llDETAILED ACTION
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 7 January 2026 has been entered.
Comments
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . 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.
Claims 21-40 are pending and examined in the instant Office action.
While the claims recite judicial exceptions, the claims recite the practical application of being more computationally efficient than conventional alignment techniques that use entire sequences because the claims recite only comparing portions of segmented DNA to the reference DNA sequence.
Withdrawn Rejections
The 35 U.S.C. 103 rejections and double patenting rejections of the previous Office action are withdrawn in view of amendments filed to the instant set of claims on 7 January 2026. All of the 35 U.S.C. 103 and double patenting rejections in this Office action are necessitated by amendment.
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
The following rejection is reiterated:
Claims 21-40 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The independent claims have been amended to recite “wherein the plurality of portions is determined based on the number of processing cores to be used for processing the plurality of partitions” In this amendment, it is unclear as to the metes and bounds of the number of portions being based on a number of processing cores in the computer system. For instance, it is unclear as to whether there is a one to one correspondence, a two to one correspondence, or etc. For the purpose of examination, any relation between the plurality of portions and a number of processing cores is interpreted to a form of basing the plurality of partitions on a number of processing cores.
Response to arguments:
Applicant's arguments filed 7 January 2026 have been fully considered but they are not persuasive. Applicant argues that the amendments to the claims overcome the rejection. This argument is not persuasive because the amendments only reword the questioned limitation and does not clarify the indefiniteness of the limitation. It is still unclear as to the metes and bounds of the determination of the plurality of portions based on the number of processing cores.
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.
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.
35 U.S.C. 103 Rejection #1:
Claim(s) 21-25, 28-32, and 35-39 is/are rejected under 35 U.S.C. 103 as being unpatentable over Pang et al. [US PGPUB 2005/0026145 A1] in view of Craig et al. [Nucleic Acids Research, volume 18, 1990, pages 2653-2660; on IDS] in view of Cronin et al. [USPGPUB 2008/0261832 A1] in view of Wunsch et al. [US PGPUB 2012/0221573 A1].
Claim 21 is drawn to a computer-implemented method of identifying one or microorganisms or DNA fragments thereof. The method comprises accessing a DNA sequence data set corresponding to a sample. The method comprises segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set. The method comprises performing an iterative alignment process using the DNA sequence data. The iterative alignment process comprises sequentially generating alignment results by comparing the plurality of portions of the DNA sequence data set to reference sequences from more than one species in a given database corresponding to the iteration until an alignment criterion for a given iteration is satisfied based on a corresponding alignment result. The method comprises predicting, based on the iterative alignment process, that the sample includes one or more microorganisms. The method comprises outputting an identification of the one or more microorganisms.
Claim 28 is drawn to similar subject matter as claim 21, except claim 28 is drawn to a system comprising processors.
Claim 35 is drawn to similar subject matter as claim 21, except claim 28 is drawn to a computer program product comprising non-transitory computer readable media.
Claims 22-25, 29-32, and 36-39 further limit the iterative alignment algorithm.
The document of Pang et al. studies computational methods for predicting intramolecular and intermolecular biopolymer interactions [title]. The cover figures and claims 51 and 53 of Pang et al. teach an iterative sequence alignment algorithm for DNA that repeats until a threshold condition is satisfied. The cover figure of Pang et al. illustrated reverting back to the original sequence in the previous database if a threshold condition is not met.
However, the objective of Pang et al. is to predict intermolecular and intramolecular DNA interactions, and not to predict source microorganisms of the DNA sequence. Pang et al. does not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. Pang et al. does not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Craig et al. studies ordering of cosmid clones covering the HSV-I genome [title]. Craig et al. uses difference in hybridization patterns of the 22 oligonucleotides in Figure 1 of Craig et al. to the four different isomers of HSV-I genomes to identify the fingerprinted virus and differentiate between the four isomers of the virus. It is interpreted that each isomer of the HSV-I virus is a different species. While the alignment/hybridization begins with one virus isomer, the reference sequences are increased to include all four isomers of the HSV-I virus.
