, or, alternatively with the aid of a generic computer as a tool to perform said calculations. These recitations are similar to the concepts of collecting information, analyzing it and providing certain results from the collection and analysis (Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations (Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in (Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind with pen and paper, and can include mathematical concepts.
Further, see MPEP § 2106.04(a)(2), subsection III. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674: noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016): holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind" (see Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016): holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
Step 2A, Prong 2 Analysis: Integration to a Practical Application
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements:
Claims 1 and 18: receiving (accessing-clm 18) genetic data sequenced from the biological sample, wherein the genetic data has been analyzed for both pathogen genetic material and mitochondrial genetic material, which are operations directed to data gathering.
Claims 8-14 are directed to operations that are routine laboratory operations and serve to get the data for computations in the abstract idea. Said operations include sequencing; sequencing with mitochondrial and pathogen material; use of probes; enrichment and amplification; capture and sequencing; read generation; and alignment of reads.
With respect to claim 18 the system recited further includes the additional element of a processor and a memory that holds instructions which when executed cause the processor to; and access genetic data sequenced from the biological sample, wherein the genetic data has been analyzed for both pathogen genetic material and mitochondrial genetic material, wherein said operations are directed to generic computer implementation using a generically recited computer with a processor executing instructions.
With respect to the additional elements in the instant claims directed to data gathering, said elements perform functions of collecting the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or on how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
With respect to routine laboratory operations, the courts have recognized the following laboratory techniques as examples of insignificant extra-solution activity. See further, the MPEP at 2106.05(d)II.): determining the level of a biomarker in blood by any means (Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017)); detecting DNA or enzymes in a sample (Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017)).
Further, the system, processor, memory and instructions are part of a general purpose computer system and there are no details herein wherein of how the specific computer structures are used to implement the judicial exceptions beyond generic computing operations, i.e., the computer elements of the claims do not provide improvements to the functioning of the computer itself (see: DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (see: Diamond v. Diehr); nor do they utilize a particular machine (see: Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the judicial exception using a computer, and therefore the claim does not provide integration into a practical application of any judicial exception.
Step 2B Analysis: Do Claims Provide an Inventive Concept
The claims are lastly evaluated using the (2B) analysis, wherein it is determined that because the claims recite abstract ideas, and do not integrate that abstract ideas into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims additional elements, the instant Specification includes that any sequencing methods may be used, including SBS sequencing, for example. [0091] Further elements directed to amplification and alignment are also laboratory techniques that are well-known and conventional in the art, as provided, for example, in the art to Amorim et al. [(2019) Mitochondrial DNA in human identification: a review. PeerJ 7:e7314; 24 pages) [pp.6-8] providing that each of said laboratory steps (including those of sequencing) as disclosed herein are directed steps that are routine, well-understood and conventional in the art.
Further, the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)II.): determining the level of a biomarker in blood by any means (Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017)); detecting DNA or enzymes in a sample (Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017)).
Last, the additional elements directed to a computer system are not those that provide an inventive concept herein as the steps are generically recited. The instant Specification provides that such systems are generic computing systems, [0113], and as such they are set forth herein at a high level of generality such that they can be met by any general purposes computer, and thus constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept (MPEP 2106.05(b)I-III).
The dependent claims have been analyzed with respect to step 2B and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 103
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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Shih et al. (Genes (2018), Vol. 9, No.49:19 pages), in view of Caldwell et al. (“Chapter 10 Mitochondrial DNA as Source Tracking Markers of Fecal Contamination” in Microbial Source Tracking: Methods, Applications, and Case Studies (2011) Hagedorn et al., eds., Springer Nature, New York; pages 229-250).
Claim 1 is directed to:
A method of performing quality control for a biological sample, the method comprising:
receiving genetic data sequenced from the biological sample, wherein the genetic data has been analyzed for both pathogen genetic material and mitochondrial genetic material;
determining whether an endogenous control is apparent in the genetic data based on whether at least a threshold amount of the genetic data includes sequences for mitochondrial genetic material; and
if the endogenous control is apparent in the genetic data, determining whether the biological sample is contaminated based on calculating a composite alternative allele fraction of the sequences for the mitochondrial genetic material.
