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.
Priority
This application is a 371 of PCT/US2021/013267, filed 13 January 2021, which claims benefit of U.S provisional application no. 62/960,476, filed 13 January 2020. The instant application has the effective filing date of 13 January 2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 11 November 2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Drawings
The drawings, submitted on 12 July 2022, are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference signs mentioned in the description: 1510, 1520, 1530, 1540, 1550, and 1560.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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 U.S.C 101 because the claimed invention is directed to an abstract idea without significantly more, as detailed in the analysis below.
Eligibility Step 1: Subject matter eligibility evaluation in accordance with MPEP § 2106:
Claims 1-7 are directed to a statutory category (method).
Claims 8-14 are directed to a statutory category (system).
Claims 15-20 are directed to a statutory category (machine).
Therefore, in accordance with MPEP § 2106.03, claims 1-20 have patent eligible subject matter.
[Eligibility Step 1: YES]
Eligibility Step 2A: This step determines whether a claim is directed to a judicial exception in accordance with MPEP § 2106.
Eligibility Step 2A -- Prong One: Limitations are analyzed to determine if the claims recite any concepts that could equate to a judicial exception (i.e. abstract idea, law of nature, or natural phenomenon).
Recitations of Judicial Exceptions:
Claim 1:
determining genetic information; (mental process)
determining, based on the genetic information, overlapping mate pairs, wherein the overlapping mate pairs are associated with a sequence and a quality score; (mental process)
determining, based on the overlapping mate pairs, at least one of a plurality of nucleotide combinations, wherein the at least one of the plurality of nucleotide combinations is associated with the sequence and the quality score; (mental process)
determining, based on the at least one of the plurality of nucleotide combinations, an error rate. (mental process, mathematical concept)
Claims 2 and 9: further comprising determining a source of an error. (mental process)
Claims 3 and 16: wherein determining the source of the error comprises identifying a device associated with an error profile. (mental process)
Claim 10: wherein, to determine the source of error, the computing device is further configured to determine a device associated with an error profile. (mental process)
Claims 4 and 11: The method of claim 2, wherein determining the source of an error comprises determining at least one nucleotide combination associated with an error profile. (mental process)
Claims 8 and 15:
determine genetic information; (mental process)
determine, based on the genetic information, overlapping mate pairs, wherein the overlapping mate pairs are associated with a sequence and a quality score; (mental process)
determine, based on the overlapping mate pairs, at least one of a plurality of nucleotide combinations; (mental process)
determining, based on the at least one of the plurality of nucleotide combinations, an error rate. (mental process, mathematical concept)
Claim 18: to determine the source of the error further cause the apparatus to identify a nucleotide combination associated with an error profile. (mental process)
As genetic information could be determined by looking at a dataset, identifying and determining secondary data based on the observables equate to analysis techniques that require no more than mere observations of data that can be completed with only the human mind and pen/paper. As such, limitations that recite these processes fall under the mental process grouping of abstract ideas.
Furthermore, determining an error rate can equate to performing a mathematical calculation on a set of information to derive secondary data. Equations that recite such techniques fall under the mathematical concepts grouping of abstract ideas.
As such claims 1-4, 8-11, and 15-18 appear to recite judicial exceptions (abstract ideas).
[Eligibility Step 2A – Prong One: YES]
Eligibility Step 2A – Prong Two: A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. If the claim contains no additional claim elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)). This step analyzes limitations that are considered additional elements to determine if they integrate the judicial exceptions into practical application.
Eligibility Step 2B: Claim elements are probed for inventive concept equating to significantly more than the judicial exception (MPEP 2106.04(II)).
Additional elements within the claimed invention include:
Claim 8: A system comprising:
a sequencing device configured to:
a computing device configured to:
Claim 15: An apparatus comprising:
one or more processors; and
memory storing processor executable instructions that, when executed by the one or more processors, cause the apparatus to:
Claim 18: The apparatus of claim 15, wherein the processor executable instructions that, when executed by the one or more processors, cause the apparatus
These limitations represent generic computer or sequencing components that generate, transmit, and/or receive data necessary to complete the steps of the claimed invention. As such, the components when viewed separately or in the context of the whole, merely act as tools to execute the judicial exceptions, but do not integrate them into practical application, per Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016).
[Eligibility Step 2A – Prong Two: YES]
The claimed invention is drawn to a method of processing and analyzing sequencing data. This technique, as claimed, was found well-understood, routine, and conventional by the courts, in University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014), which recognized nucleic acid sequencing; and Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, which recognized the analysis of DNA to provide sequence information.
[Eligibility Step 2B: NO]
Additional Elements that may be categorized differently include:
Claim 5, 12, 19: The method of claim 1, wherein the genetic information comprises at least one DNA sequence.
Claim 6, 13, 20: The method of claim 1, wherein the sequence comprises at least one base pair.
Claim 7, 14: The method of claim 1, wherein the quality score comprises a read value.
These limitations specify the format and length of data gathered or analysis technique to be performed. Selecting a particular data source or type of data to be manipulated is classified as an insignificant extra-solution activity and does not integrate the judicial exceptions of the claimed invention, when evaluated separately or as a whole, into practical application per MPEP 2106.05(g) and Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1354-55, 119 USPQ2d 1739, 1742 (Fed. Cir. 2016).