Pang et al. and Craig et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. Pang et al. and Craig et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the iterative sequence alignment to predict molecular interactions of Pang et al. by use of the alignment by hybridization to identify source virus isomers of Craig et al. because it is obvious to substitute known elements in the prior art to yield a predictable result. In this instance using alignment to identify source microorganisms is an alternative to using alignment to predict molecular interactions. There would have been a reasonable expectation of success in combining Pang et al. and Craig et al. because the iterative alignment of Pang et al. is robust and generally applicable to using alignment/hybridization to identify source microorganisms of Craig et al.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the iterative sequence alignment to predict molecular interactions of Pang et al. and the alignment by hybridization to identify source virus isomers of Craig et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the iterative sequence alignment to predict molecular interactions of Pang et al., the alignment by hybridization to identify source virus isomers of Craig et al., and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
Response to arguments:
Applicant's arguments filed 7 January 2026 have been fully considered but they are not persuasive.
Applicant argues that Hubbell et al. does not teach the amended limitations of the claims. Hubbell et al. is replaced by Wunsch et al. and is not cited in the instant Office action
The following rejection is necessitated by amendment:
35 U.S.C. 103 Rejection #2:
Claim(s) 26-27, 33-34, and 40 is/are rejected under 35 U.S.C. 103 as being unpatentable over Pang et al. in view of Craig et al. in view of Cronin et al. in view of Wunsch et al. as applied to claims 21-25, 28-32, and 35-39 above, in further view of Gladyshev et al. [US PGPUB 2011/0178072 A1].
Claims 26-27, 33-34, and 40 are further limiting wherein the source microorganism comprises a bacterium or fungus.
Pang et al., Craig et al., Cronin et al., and Wunsch et al. make obvious using sequence alignment to predict isomer of virus.
Pang et al., Craig et al., Cronin et al., and Wunsch et al. do not teach using sequence alignment to predict bacterium or fungus identify.
Example 5 of Gladyshev et al. teaches using sequence alignment to identify yeast sequences in bacteria and fungi.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the iterative sequence alignment to predict molecular interactions of Pang et al., the alignment by hybridization to identify source virus isomers of Craig et al., the comparison of segmented probe sets/arrays to full reference sequences of Cronin et al., and the computer automation of DNA analysis of Wunsch et al. by use of the sequence alignment is bacteria and fungi of Gladyshev et al. because it is obvious to substitute known elements in the prior art to yield a predictable result. In this instance using alignment to identify source bacteria and fungi is an alternative to using alignment to predict virus isomers. There would have been a reasonable expectation of success in combining Craig et al. and Gladyshev et al. because the alignment to predict virus isomer of Craig et al. is robust and generally applicable to using alignment to predict source bacteria or fungi of Gladyshev et al.
Response to arguments:
Applicant has no arguments specific to Gladyshev et al.
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.
The following rejection is necessitated by amendment:
Double Patenting Rejection #1:
Claims 21, 28, and 35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 14, respectively, of U.S. Patent No. 11,437,122 B2 [on IDS] in view of Cronin et al. in view of Wunsch et al. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism.
The claims of ‘122 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘122 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #2:
Claims [22, 23, or 24], [29, 30, or 31], and [36, 37, or 38] are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 14, respectively, of U.S. Patent No. 11,437,122 B2 in view of Pang et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘122 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘122 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘122 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Pang et al. studies computational methods for predicting intramolecular and intermolecular biopolymer interactions [title]. The cover figures and claims 51 and 53 of Pang et al. teach an iterative sequence alignment algorithm for DNA that repeats until a threshold condition is satisfied. The cover figure of Pang et al. illustrated reverting back to the original sequence in the previous database if a threshold condition is not met.
The claims of ‘122 and Pang et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘122 and Pang et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 to include the iterative sequence alignment of Pang et al. wherein the motivation would have been that the iterative sequence alignment limitations of Pang et al. increase the accuracy of sequence alignment [claims 51 and 53 of Pang et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 and the iterative sequence alignment of Pang et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122, the iterative sequence alignment of Pang et al., and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #3:
Claims 25, 32, and 39 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 14, respectively, of U.S. Patent No. 11,437,122 B2 in view of Craig et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘122 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘122 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘122 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Craig et al. studies ordering of cosmid clones covering the HSV-I genome [title]. Craig et al. uses difference in hybridization patterns of the 22 oligonucleotides in Figure 1 of Craig et al. to the four different isomers of HSV-I genomes to identify the fingerprinted virus and differentiate between the four isomers of the virus. While the alignment/hybridization begins with one virus isomer, the reference sequences are increased to include all four isomers of the HSV-I virus.
