DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claim Objections
Claim 1 is objected to because of the following informalities: line 3 recites “fist call” which appears to be a typographical error. Applicant is required to amend “fist call” to “first call” the apparent intended wording. 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.
Claim 1 is 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 Guidance published in the Federal Register notice titled 2019 Revised Patent Subject Matter Eligibility Guidelines (Vol. 84, No. 4, Monday January 7, 2019 at 50) and the October 2019 Updated Subject Matter Eligibility Guidance (hereinafter both referred to as the “Guidance”).
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Are the claims directed to a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea (Prong One); If the claims are directed to a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims are directed to a judicial exception and do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
With regard to (1), the instant claims recite a “computer-implemented method”, and therefore the answer is "yes".
With regard to (2A), Prong One, under the broadest reasonable interpretation (BRI), instant claim 1 recites an abstract idea of the type that is in the grouping of “mental process” or math (See MPEP 2106.04(a)(2) subsections (I) and (III)) because the focus of claim 1 is obtaining sequencing data, determining a call, calculating a quality value for that call, and evaluating the quality of the run using the value. At the level claimed, these are information collection, evaluation, and judgement steps. The “calculating” limitation also encompasses a mathematical calculation because neither a particular quality metric nor a technical algorithm is recited. The claim does not require any data volume or any operation that could not be easily performed by a user or laboratory technician observing values and applying rules or calculations, which are mental-process and mathematical-concepts which under the BRI, cover performance of the limitations in the mind. Thus, if a claim, under its BRI, covers performance of the limitation in the mind, but for the recitation of generic computer, then it falls within the “mental processes” grouping of abstract ideas (see MPEP 2106.04(a)(2)(III)(C)).
Because the claim is directed to an abstract idea, the claim must further be analyzed under Prong Two to determine if said judicial exceptions are integrated into a practical application as determined by further assessment of the “additional steps” recited in the claim. With respect to Prong Two, the additional steps and the rationale pertaining to why the additional elements are not integrated are as follows:
(a) Claim 1 recites mental steps/math calculations (judicial exception) which are not integrated into a practical application because “receiving data from a sequencing instrument” supplies the information to be analyzed and limits the field of use. But the claim does not require a resultant action/step that is taken by applying the obtaining, determining, calculating and evaluating of data that would add a meaningful limitation to the abstract idea;
(b) Although the claim recites a sequencing instrument as the source for the data, the claim does not apply the exception, as the claim does not transform the data into a different state or thing beyond its ordinary purpose (See MPEP 2106.05(f) and MPEP 2106.05(c)); and
(c) the method is recited at a high level of generality (as a generic and well-known structure) such that it is no more than mere instructions to apply the exception using a generic computer/diagnostic system (see MPEP 2106.04(a)(2)(III)(C) and MPEP 2106.05(d-f).
As such, the additional elements in the claim do not integrate the abstract idea into a practical application because they do not impose meaningful limits on practicing the abstract idea.
Because the claim fails under (2A), the claim is further evaluated under (2B). The claim herein do not include additional elements that are sufficient to amount to significantly more than the judicial exception under (2B) because, as discussed above with regard to integration of the recited abstract idea into a practical application, the additional elements herein amount to no more than a generic computer implementation and a conventional sequencing-data source (See MPEP 2106.05(g) The specification itself describes conventional processors, computers, communications and sequencing instruments, while the claim supplies no unconventional implementation in detail.
Additionally, MPEP 2106.04(a)(2)(III)(C) states methods of performing mental steps on a generic computer, performing a mental process in a computer environment, or using a computer as a tool to perform a mental process are considered an abstract idea. Considering the elements individually and as an ordered combination, claim limitations merely recite generic computing/mental processes to perform the abstract analysis and not significantly more.
Thus, in light of the above considerations the claim is non-statutory and not patent eligible under 35 U.S.C. 101.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim 1 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over
Greiner et al., (US 2010/0129810; already of record, hereafter “Greiner”) in view of Mann (US 2010/0088255).
Regarding claim 1, Greiner teaches a data acquisition, analysis and control units in an automated next-generation sequencing instrument (Fig. 1; description of unit 140) that performs data acquisition/analysis; color measurements and error metrics; aggregates matching statistics used to assess each sequency run as satisfactory or poor. Greiner teaches sequencing with color measurements and matching/mismatch result. To the extent Greiner does not explicitly identify a per-sample first call, Mann expressly teaches comparing image intensities to obtain a base call and a computer identifying each nucleotide base (Mann- Fig. 7 and associated description in particular step 710). Mann teaches a processor that determines a quality variable associated with each base prediction, including non-training data (Mann- Figs. 1,2 and 7 and associated description). Greiner uses sequencing error rates and aggregate matching statistics to assess the quality of each sequencing run, describing low mismatch as satisfactory and high mismatch as poor. In combination, Mann’s known per-call quality value is one of the known call-derived quality inputs used to make Greiner’s run-level assessment. Accordingly, one of ordinary skill in the sequencing art to have had reason to use Mann’s per-base quality value as an input in Greiner’s run-quality evaluation, since Greiner seeks standardized, sensitive metrics that distinguish satisfactory from poor runs, and already relies on call-derived mismatch/error statistics. That is, supplementing or substituting Greiner’s per-call error with Mann’s quality score would predictably improve the granularity, permit thresholding, or aggregation and support the same pass/ fail run determination since both references address sequencing-data quality using a computer of instrument signals, so the combination would provide a known quality metric for its established purpose in the same field of art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1 is rejected on the grounds of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11,135,699 and claims 1-20 of U.S. Patent No. 9,727,032. Although the claims at issue are not identical, they are not patentably distinct from each other because: the conflicting patent claims in both parents recite receiving control and sample data from a sequencing instrument, determining control and sample quality values, comparing them to expected values to determine quality scores, identifying a source problem, and instructing the instrument to modify the run. The instant claim 1 broadly claims the core sequence of receiving sequencing data, determining a call, calculating call quality and evaluating run quality. The patented claims in ‘699 and ‘032 encompass or render obvious the subject matter of instant claim 1. Omitting the patented claims’ control data, expected-value comparison, problem source and event handling merely broadens the instant claim and does not create a patentably distinct invention.
Citations to art
In the above citations to documents in the art, an effort has been made to specifically cite representative passages, however rejections are in reference to the entirety of each document relied upon. Other passages, not specifically cited, may apply as well.
Pertinent Prior Art
The following prior art is hereby made of record. Although the prior art is not currently being applied with respect to the claim, the examiner considers the listed prior art relevant to the applicant’s invention and may be relied upon in a future rejection.
Garcia et al. (US 2012/0020537) teach methods and systems for analysis of image data generated from various reference points. Particularly, the methods and systems provided are useful for real time analysis of image and sequence data generated during DNA sequencing methodologies.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to P. Kathryn Wright whose telephone number is (571)272-2374. The examiner can normally be reached between 9:30am-7pm EST.
Examiner interviews are available via telephone 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.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Charles Capozzi can be reached on 571-270-3638. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/P. Kathryn Wright/Primary Examiner, Art Unit 1798
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