[Eligibility Step 2A – Prong Two: YES]
Considering the types of data (DNA sequence) and techniques (read-associated value) are also well-understood, routine, and conventional within the art, per Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, the elements are further found to lack inventive concept.
[Eligibility Step 2B: NO]
Additional elements that may be categorized differently include:
Claim 8:
transmit genetic information
receive genetic information;
These limitations complete necessary data gathering activities for the claimed invention and do not place necessary limits on or integrate the abstract ideas into practical application per MPEP 2106.05(f) and Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016).
[Eligibility Step 2A – Prong Two: YES]
Such data gathering activities that use a computer to transmit and receive data are further classified as insignificant extra-solution activities and considered well-understood, routine, and conventional per buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014).
[Eligibility Step 2B: NO]
As such claims 1-20 are directed to judicial exceptions and rejected under 35 U.S.C 101, in accordance with Alice/Mayo, MPEP 2143 evaluation.
Claim Rejections - 35 USC § 102
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 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.
(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 1-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen-Harris et al. (IDS reference; filed on 11/11/2022; Non-Patent Literature; cite no. 1; 2013).
Claims 1, 8, and 15 are directed to methods, systems, and machines that obtain genetic information. The genetic information includes overlapping mate pairs, associated with a sequence, quality score, and at least one combination of nucleotides. The methods use this information to generate an error rate.
Claim 8 is further directed to a system with a sequencing device that obtains and transmits genetic information to a computing device, that receives it.
Claim 15 is further directed to a machine capable of executing the method/system described.
Chen-Harris et al. describes a method of modeling sequencing data errors via overlapping read pairs (ORPs). Chen-Harris et al. teaches carrying out Illumina paired-end sequencing to generate overlapping read pairs (page 2, column 2); and using mismatched read pairs, defined as incongruent nucleotides (page 11, column 1), to calculate mismatch rates (page 11, column 1) and examine them, in association with quality scores from the sequencers (page 8, column 1).
Chen-Harris et al. further teaches estimating sequencing errors directly from mismatch rates in the ORP (page 8, column 1) and calculating error rates as a ratio between the total number of candidate base calls differing from the consensus nucleotides summed across the genome and the total number of base calls made across the genome (page 10, column 2).
Regarding claim 8, Chen-Harris et al. teaches that the sequencing of three natural samples and the two control plasmids, was carried out using an Illumina Genome Analyzer II (page 10, column 1), and table 1 summarizes the output generated in the sequencing run (page 10, column 1). Therefore, a computing device received genetic information obtained and transmitted by a sequencing device.
Regarding claim 15, Chen-Harris et al. teaches results that demonstrate a practical sequencing and computational analytic approach to studying viral evolution with an unprecedented level of genetic resolution (page 2, column 2). Therefore, the results of the method and system described are executable by a computer (machine).
Claims 2, 9, and 16 are directed to finding a source of error.
Chen-Harris et al. teaches a method that demonstrates how PCR amplification can become the dominant source of error over the sequencer’s error, even when using a high fidelity polymerase (page 2, column 1).
Claims 3, 10, and 17 are directed to finding a device associated with information about an error.
Chen-Harris et al. teaches that the number of erroneous matching ORPs was relatively constant with respect to Q-scores, which suggests that they were dominated by PCR errors and not sequencing errors (page 4, column 2). Chen-Harris et al. further teaches comparing error rates between two different sequencers (page 10, column 1) and identifying a high variation in error rates between them (page 2, column 1). Chen-Harris et al. further teaches the difference can be attributed to the Q-score calibration of the two instruments (page 3, column 2), underscoring the utility of using ORP to recover an empirical sequencing error rate and minimize technical artifacts introduced by the sequencer (page 4, column 1).
Claims 4, 11, and 18 are directed to finding at least one combination of nucleotides that are associated with an error.
Regarding claims 4, 11, and 18, Chen-Harris et al. teaches that at a given locus, any polymorphisms in the ORPs that deviated from the known consensus nucleotide are taken as errors introduced either through PCR amplification or sequencing (page 5, column 1).
Claims 5, 12, and 19 are directed to the genetic information obtained including at least one DNA sequence.
Regarding claims 5, 12, and 19, Chen-Harris et. al teaches that library preparation yielded a target DNA fragment that was 142bp long (page 2, column 2).
Claims 7 and 14 are directed to the quality scores including a read value.
Regarding claims 7 and 14, Chen-Harris et al. teaches that the Q-score (quality score) of 2 is a ‘read segment control indictor’ in the FASTQ format that tags specific final portion of the read as unreliable and unfit for downstream analyses (page 4, figure 3) and that Q=2 reads comprised a disproportionally large fraction of mismatched read pairs is consistent with the fact that mismatched ORPs result from error during sequencing (page 4, figure 3).
Claims 6, 13, and 20 are directed to the sequence having at least one base pair.
Chen-Harris et al. teaches that the paired end reads had an average overlap of 88bp (page 2, column 2) and at every base, all overlapping read pairs were separated into two categories: matching and non-matching base pairs (page 11, column 1).
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Milana Thompson whose telephone number is (571)272-8740. The examiner can normally be reached Monday - Friday, 9:00-6:00 ET.
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/M.K.T./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687