The prior art to Shih et al. disclose the application of probe capture enrichment of mitochondrial DNA, wherein “library prepared from a limited DNA source can be enriched for mtDNA as well as nuclear markers by hybrid capture with the relevant probe panels” (abstract-p. 1). Shih et al. disclose that “mitochondrial DNA, as a haploid lineage marker, is also valuable for the de-convolution of mixtures since each individual contributes only one sequence rather than two alleles. Presence of two nucleotides in a single mt genome position would either indicate a mixture or presence of heteroplasmy” (p. 2). The method of Shih et al. includes further the improves[ment] [of] “the capture of forensically challenging DNA samples such as DNA from telogen hair roots, telogen hair shafts, and touch-DNA. This strategy allows the capture of both mtDNA and nuclear SNP markers from a single shotgun DNA library without consuming additional DNA extracts of limited forensic biological samples” (p. 4). Shih et al. further establish that “setting thresholds based on the initial copy number can reduce the stochastic effects posed by possible allele dropouts with limited DNA samples during the probe capture enrichment process” (p. 15).
The prior art to Shih et al. does not specifically disclose mtDNA as endogenous control when assessing pathogen and mitochondrial genetic material, as in claim 1. However, the prior art to Caldwell et al. discloses using mtDNA to assess contamination in environmental surface waters (p. 230; p. 233). Caldwell et al. disclose that mtDNAs are used as typing markers for several fields such as in forensics and food industry applications (p. 232).
As such, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized mtDNA to distinguish contamination, such as in the methods disclosed in Caldwell et al. that provide ability to test for mtDNA in water samples as indicative of fecal contamination rather than testing specific bacterial species by using capture techniques such as in Shih et al. because as disclosed Caldwell et al., mtDNA is uniquely found in the cells of eukaryotes (p. 231-Caldwell) and provides for robust signals in assay platform (p. 233). Distinguishing mtDNA in mixture of samples, as in Shih et al., would be obvious given the references, and one would have had a reasonable expectation of success in so doing as mtDNA is routinely used for mixture analysis in forensics, for example, as disclosed by Shih et al. (abstract), providing that mtDNA is a viable source for control analyses.
With respect to claim 2, Shih et al. disclose alternative allele fraction variants detection (abstract).
With respect to claim 3, Shih et al. disclose threshold determinations (p. 15).
With respect to claims 4, 5, and 7 and specific thresholds set, Shih et al. discloses variant allele detection using GeneMarker® HTS, which is a platform to distinguish major and minor variants (Figure 1; p. 7). Shih et al. discloses that custom filters may be set to meet threshold requirements (p. 7). As such, it would be obvious to set a threshold for assay needs as set by a researcher.
With respect to claim 6, Caldwell et al. disclose assessment of human material from that of other (p. 233).
With respect to claim 8, Shih et al. disclose sequencing material (p. 5, Figure 1).
With respect to claim 9, Shih et al. disclose sequencing mixtures and it would be an obvious variation to include pathogens (bacteria) as would be present also in the samples as disclosed by Caldwell et al. which utilize mtDNA as an indicator of contamination (or not) (see above).
With respect to claims 10-12, Shih et al. disclose probe capture, enrichment, and sequencing (p. 5, Figure 1).
With respect to claim 13, Shih et al. disclose fragments that extend across the mt genome (p. 5, Figure 1).
With respect to claim 14, Shih et al. disclose mtDNA alignment for variant separation at p. 5, Figure 1.
With respect to claim 15, Shih et al. disclose assessment of mitochondrial contigs at least at 20% (p. 7-8).
With respect to claim 16, Shih et al. include setting threshold limitations as described above.
With respect to claim 17, Shih et al. disclose variant calling at p. 5, Figure 1.
With respect to claims 18-20, the claims are further directed to a system that includes a processor to perform said operations as disclosed above. The prior art to Shih et al. disclose implementation of computer analyses using calculations of variant allele fractions, such as disclosed at p. 5, Figure 1, wherein data are assessed as provided from probe capture, enrichment and sequencing laboratory steps.
Conclusion
No claims are allowed.
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/Lori A. Clow/ Primary Examiner, Art Unit 1687
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