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 .
Priority
This application filed 03/21/2023 is a Continuation of 16241725, filed 01/07/2019, now abandoned, and claims priority from Provisional Application 62614828, filed 01/08/2018. The claims are therefore examined as filed on 01/08/2018, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Claim Status
Claims 1-18 are pending.
Claims 1, 10 and 14 are objected to.
Claims 1-18 are examined.
Claims 1-18 are rejected.
Information Disclosure Statement
The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered.
Claim Objections
Claims 1, 10 and 14 are objected to because of the following informalities:
Claims 1 lines 21-22 and claim 10 lines 17-18 should read “an existence of at least one structural variant at the given genome position in at least two full genome samples of the plurality of full genome samples…” (missing plural)
Claim 14 part b) should read “comprising selecting
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1 and 10 recite the limitation of obtaining a “weak evidence metric,” but there is not sufficient written description explaining what this metric is or how it is computed, and the limitations of the claim only describe what it is associated with. The only mention of this metric in the specification [0049] states that “the computational protocol will extend GROM's score at each genome position, produced for all variants (SNVs, indels, SVs, CNVs), to take into account co-occurrence of breakpoints in several samples and thus provide a robust "weak evidence" metric” - but there is no instruction on how to actually compute/determine the metric. Therefore, these claims fail to comply with the written description requirement.
Claims 2-9 and 11-18 also fail to comply with the written description requirement, as they depend from claims 1 and 10, respectively and do not resolve the above issues.
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 1-18 are also 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.
Claims 1 and 10 are unclear with respect to the final phrase “wherein the determining of the at least one particular structural variant from the co-occurring structural variants has a superior accuracy than a same DNA sequencing technique excluding the analysis based at least in part on the weak evidence metric of the co-occurring structural variants.” The phrase itself is unclear due to the wording and sentence structure. As a guess, the phrase is interpreted to mean that the previous determining step of determining a particular structural variant is more accurate compared to a method that does not use a “weak evidence metric” in its analysis.
Given this interpretation, it is also unclear whether this phrase is a functional limitation or if it is an intended or inherent property that results from the previous claimed steps.
Further, the term “superior accuracy” in claims 1 and 10 is a relative term which renders the claim indefinite. The term “superior accuracy” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear how one would determine that the accuracy of the claimed method is superior to “a same DNA sequencing technique.”
Further, the phrase “weak evidence metric” in claims 1 and 10 is also unclear, as it cannot be determined from the claims or specification what this metric is measuring or how it is computed (see written description rejection above). The metes and bounds of what constitutes a “weak evidence metric” are therefore unclear.
Because of these reasons, claims 1 and 10 are indefinite due to lack of clarity.
Claims 2-9 and 11-18 are also indefinite, as they depend from claims 1 and 10, and do not resolve the above issues.
Claims 4-9 are also unclear as they all refer to “the subject”, with limitations referring either to a body part of the subject (claim 4) or the at least one genome of the subject. There is insufficient antecedent basis for these limitations in the claims, as claim 1, from which they depend, refers to receiving sequencing data “of a plurality of full genome samples of a plurality of subjects” rather than a single subject. Therefore, it is unclear if the claim limitations refer to any subject within these subjects, or each subject from which samples were received, or something else.
Claims 17-18 are also unclear with respect to the phrase “obtaining a subject.” It is unclear if “obtaining a subject” means that data from a subject is obtained, or if “obtain” in this case means something else. Therefore, these claims are indefinite due to lack of clarity. Based on the remainder of the claims, this is currently interpreted to mean obtaining data from a subject consisting of genomic data, for the sake of further examination.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-9 are directed to a product (a DNA sequence analysis system comprising a non-transitory computer readable medium and processor), and claims 10-18 are directed to a process (a method).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. The claims recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Perform an analysis at analyze each position in each full genome sample of the plurality of full genome samples to obtain a weak evidence metric corresponding to at least one particular structural variant associated with a particular disease so as to identify the at least one particular structural variant as a corresponding biomarker to the particular disease (mental process/mathematical concept; the human mind is capable of comparing a reference sequence to a subject sequence at various positions to determine a difference as a metric and associating it with a structural variant and disease; using data to determine/compute a metric is equivalent to performing a calculation; claims 1, 10)
Utilizing a plurality of types of next-generation sequencing (NGS) evidence to identify co-occurring structural variants based at least in part on a given genome position across the plurality of full genome samples, and an existence of at least one structural variant at the given genome position in at least two full genome samples (mental process; the human mind is capable of using provided sequencing data to identify variants by comparing sequence position to a reference and associating them with structural variants; claims 1, 10)
Determining, for each full genome sample, the weak evidence metric at the given genome position based at least in part on the co-occurring structural variants in the plurality of full genome samples (mental process/mathematical concept; the human mind is capable of determining a metric at a sequence position based on data; determining a metric from data is equivalent to performing a calculation; claims 1, 10)
Determining the at least one particular structural variant from the co- occurring structural variants based at least in part on the weak evidence metric at the given genome position and at least one threshold (mental process/mathematical concept; the human mind is capable of making a determination based on data and a metric, and comparing a value to a threshold; these are also mathematical concepts; claims 1, 10)
