DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim status
Claims 1-13 are cancelled.
Claims 14-21 are pending and are examined on the merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of EUROPEAN PATENT OFFICE (EPO) 16202691.8 filed 12/7/2016 is acknowledged.
Specification
The disclosure is objected to because it contains embedded hyperlinks and/or other form of browser-executable code. 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.
Specification has the following active web links:
http://www.pnas.org/conten/101/10/3504.long on page 5;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5232416/table/T1/ on page 5;
http://www.multplicom.com/sites/default/files/cftr mastr_dx_v1511_0_0.pdf and
http://www.multiplicom.com/product/cftr-mastr-dx on page 18; and
https://www.agilent.com/cs/library/datasheets/public/Performance%20characteristics%20CFTR%20MASTR%20Dx%205991-8425ENE.pdf on page 34.
Correction is required.
Claim Rejections - 35 USC § 112
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.
Claims 15-16 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.
Claim 15 recites the limitation "the basic motif" in the 2nd line. There is insufficient antecedent basis for this limitation in the claim.
Claim 16 recites the limitation "the measured probability distribution" in the 3rd line. There is insufficient antecedent basis for this limitation in the claim.
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 14-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 14-21 are directed to a process, here a “method”, with a series of functional steps.
Step 2A Prong One: Identification of Abstract Ideas
The claim(s) recite(s):
(c) For each of the repeat patterns:
(i) Measuring a distribution of the length of the repeat pattern, in the plurality of control data sequence reads;
This step reads on a process that can be performed by the human mind and is therefore an abstract idea.
(ii) For each possible combination of genomic variants corresponding to alleles of the repeat pattern, estimating the expected distribution among reads of the length of the repeat pattern for this genomic variant as a function of this genomic variant and of the measured distribution of the length of the repeat pattern in the plurality of control data sequence reads;
This step reads on a process that can be performed by the human mind and is therefore an abstract idea.
(iii) Measuring a patient distribution of the length of the repeat pattern in the plurality of patient data sequence reads;
This step encompasses a process that generating a bar chart wherein the different bars stand for different repeat patterns and the bar heights stand for the length of the repeat patterns (data come from the patients). Hence this step reads on a process that can be performed by the human mind with the help of a pen and paper and is therefore an abstract idea.
(iv) Identifying the combination of genomic variants corresponding to alleles of the repeat pattern which results in the closest comparison with the measured patient distribution of length among reads and assigning these alleles to the patient sample;
This step encompasses a process that generating a patient population bar chart wherein the different bars stand for different repeat patterns and the bar heights stand for the length of the repeat patterns (this chart actually generated in the previous step, step (c.iii)), then aligning the individual repeat pattern identified to this “standard chart”. This step reads on a process that can be performed by the human mind with the help of a pen and paper and is therefore an abstract idea.
(d) For each genomic variant scenario possible based on the alleles identified for each repeat pattern in step (c), estimating the expected distribution of the joint length of the repeat patterns in the plurality of control data sequence reads, each genomic variant scenario being obtained with alleles of the different repeat patterns localized on the same sequencing reads;
This step encompasses a process that generating a patient population bar chart wherein the different bars stand for different repeat patterns and the bar heights stand for the length of the repeat patterns (this chart actually generated in the previous step, step (c.iii)), then aligning the individual repeat pattern identified to this “standard chart” (done in step (d)), then add the bar heights for each genomic variant scenario identified from the same sequencing read. This step reads on a process that can be performed by the human mind with the help of a pen and paper and is therefore an abstract idea.
(e) Measuring the distribution of the joint length of the different repeats among reads in the plurality of patient data sequence reads; and
This step encompasses a process that generating a patient population bar chart wherein the different bars stand for different repeat patterns and the bar heights stand for the length of the repeat patterns (this chart actually generated in the previous step, step (c.iii)), then aligning the individual repeat pattern identified to this “standard chart” (done in step (d)), then add the bar heights of different repeat bars identified from the plurality of patient data sequence reads. This step reads on a process that can be performed by the human mind with the help of a pen and paper and is therefore an abstract idea.
(f) Selecting the expected joint distribution of lengths that results in the closest comparison with the measured patient distribution of joint lengths in the plurality of patient data sequence as the genomic variant scenario characterizing the actual genomic variant scenario for the patient sample.