The claims of ‘122 and Craig et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘122 and Craig et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 to include the set of four isomers of viral sequences of Craig et al. wherein the motivation would have been that the additional reference sequences of Craig et al. increase the accuracy of virus identification prediction [Figure 5 of Craig et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 and the probe set comparison to identify microorganisms of Craig et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #4:
Claims [26 or 27], [33 or 34], and 40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 14, respectively, of U.S. Patent No. 11,437,122 B2 in view of Cronin et al. in view of Wunsch et al. in view of Gladyshev et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘122 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘122 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The claims of ‘122 do not teach all of the source microorganism limitations of the claims.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
The claims of ‘122 and Gladyshev et al. do not teach all of the source microorganism limitations of the claims.
Example 5 of Gladyshev et al. teaches using sequence alignment to identify yeast sequences in bacteria and fungi.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122, the comparison of probe sets to reference DNA sequences of Cronin et al., and the computer analysis of DNA arrays of Wunsch et al. to include the bacteria and fungi of Gladyshev et al. wherein the motivation would have been that the additional pool of source microorganisms et al. of Gladyshev et al. increase the robustness of using iterative sequence alignment to predict source microorganisms [Example 5 of Gladyshev et al.].
The following rejection is necessitated by amendment:
Double Patenting Rejection #5:
Claims 21, 28, and 35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, and 19, respectively, of U.S. Patent No. 10,204,209 B2 [on IDS] in view of Wunsch et al. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment and segmenting to predict a source microorganism.
The claims of ‘209 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209 by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #6:
Claims [22, 23, or 24], [29, 30, or 31], and [36, 37, or 38] are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, and 19, respectively, of U.S. Patent No. 10,204,209 B2 in view of Pang et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘209 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘209 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘209 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Pang et al. studies computational methods for predicting intramolecular and intermolecular biopolymer interactions [title]. The cover figures and claims 51 and 53 of Pang et al. teach an iterative sequence alignment algorithm for DNA that repeats until a threshold condition is satisfied. The cover figure of Pang et al. illustrated reverting back to the original sequence in the previous database if a threshold condition is not met.
The claims of ‘209 and Pang et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘209 and Pang et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209 to include the iterative sequence alignment of Pang et al. wherein the motivation would have been that the iterative sequence alignment limitations of Pang et al. increase the accuracy of sequence alignment [claims 51 and 53 of Pang et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209 and the iterative sequence alignment of Pang et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209, the iterative sequence alignment of Pang et al., and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #7:
Claims 25, 32, and 39 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, and 19, respectively, of U.S. Patent No. 10,204,209 B2 in view of Craig et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘209 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘209 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘209 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Craig et al. studies ordering of cosmid clones covering the HSV-I genome [title]. Craig et al. uses difference in hybridization patterns of the 22 oligonucleotides in Figure 1 of Craig et al. to the four different isomers of HSV-I genomes to identify the fingerprinted virus and differentiate between the four isomers of the virus. While the alignment/hybridization begins with one virus isomer, the reference sequences are increased to include all four isomers of the HSV-I virus.
The claims of ‘209 and Craig et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘209 and Craig et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209 to include the set of four isomers of viral sequences of Craig et al. wherein the motivation would have been that the additional reference sequences of Craig et al. increase the accuracy of virus identification prediction [Figure 5 of Craig et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209 and the probe set comparison to identify microorganisms of Craig et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘209 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #8:
Claims [26 or 27], [33 or 34], and 40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 10, and 19, respectively, of U.S. Patent No. 10,204,209 B2 in view of Cronin et al. in view of Wunsch et al. in view of Gladyshev et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘209 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘209 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The claims of ‘209 do not teach all of the source microorganism limitations of the claims.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
The claims of ‘209 and Gladyshev et al. do not teach all of the source microorganism limitations of the claims.
