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 .
Claims Status
Claims 5, 6, 9, 14, 17, 19-22, 25, 27, 30 and 32-34 are cancelled.
Claims 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 are currently pending and under examination herein.
Claims 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 are rejected.
Priority
The instant application claims the benefit of priority to Provisional Application No. 63/337510, filed 02 May 2022. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.78. As such, the effective filing date of claims 1-35 is 02 May 2022.
Information Disclosure Statement
The Information Disclosure Statement(s) filed on 01 May 2023 is in compliance with the provisions of 37 CFR 1.97 and has been considered. A signed copy of list of references cited from the IDS is included with this Office Action.
Drawings
The drawings are objected to because Fig. 1 has labeling that is faded and difficult to see. 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. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. 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.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see ¶ [0056]). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of trademarks has been noted in this application. Trademarks can be found in ¶ [00146, 00147, 00174, 00181, 00183, 00184, 00186, 00188, 00189, 00191]. The terms should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
All trademarks found within the instant application appear to be in compliance with MPEP § 608.01.
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 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more.
Step 2A, Prong 1 Considerations
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/law of nature/natural phenomenon:
Claims 1, 10 and 23 recite identifying one or more D gene segments in a GDJ or VDDJ sequence comprising obtaining data sets, determining scores, and identifying D gene segment regions.
Claims 4, 13 and 26 recite applying predetermined scoring adjustment factors, identifying potential alignments with the highest score and identifying additional D gene segments.
Claims 7 and 8 recite determining scores as well as mathematical formulas.
Claims 15, 16, 18, 28, 29 and 31 recite scoring schemas (addition and/or subtraction, mathematical calculations)
Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. While claims the claims recite performing aspects of the analysis in computer environments, use a “computer-readable medium,” or comprise a processing unit, alignment engine, scoring engine or an identification engine, there are no additional limitations that indicate that this analysis engine 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 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 recite an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1 : YES).
Step 2A, Prong 2 Considerations
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 affect a particular 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 computer medium and/or use of a hardware processor. Specifically, the claims recite the following additional elements:
Claims 1, 10 and 23 recite aligning VDJ sequences to reference sequences thereby generating first and second potential alignments.
Claims 2, 11, and 24 recite applying affine gap penalty functions.
Claims 4, 13 and 26 recite applying scoring adjustment factors to the scores of the alignments.
There are no limitations that indicate that the claimed system, method or storage medium require anything other than generic computing systems or involve insignificant extra-solution activity. 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 steps for performing sequence alignments of D gene segments in a VDJ or VDDJ sequence using computational means are well-understood, routine and conventional functions such as performing repetitive calculations and mere data extracting (see MPEP 2106.05(d)(2)). The steps for aligning D gene segments amount to insignificant extra-solution activity (see MPRP 2106.05 (g). As such, claims 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
Step 2B (MPEP 2106.05.A i-vi)
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 following additional elements:
Claims 10, 11, 12, 13, 15, 16, and 18 recite a computer-readable medium.
Claims 23, 24, 26, 28 and 29 recite a system comprising a processing unit, an alignment engine, a scoring engine and an identification engine.
As discussed above, there are no additional limitations to indicate that the claimed system and method 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 limitation for use of a computer-implemented system, one or more hardware processes, or use of a non-transitory computer-readable storage system amount to mere instructions to apply the judicial exception in a generic way because the executable steps are so generically recited. MPEP 2106.05(d) discloses that a claim to an abstract idea requiring no more than a generic computer to perform generic computer functions that are well-understood, routine and conventional activities previously known to the industry are not enough to qualify as “significantly more” when recited in a claim with a judicial exception. 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 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 are not patent eligible.
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)(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.
Claim(s) 1, 10 and 23 and 35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Russ (Russ et al. 2015 BMC Bioinformatics 16(170) pgs. 1-11).
Claims 1, 10 and 23 recite a method for identifying one or more D gene segments in a VDJ or VDDJ sequence. Russ teaches a D matching alignment algorithm (see pg. 4 § “D matching alignment algorithm”).
Claims 1, 10 and 23 recite obtaining a B cell and/or T cell receptor data set comprising a VDJ sequence. Russ teaches a data set comprising peripheral blood mononuclear cells, which includes B and T cells (see pg. 5 § “Comparison with a standard dataset of biological VDJ rearrangements”).
Claims 1, 10 and 23 recite aligning the VDJ sequence to one or more reference sequences and determining scores for alignments. Russ teaches D matching alignment and scoring alignments (see pg. 4 § “D matching alignment algorithm”).
