DETAILED ACTION
Claim Status
Claims 1-17 are rejected.
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Priority
This application is a continuation of application # 16145373, itself a divisional of application # 13787221. This application claims Domestic Benefit to application # 61640288, filed 04/30/2012. Domestic Benefit is acknowledged. Therefore, the effective filing date of claim(s) is 04/30/2012.
Information Disclosure Statement
The Information Disclosure Statement(s) filed on 06/02/2023 are in
compliance with the provisions of 37 CFR 1.97 and have been considered in full. A signed copy of list of
references cited from each IDS is included with this Office Action.
Drawings
The drawings filed on 01/11/2023 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 1-17 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:
Independent claim 1 recites a computer-mediated process of analyzing overlapping polynucleotide sequence data of a first and second polynucleotide sequence derived from a polynucleotide sequencer, comparing and aligning the overlapping sequences, analyzing concordance and discordance at positions in the overlapping sequences, calculating a weighted average at positions of discordance, and determining a base call and quality value for each position of discordance.
Independent claim 10 recites a computer that executes the process of claim 1.
Dependent claims 4 and 12 further recite a mental process of analyzing weights based on accuracies of a position.
Dependent claims 5 and 13 further recite a mental process of considering data of quality values that are higher for a position with concordance than a position with discordance.
Dependent claims 6 and 14 further recite a mental process of comparing data of initial base calls at a position.
Dependent claims 7 and 15 further recite a mental process of aligning data of initial base calls at a position.
Dependent claims 8 and 16 further recite a mental process of mapping flow space information to corresponding bases and aligning data at positions.
Dependent claims 9 and 17 further recite a mental process of analyzing data of empty flow information at base sequences.
Claims 1, 3-9, 10 and 11-16 recite, but for the limitation of using a generic computer in claims 1 and 10, the mental process grouping of abstract ideas. Independent claims 1 and 10 also recite the mathematical concept grouping of abstract ideas. A human being with a pen and paper could look at two overlapping sequences, find concordance and discordance, calculate a weighted average, and determine base call and quality value. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. While claims 1 and 10 recite performing some aspects of the analysis with a computer, there are no additional limitations that indicate that this computer 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 1-17 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 or mere instructions to apply the recited judicial exception via a generic treatment. Specifically, the claims recite the following additional elements:
the additional elements of a computer processor in claims 1 and 10 do not improve the functioning of a generic computer and do not integrate the recited judicial exception into a practical application.
The additional element of obtaining data in claims 1, 7, and 10 are a data gathering process that does not integrate the recited judicial exception into a practical application.
The additional element of outputting data in claims 1 and 10 is an extra-solution process that does not integrate the recited judicial exception into a practical application.
The additional element of paired-end sequencing in claim 2, is a data gathering process that does not integrate the recited judicial exception into a practical application.
Dependent claims 3 and 11 further limit the information being received to a first and second flow space information.
There are no limitations that indicate that the claimed computer 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. The remaining additional elements amount to obtaining and outputting data, similar to selecting information, based on types of information and availability of information in a power-grid environment, for collection, analysis and display, Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350, 1354-55, 119 USPQ2d 1739, 1742 (Fed. Cir. 2016). As such, claims 1-17 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 the additional elements recited above, in the section on step 2A.
As discussed above, there are no additional limitations to indicate that the claimed computer 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 element of paired-end sequencing in claim 2 is conventional. The conventionality of paired-end sequencing is shown in Holt et al. (Genome Research vol. 18, pages 839-846 (2008), IDS Reference). Holt et al. reviews commercially available sequencing apparatus. Holt et al. shows on pages 841-842 that commercially available sequencing apparatus can perform paired-end sequencing. The data gathering elements are conventional, similar to Presenting offers and gathering statistics, OIP Techs., 788 F.3d at 1362-63, 115 USPQ2d at 1092-93.
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 1-17 are not patent eligible.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
Claims 1-2, 4-6, 10, and 12-14 are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Masella et al (BMC Bioinformatics 2012, 13:31, henceforth “Masella”).