Example 5 of Gladyshev et al. teaches using sequence alignment to identify yeast sequences in bacteria and fungi.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘122, the comparison of probe sets to reference DNA sequences of Cronin et al., and the computer analysis of DNA arrays of Wunsch et al. to include the bacteria and fungi of Gladyshev et al. wherein the motivation would have been that the additional pool of source microorganisms et al. of Gladyshev et al. increase the robustness of using iterative sequence alignment to predict source microorganisms [Example 5 of Gladyshev et al.].
The following rejection is necessitated by amendment:
Double Patenting Rejection #9:
Claims 21, 28, and 35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 15, respectively, of U.S. Patent No. 9,971,867 B2 [on IDS] in view of Wunsch et al. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment and segmenting to predict a source microorganism.
The claims of ‘867 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #10:
Claims [22, 23, or 24], [29, 30, or 31], and [36, 37, or 38] are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 15, respectively, of U.S. Patent No. 9,971,867 B2 in view of Pang et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘867 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘867 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Pang et al. studies computational methods for predicting intramolecular and intermolecular biopolymer interactions [title]. The cover figures and claims 51 and 53 of Pang et al. teach an iterative sequence alignment algorithm for DNA that repeats until a threshold condition is satisfied. The cover figure of Pang et al. illustrated reverting back to the original sequence in the previous database if a threshold condition is not met.
The claims of ‘867 and Pang et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 and Pang et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 to include the iterative sequence alignment of Pang et al. wherein the motivation would have been that the iterative sequence alignment limitations of Pang et al. increase the accuracy of sequence alignment [claims 51 and 53 of Pang et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 and the iterative sequence alignment of Pang et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867, the iterative sequence alignment of Pang et al., and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #11:
Claims 25, 32, and 39 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 15, respectively, of U.S. Patent No. 9,971,867 B2 in view of Craig et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘867 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘867 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Craig et al. studies ordering of cosmid clones covering the HSV-I genome [title]. Craig et al. uses difference in hybridization patterns of the 22 oligonucleotides in Figure 1 of Craig et al. to the four different isomers of HSV-I genomes to identify the fingerprinted virus and differentiate between the four isomers of the virus. While the alignment/hybridization begins with one virus isomer, the reference sequences are increased to include all four isomers of the HSV-I virus.
The claims of ‘867 and Craig et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 and Craig et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 to include the set of four isomers of viral sequences of Craig et al. wherein the motivation would have been that the additional reference sequences of Craig et al. increase the accuracy of virus identification prediction [Figure 5 of Craig et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 and the probe set comparison to identify microorganisms of Craig et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #12:
Claims [26 or 27], [33 or 34], and 40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 8, and 15, respectively, of U.S. Patent No. 9,971,867 B2 in view of Cronin et al. in view of Wunsch et al. in view of Gladyshev et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘867 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The claims of ‘867 do not teach all of the source microorganism limitations of the claims.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
The claims of ‘867 and Gladyshev et al. do not teach all of the source microorganism limitations of the claims.
Example 5 of Gladyshev et al. teaches using sequence alignment to identify yeast sequences in bacteria and fungi.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘867, the comparison of probe sets to reference DNA sequences of Cronin et al., and the computer analysis of DNA arrays of Wunsch et al. to include the bacteria and fungi of Gladyshev et al. wherein the motivation would have been that the additional pool of source microorganisms et al. of Gladyshev et al. increase the robustness of using iterative sequence alignment to predict source microorganisms [Example 5 of Gladyshev et al.].
The following rejection is necessitated by amendment:
Double Patenting Rejection #13:
Claim 21, 28, or 35 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of U.S. Patent No. 9,589,101 B2 [on IDS] in view of Wunsch et al. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment and DNA sequence segmenting to predict a source microorganism.
The claims of ‘101 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #14:
Claims [22, 23, or 24], [29, 30, or 31], or [36, 37, or 38] is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of U.S. Patent No. 9,589,101 B2 in view of Pang et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘101 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘101 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘209 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Pang et al. studies computational methods for predicting intramolecular and intermolecular biopolymer interactions [title]. The cover figures and claims 51 and 53 of Pang et al. teach an iterative sequence alignment algorithm for DNA that repeats until a threshold condition is satisfied. The cover figure of Pang et al. illustrated reverting back to the original sequence in the previous database if a threshold condition is not met.