Claims 1, 10 and 23 recite identifying D gene segment regions associated with the highest of the first and second scores. Russ teaches scoring for D segments (see pg. 5 § “Results”, Fig. 5 and pg. 7 col.1).
Claim 35, dependent from claim 23, recites identification of a D gene segment. Russ teaches a D matching alignment algorithm (see pg. 4 § “D matching alignment algorithm”).
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.
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 non-obviousness.
Claims 2, 11 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Russ as applied to claims 1, 10 and 23 above, and further in view of Khan (Khan et al. 2016 Sci. Adv. 2(e1501371) pgs. 1-15).
Claims 2, 11 and 24 1st elements recite applying affine gap penalty functions. Russ does not explicitly teach use of an affine gap penalty function wherein aligning determines alignment scores.
Khan teaches use of an affine gap penalty function to VDJ sequence alignments, as well as scoring alignments (see pg. 2 § “VDJ annotation” ¶2).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Russ and Kahn to use affine gap penalty functions and determine alignment scores in order to avoid the introduction of gaps through mutations in the alignment.
Claims 3 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Russ and Khan as applied to claims 2, 11 and 24 above, and further in view of Russ.
Claims 3 and 12 recite gap penalization at various rates for insertions, deletions and extensions. Russ teaches gap penalization for insertions, deletions or mutations (see pg. 2 § “The approximate backwards algorithm”).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Russ and Khan in order to produce more accurate alignment boundaries.
Claims 4, 13 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Russ as applied to claims 1, 10 and 23 above, and further in view of Mills (Mills et al. 2013 Bioinformatics 29(23) pgs. 3007-3019).
Claims 4 ,13 and 26 recite applying a pre-determined scoring adjustment factor to the alignments, identifying the highest scoring potential alignment, and/or identifying an additional D gene segment. Russ teaches high score selection (see pg. 2 col.1) and identification of additional D gene segments (see pg. 5 § “ Comparison with a standard dataset of biological VDL arrangements”). Russ does not explicitly teach scoring adjustment factors. Mills teaches a scoring adjustment factor (see pg. 3008 § “Scoring matrix adjustment”).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Russ and Mills in order to produce more accurate alignment boundaries.
Claims 16 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Russ as applied to claims 1 and 23 above, and further in view of Khan.
Claims 16 and 29 recite a scoring schema that subtracts points from alignment scores for base mismatch, insertions, gap openings and gap extensions. Russ does not explicitly teach a scoring schema. Khan teaches adjustment of alignment scores for mismatch, insertions, and deletions (see pg. 12 § “MAF error and bias correction pipeline”).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Russ and Khan in order to account for error correction in sequence alignments.
Claims 18 and 31 are rejected under 35 U.S.C. 103 as being unpatentable over Russ and Khan as applied to claims 16 and 29 above, and further in view of Khan. Claims 18 and 31 recite further limitations on the scoring schema where points are subtracted for gap extensions between V and D, and D and J sequences. Russ does not explicitly teach a scoring schema. Khan teaches adjustment of alignment scores for mismatch, insertions, and deletions (see pg. 12 § “MAF error and bias correction pipeline”).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Russ and Khan in order to account for error correction in sequence alignments.
Claim 28 is rejected under 35 U.S.C. 103 as being unpatentable over Russ as applied to claim 23 above, and further in view of Khan. Claims 28 recites further limitations on the scoring schema where points are added for base matches of potential alignments. Russ does not explicitly teach a scoring schema. Khan teaches adjustment of alignment scores for mismatch, insertions, and deletions (see pg. 12 § “MAF error and bias correction pipeline”).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Russ and Khan in order to account for error correction in sequence alignments.
Conclusion
Claims 1-4, 7-8, 10-13, 15-16, 18, 23-24, 26, 28-29, 31 and 35 are rejected.
Prior art for claims 7 and 8, applying a binomial function to a bit score, was not found during examiner search. Applicant has introduced a binomial probability to the bit score used in the alignment algorithm [¶ 00125]. Probabilities have been introduced to bit scores as is found in the prior art (see Eddy 2008 PLOS Comp Biol 4(5): e1000069; Bastien 2008 Evol Bioinfo 4 pgs. 41-45; and Altschul 2010 PLOS Comp Biol 6(7): e1000852). However, the specific mathematical manipulations are not taught in the prior art as follows: 2.2 times a bit score and scaling values 3l/4n.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Maranda S Cantrell whose telephone number is (571)270-5651. The examiner can normally be reached Monday - Thursday 7:30-4:30 pm.
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/M.S.C./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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