This step reads on a process that can be performed by the human mind and is therefore an abstract idea.
Dependent claims 15-16 and 19 further recite additional limitations characterizing the genomic variant scenario, by processes that read on mental steps. The dependent claims are therefore drawn to further abstract idea steps.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of reporting at a user interface the selected genomic variant scenario and the comparison results for each genomic variant scenario comparison, which are insignificant extra-solution activities. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
(a) Obtaining a plurality of patient data sequence reads from an enriched genomic sample of a patient using next generation sequencing, wherein obtaining the enriched genomic sample of the patient comprises targeting and enriching sub-regions of a genomic sample of the patient corresponding to the at least two regions containing the repeat patterns (claim 14);
(b) Obtaining a plurality of control data sequence reads from an enriched genomic control sample using next generation sequencing, wherein obtaining the enriched genomic sample of the control data sequence reads comprises targeting and enriching sub-regions of a genomic control sample corresponding to the at least two regions containing the repeat patterns (claim 14);
Reporting, with a processor, through a user interface, the selected genomic variant scenario (claim 17).
Reporting, with a processor, through a user interface, the comparison results for each genomic variant scenario comparison (claim 18).
A genomic data analyzer (claim 20).
A genomic analysis software platform (claim 21).
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of obtaining data of sequence reads through target enrichment sequencing and reporting analytical results in user interface. The following art exemplified the conventionality of these additional element (emphasis added):
Mantovani, Vilma, et al. "Simple method for haplotyping the poly (TG) repeat in individuals carrying the IVS8 5T allele in the CFTR gene." Clinical Chemistry 53.3 (2007): 531-533. Newly cited
Huang, Qin, Wei Ding, and Mu-Xin Wei. "Comparative analysis of common CFTR polymorphisms poly-T, TG-repeats and M470V in a healthy Chinese population." World journal of gastroenterology: WJG 14.12 (2008): 1925. Newly cited
Trujillano, D., et al. "Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR." Journal of Medical Genetics 50.7 (2013): 455-462. Newly cited
Lee, S., et al. "Replacing CFTR Sanger sequencing in the clinical lab with a reliable, targeted next-generation sequencing assay." J Genet Genom Res 1.1 (2014). Newly cited
Fungtammasan, Arkarachai, et al. "Accurate typing of short tandem repeats from genome-wide sequencing data and its applications." Genome research 25.5 (2015): 736-749. Newly cited
Utiramerur (“Systems and Methods For Detecting Homopolymer Insertions /Deletions“, US 20140052381 A1, date published 2014-02-20. Newly cited)
The highlighted parts tells the targeted sequencing for the CFTR poly(T) and poly(TG) repeats investigation had been practiced for years before the instant application filed. The CFTR poly(T) and poly(TG) repeats for the CFTR gene is a well-known genetic disease in some human patients.
Utiramerur disclosed a method for detecting and characterizing, with a processor, a genomic variant scenario as a combination of at least two genomic sequence variants associated with nucleotide repeat patterns in a patient sample (abstract, and [65] “determining a presence of an indel variant in a reference homopolymer”, [79] “determining a presence or absence of an insertion/deletion variant in a reference homopolymer”)
Obtaining patient samples and obtaining control samples for a comparative study, is a well-known and conventional way in human disease research. Using a graphic user interface (GUI) to present data and report analytical results, is a common and conventional practice in modern day research.
Other elements of the method include “a genomic data analyzer” (claim 20) and “a genomic analysis software platform” (claim 21), which are recitations of generic computing components that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself.
Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
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 14-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 12-13 of U.S. Patent No. US11990206B2. Although the claims at issue are not identical, instant claim 14 is broader than the reference claim 1 and is anticipated by the reference claim 1. Instant claims 15-21 are not patentably distinct from reference claims 2-6 and 12-13.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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 nonobviousness.
This application 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.