Regarding claim 1, Masella’s PANDAseq method obtains first and second polynucleotide signal information, and proceeds with sequencing by finding overlapping information (pg 2 left col ¶ 1). A computer implementation of the method is given on a GITHUB® page (pg 6 right col ¶ 2).
Overlapping regions of the sequences are aligned (see fig. 1 of Masella) and compared for discordance or concordance (pg 2 left col ¶ 1-2).
Masella uses a weighted average of two quality scores to calculate a quality value (pg 2 left col ¶ 2) and a base call when discordance is identified, and uses them to produce a sequence (pg 2 right col ¶ 2-4).
Concerning claim 2, the primers of the sequences extend in opposite directions, see fig. 1 of Masella.
Moving on to claim 4, the weights are based on accuracies of the sequence information (pg 2 left col ¶ 2, pg 3 right col ¶ 4).
With respect to claim 5, the quality score equation given ensures that the score value will be higher for concordance than discordance. Masella states on page 3 left col ¶ 4: “If the bases agree, the base is included and the quality of this base is assumed to be Pr[ˆ X = ˆ Y|X = Y]. If the bases disagree, the base with the higher quality score is chosen and the quality of this base is assumed to be Pr[ˆ X = ˆ Y|X̸ = Y].” These equations are given on pg 2 right col ¶ 1-2. The fraction constants in the terms of the mismatch equation ensure that disagreeing bases will have lower quality values.
For claim 6, initial base calls are compared in the comparison stage (pg 3 right col ¶ 4).
Claims 10 and 12-14 are the same as claims 1 and 4-6, only differing in that they are drawn to a system rather than a method. The arguments against claims 1 and 4-6 apply, mutatis mutandis.
Claim Rejections - 35 USC § 103
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.
Claims 3, 7-9, 11 and 15-17 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Masella as applied to claim 1-2, 4-6, 10 and 12-14 above, and further in view of Margulies et al (Nature, Vol 437|15 September 2005, henceforth “Margulies”).
Masella teaches the limitations these claims are dependent upon.
Regarding claim 3, Margulies discloses a pyrosequencing workflow that uses flow space information (pg 377 right col ¶ 2).
Concerning claim 7, Masella teaches obtaining the base sequences (pg 2 left col ¶ 1) and comparing by overlap (pg 2 left col ¶ 1).
Moving on to claim 8, Masella teaches mapping the sequence information to align the overlapping region, see fig. 1 of Masella.
With respect to claim 9, fig. 3 of Margulies shows how empty flow information is combined with flow order information to produce sequence information.
In the discussion, Margulies suggests that the method can be adapted to use paired-end sequencing in combination with the pyrosequencing method using flow space information, and provides supplementary methods for their plan to add this capability (pg 379 right col ¶ 1).
Claims 11 and 15-17 are the same as claims 3 and 7-9, only differing in that it is drawn to a system rather than a method. The arguments against claim 3 and 7-9 apply, mutatis mutandis.
Regarding claims 3, 7-9, 11 and 15-17, 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. Margulies suggests that the method can be adapted to use paired-end sequencing in combination with the pyrosequencing method using flow space information, in order to adapt the method to handle the de novo assembly of larger genomes. (pg 379 right col ¶ 1). There would be a reasonable expectation of success in making this combination to a person of ordinary skill in the art, as the steps towards this goal are explained by Margulies. Therefore, it would have been prima facie obvious to one of ordinary skill in the art at the time to modify the method of Masella by modifying it to work based on pyrosequencing as suggested by Masella, in order to adapt the method to large de novo genome assembly (pg 379 right col ¶ 1).
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.
Claims 1, 3, 10 and 11 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3 of Patent No. 11,566,281 (reference application, henceforth ‘281). Although the claims at issue are not identical, they are not patentably distinct from each other because the only difference is that “degree of agreement” is instead phrased as “identification of concordance or discordance”.
Claims 1 and 10 are taught by claim 1 of ‘281. Claims 3 and 11 are taught by claim 3 of ‘281.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
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/G.M.H./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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