The claims of ‘101 and Pang et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘101 and Pang et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 to include the iterative sequence alignment of Pang et al. wherein the motivation would have been that the iterative sequence alignment limitations of Pang et al. increase the accuracy of sequence alignment [claims 51 and 53 of Pang et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 and the iterative sequence alignment of Pang et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101, the iterative sequence alignment of Pang et al., and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #15:
Claim 25, 32, or 39 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of U.S. Patent No. 9,589,101 B2 in view of Craig et al. in view of Cronin et al. in view of Wunsch et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘101 do not teach all of the sequence alignment limitations in the instant set of claims. The claims of ‘101 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Craig et al. studies ordering of cosmid clones covering the HSV-I genome [title]. Craig et al. uses difference in hybridization patterns of the 22 oligonucleotides in Figure 1 of Craig et al. to the four different isomers of HSV-I genomes to identify the fingerprinted virus and differentiate between the four isomers of the virus. While the alignment/hybridization begins with one virus isomer, the reference sequences are increased to include all four isomers of the HSV-I virus.
The claims of ‘101 and Craig et al. do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘101 and Craig et al. do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 to include the set of four isomers of viral sequences of Craig et al. wherein the motivation would have been that the additional reference sequences of Craig et al. increase the accuracy of virus identification prediction [Figure 5 of Craig et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 and the probe set comparison to identify microorganisms of Craig et al. by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
The following rejection is necessitated by amendment:
Double Patenting Rejection #16:
Claim [26 or 27], [33 or 34], or 40 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 9 of U.S. Patent No. 9,589,101 B2 in view of Cronin et al. in view of Wunsch et al. in view of Gladyshev et al.
Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn to iteratively conducting sequence alignment to predict a source microorganism. The claims of ‘101 do not teach segmenting the DNA sequence data set to produce a plurality of portions of the DNA sequence data set wherein the portions of the segmented DNA sequence are compared to the reference DNA sequence. The claims of ‘867 do not teach a number of portions in the plurality of portions is determined based on a number of processing cores to be used in the computer system.
The claims of ‘101 do not teach all of the source microorganism limitations of the claims.
The document of Cronin et al. studies arrays of nucleic acid probes for detecting cystic fibrosis [title]. Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al. teach comparing arrays of segmented DNA probes sets to reference DNA sequences.
Wunsch et al. also teaches DNA probe sets are arrays [paragraph 46 of Wunsch et al.]. Figure 14 and paragraphs 74-75 teach processing cores (i.e. CPUs) that use parallel processing to analyze the DNA probe sets and arrays.
The claims of ‘101 and Gladyshev et al. do not teach all of the source microorganism limitations of the claims.
Example 5 of Gladyshev et al. teaches using sequence alignment to identify yeast sequences in bacteria and fungi.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 by use of the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. wherein the motivation would have been that comparing only portions of probes sets to reference sequences facilitates identifying the reference sequences without requiring a complete comparison of the full DNA sequence to the reference DNA sequences [Figure 1 and paragraphs 18-19, 60, and 64 of Cronin et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101 and the comparison of segmented portions/arrays of DNA sequences to reference DNA sequences of Cronin et al. by use of the computer analysis of Wunsch et al. wherein the motivation would have been that automation of data analysis facilitates accuracy and efficiency of data analysis [In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958); MPEP Section 2144.04 Section III].
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the claims of ‘101, the comparison of probe sets to reference DNA sequences of Cronin et al., and the computer analysis of DNA arrays of Wunsch et al. to include the bacteria and fungi of Gladyshev et al. wherein the motivation would have been that the additional pool of source microorganisms et al. of Gladyshev et al. increase the robustness of using iterative sequence alignment to predict source microorganisms [Example 5 of Gladyshev et al.].
Response to Arguments Regarding Double Patenting
Applicant requests that the non-statutory double patenting rejections be held in abeyance.
E-mail Communications 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.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/Primary Examiner, Art Unit 1686 20 February 2026