Claims 14-18 and 20-21 are rejected under 35 U.S.C. 103 as being unpatentable over Utiramerur (“Systems and Methods For Detecting Homopolymer Insertions/Deletions“, US 20140052381 A1, date published 2014-02-20. Newly cited), in view of Parmigiani (“Determining Carrier Probabilities for Breast Cancer–Susceptibility Genes BRCA1 and BRCA2,” AJHG, Volume 62, Issue 1, January 1998, Pages 145-158. Newly cited), and Bhattacharjee (“Methods and Systems for Screening Diseases in Subjects”, US 20160281166 A1, Date Published 2016-09-29. Newly cited).
Claim 14 is directed to a method to detect and characterize genomic variants of nucleotide repeat patterns. Utiramerur also is directed to a method for detecting and characterizing, with a processor, a genomic variant scenario as a combination of at least two genomic sequence variants associated with nucleotide repeat patterns in a patient sample (abstract, and [65] “determining a presence of an indel variant in a reference homopolymer”, [79] “determining a presence or absence of an insertion
/deletion variant in a reference homopolymer”).
Regarding the recited (a) obtaining a plurality of patient data sequence reads from an enriched genomic sample of a patient, this reads on Utiramerur’s “for a plurality of sample reads” ([0077]). It is implied that these samples can be from a patient ([0006]), variations are detected to identify diseases).
The recited (b) obtaining a plurality of control data sequence reads from an enriched genomic control sample reads on Utiramerur’s “a reference homopolymer” ([0065]).
Utiramerur does not teach enrich sub-regions of a genomic sample. Bhattacharjee ([0062]) provides “the methods and systems described herein can utilize a targeted next-generation sequencing (TNGS) assay which can cost-effectively addresses second-tier and diagnostic testing of newborns (FIG. 1A) by selectively sequencing genomic regions of interest, e.g., coding exons, by enrichment in a physical DNA capture step (FIG. 1B)”, which teaches enriching selective genomic regions of interest.
Step (c.i) recites measuring a patient distribution of the length of the repeat pattern, in the plurality of control data sequence reads, as the expected probability distribution length of the first repeat pattern of the control sample, the repeat pattern comprising at least two repeats of a basic motif, the basic motif being a sequence of one or more nucleotides. The recited step (c.i) reads on Utiramerur’s "distribution of matched-filter residuals can be fit to uni-modal and bi-modal distributions" ([0069]), where the matched-filter residuals are homopolymer lengths ([0063] also pertains).
Step (c.ii) recites that for each possible genomic variant of the first repeat pattern relative to the control data first repeat pattern, estimating the expected probability distribution of the length of the first repeat pattern for this genomic variant as a function of this genomic variant and of the measured probability distribution of the length of the first repeat pattern in the plurality of control data sequence. The recited step (c.ii) reads on Utiramerur’s “bi-modal Gaussian model” for homozygous genomic variant, “uni-model Gaussian model” for heterozygous genomic variant ([72-73]);
The recited (c.iii) measuring a probability distribution of the length of the first repeat pattern in the plurality of patient data sequence reads reads on Utiramerur’s "distribution of matched-filter residuals can be fit to uni-modal and bi-modal distributions" ([69]), it is implied that these samples can be from a patient ([6]).
Step (c.iv) recites that selecting an estimated patient probability distribution of the first repeat pattern length, characterizing a first genomic sequence variant of the patient sample as the expected probability distribution, which results in the closest comparison with the measured patient probability distribution. The recited step (c.iv) reads on Utiramerur’s teaching of determining a distribution of base calling residuals based on measured values for a homopolymer region (which is equivalent to the probability distribution of the length of the first repeat pattern), fit this distribution to a uni-modal and bi-modal model (comparing to the first repeat pattern of the genomic variants) and identify the genomic variant based on the best fitting model (which is equivalent to the closest comparison with the measured patient probability distribution) ([77-78]).
The recited (d) reads on Utiramerur’s teaching of comparing the repeat length (either a homopolymer indel or a non-homopolymer indel) from a candidate (a patient) vs the length from a reference sequence (from a control sample) ([62]). Utiramerur also teaches the uni-modal and bi-modal Gaussian distributions ([67]).
The recited step (d) is also directed to various joint probabilities among the two repeats of mutations. Utiramerur does not teach these joint probability distributions. Parmigiani does teach joint probability distributions between BRCA1 and BRCA2 mutations, which also are discussed in the instant specification (pg 1, last para). The step (d) reads on Parmigiani as the two repeats discussed above, involving the BRCA1 and the BRCA2 genes, are genetic variations or mutations.