Identifying the at least one abnormal genotype difference, by jointly comparing each subject-specific genome variant identified in a first genome of the at least one diseased body part of the subject to each subject-specific genome variant identified in a second genome of the non- diseased body part of the subject (mental process; the human mind is capable of comparing variants in diseased and non-diseased states to identify a difference; claim 4)
Evaluating each respective genome position of the at least one genome of the subject using a joint analysis of all distinct data type outputs of the at least one structural variant of each position identifying data type outputs (mental process/mathematical concept; the human mind is capable of doing a joint analysis of distinct data type outputs of the variants; doing so is equivalent to performing a calculation; claim 5-9)
Identify at least one genome variant from the at least one potential reference genome variant of sequence reads by using joint statistical evaluation for different variant types (mental process/mathematical concept; the human mind is capable of using joint statistical evaluation for different variant types, and doing so is equivalent to performing a calculation; claim 5)
Applying during the evaluation a nucleotide content weighting method for each genome position (mental process/mathematical concept; the human mind is capable of applying a weighting method for each genome position; doing so is equivalent to performing a calculation; claim 6)
Applying during the evaluation a nucleotide content bias normalization for each genome position (mental process/mathematical concept; the human mind is capable of applying a nucleotide content bias normalization for each genome position; doing so is equivalent to performing a calculation; claim 7)
Applying during the evaluation a dinucleotide repeat bias normalization for each genome position (mental process/mathematical concept; the human mind is capable of applying during the evaluation a dinucleotide repeat bias normalization for each genome position; doing so is equivalent to performing a calculation; claim 8)
Utilize at least one sequence window with independently sliding borders for finding copy number changes based on read depth, and add at least one window with the copy number change borders to a plurality of potential genome variants supporting deletion and duplication type variants (mental process; the human mind is capable of adding a window with sliding borders to sequence data; claim 9)
Determining, if the plurality of full genome samples comprises a particular validated genome variant associated with a cancer, identifying that at least one full genome of a subject comprises the particular validated genome variant associated with the cancer, comprising selecting at least one of a monitoring method or a diagnostic method relating to monitoring or diagnosing the cancer (mental process; the human mind is capable of determining if a genome contains a particular variant associated with cancer and selecting a monitoring or diagnosing method; claim 14)
Identifying that the at least one full genome of a subject comprises the particular validated genome variant associated with the cancer, comprising selecting the subject as in need of at least one therapeutic regimen (mental process; the human mind is capable of identifying if a genome contains a variant associated with cancer and selecting a subject in need of a therapy; claim 16)
Determining if a genome of the subject comprises a particular validated genome variant associated with a cancer, wherein if the particular validated genome variant associated with the cancer is not detected in the subject's genome, a proposed treatment regimen of the cancer in the subject based on the preliminary diagnosis is not recommended (mental process; the human mind is capable of making a recommendation or not based on if a genome contains a particular variant; claim 17)
Determining if a genome of the subject comprises a particular validated genome variant associated with a cancer, wherein if the particular validated genome variant associated with the cancer is not detected in the subject's genome, the preliminary diagnosis of the cancer in the subject is identified as a false positive diagnosis of the cancer in the subject (mental process; the human mind is capable of determining if a diagnosis is a false positive or not based on if a genome contains a particular variant; claim 18)
Dependent claims 2-3 and 11-13 further limit the abstract ideas recited in the independent claims, and do not change their characterization as abstract ideas.
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claim 1 and its dependents recite the additional element of a system comprising a non-transitory computer readable medium and a processor for performing the steps in the claims. Claim 10 and its dependents similarly recite the additional element of a computer processor for performing the steps of the method. The claims also recite the additional elements of receiving DNA sequencing data from subject samples, and receiving at least one DNA reference sequence and reference DNA alignment data. Claims 17-18 further recite the additional element of “obtaining a subject” interpreted to mean obtaining subject data.
Claim 14 also recites the additional element of performing a monitoring method or the diagnostic method relating to monitoring or diagnosing the cancer in the subject, with claim 15 further defining the monitoring method or the diagnostic method as a blood test, an imaging protocol, a biopsy, or a histopathological analysis.
While the claims recite the additional element of receiving or obtaining data, such steps that only amount to necessary data gathering and outputting, without any technical details of how the data is obtained/output that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). Similarly, the additional element of monitoring or diagnosing the cancer in the subject, with at least a blood test, an imaging protocol, a biopsy, or a histopathological analysis, is an insignificant extrasolution activity for further data gathering (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition, while the claims recite additional elements related to the use of computers, they do not provide any specific details by which the system, computer readable medium or processor performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the computer are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)). Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather or produce data do not provide an inventive concept. Non-particular instructions to gather data, either using computer methods or through laboratory methods, are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, and “Determining the level of a biomarker in blood by any means” from Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017) are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R. Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARY C LEVERETT/Examiner, Art Unit 1687
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