The recited (e) is rejected similarly as discussed for step (d) above.
The recited step (e) is also directed to various joint probabilities among the two repeats of mutations. Utiramerur does not teach these joint probability distributions. Parmigiani does teach joint probability distributions between BRCA1 and BRCA2 mutations, which also are discussed in the instant specification (pg 1, last para). The step (e) reads on Parmigiani as the two repeats discussed above, involving the BRCA1 and the BRCA2 genes, are genetic variations or mutations.
The recited step (f) reads on Utiramerur’s teaching of determining a distribution of base calling residuals based on measured values for a homopolymer region (which is equivalent to the probability distribution of the length of the first repeat pattern), fit this distribution to a uni-modal and bi-modal model (comparing to the first repeat pattern of the genomic variants) and identify the genomic variant based on the best fitting model (which is equivalent to the closest comparison with the measured patient probability distribution) ([77-78]).
The recited step (f) is also directed to various joint probabilities among the two repeats of mutations. Utiramerur does not teach these joint probability distributions. Parmigiani does teach joint probability distributions between BRCA1 and BRCA2 mutations, which also are discussed in the instant specification (pg 1, last para). The step (f) reads on Parmigiani as the two repeats discussed above, involving the BRCA1 and the BRCA2 genes, are genetic variations or mutations.
Claim 15 further specifies the genomic variant comprising at least one insertion or one deletion on one allele of the basic motif relative to the repeat pattern of the control data, which reads on Utiramerur’s “detecting homopolymer insertions/deletions, in homopolymer regions, and thereby detecting heterozygosity” ([6]).
Claim 16 specifies a method for estimating an expected probability distribution of lengths of repeat patterns, which reads on Utiramerur’s two hypothesis evaluation on the matched-filter residue and the formula to calculate a DELTA ([62-63]).
Claims 17 and 18 recite reporting of a selected genomic variant scenario through a user interface, which reads on Utiramerur’s “DISPLAY” module (Fig 1, and [34-35]).
Claim 20 recites a genomic data analyzer, which reads on Utiramerur’s Fig. 4 (Fig 4, and [86-102]).
Claim 21 recites a genomic analysis software platform, which reads on the “Pre-processing Module 412”, “Mapping Module 414”, and “Variant Calling Module 416” in Utiramerur’s Fig. 4 (Fig 4, and [86-102]).
It would have been prima facie obvious to combine Utiramerur’s method for detecting homopolymer / non-homopolymer insertions / deletions in sample sequence using a single probability distribution with Parmigiani’s joint probability distribution for two mutational events, and Bhattacharjee’s enrichment for sub-regions. As all of Utiramerur, Parmigiani and Bhattacharjee teach detecting variations in NGS sequence, then they enhance each other technically. This would have been an example of combining prior art elements according to known methods to yield predictable results (MPEP §2143.I.A).
Claim19 is rejected under 35 U.S.C. 103 as being unpatentable over Utiramerur and Parmigiani as applied to claims 14-18 and 20-21 above, and further in view of Xiao (“Molecular epidemiology of cryptosporidiosis”: An update, Experimental Parasitology 124 (2010) 80–89. Newly cited)
Claim 19 require an embodiment of TGA trinucleotide repeats and a T single repeats, which reads on: Xiao’s heteropolymer of TCA repeats, because the TCA repeats is reverse-complementary to the TGA repeats, and Utiramerur’s homopolymer of T repeats ([62]).
It would have been prima facie obviousness to combine Utiramerur’s method for detecting homopolymer / non-homopolymer insertions / deletions in sample sequence using a single probability distribution, Bhattacharjee’s teaching of enhancement of sub-regions, with Parmigiani’s joint probability distribution for two mutational events, and Xiao’s teaching of detecting TGA trinucleotide repeats. As Utiramerur, Parmigiani, Bhattacharjee and Xiao each teach detecting variations in NGS sequence, then they enhance each other technically. This would have been an example of combining prior art elements according to known methods to yield predictable results (MPEP §2143.I.A).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GUOZHEN LIU whose telephone number is (571)272-0224. The examiner can normally be reached Monday-Friday 8-5.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights