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 .
Status of the Claims
Claims 70-93 are pending and examined herein. Claims 1-69 are canceled.
Priority
As detailed on the 21 July 2022 filing receipt, the application claims priority as early as 09 March 2021. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Information Disclosure Statement
The information disclosure statement (IDS) was submitted on 15 July 2022. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
Specification
The disclosure is objected to because of the following informality: the phrase “Figure 12 is block diagram” should read “Figure 12 is a block diagram”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
Claim 74 is 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 74 depends on claim 5, which has been canceled, and thus the antecedence of claim 74 is unclear. For compact examination, it is assumed the claim will be amended to recite dependent on claim 70.
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 70-93 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements both individually and in combination, do not amount to significantly more than the abstract idea of tumor detection based on non-target sequences.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a method (claims 70-93), which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Mathematical concepts recited in the claims include determining quantitative measures (claim 70), determining normalized quantitative measures (claim 70), and estimating a copy number of tumor cells (claim 70). Determining quantitative measures, normalizing the quantitative measures, and estimating copy number are interpreted as verbal descriptions of mathematical concepts. A mathematical relationship may be expressed in words and there is no particular word or set of words that indicates a claim recites a mathematical calculation (MPEP 2106.04(a)(2)).
Mental processes, defined as concepts practically performed in the human mind such as steps of observing, evaluating, or judging information, recited in the independent claim include generating an alignment (claim 70), determining off-target sequences and on-target sequences (claim 70), and determining off-target segments (claim 70). These steps are considered mental processes because they are interpreted to recite: alignment, which is pattern recognition, to areas of a target and not of a target; and segmenting the off-target regions. These are steps which the human mind is practically equipped to perform.
Claim 71 recites the quantitative measure involves counting, which is a mathematical operation.
Claim 72 recites additional information about the quantitative measure being a median, which is math.
Claim 73 recites counting, determination of a frequency, and normalization, which are mathematical concepts.
Claim 74 recites determining a mappability score, determining a frequency, and normalization, which are interpreted as mathematical concepts.
Claim 75 recites determining an alignment, which is a mental process of pattern recognition, and determining quantitative measures, which is a mathematical concept.
Claim 76 recites generating alignments, determining off-target alignments, and obtaining quantitative measures for additional data and thus are abstract ideas as explained above.
Claim 77 recites determining on-target alignments, which is a mental process, and determining quantitative measures and copy number, which are mathematical concepts.
Claim 78-80 recite additional information about the quantitative measures, which is interpreted as directed to the mathematical concepts.
Claims 81-85 recite determining size metrics, which is interpreted as a mathematical concept.
Claims 86-87 recite determining parameters for a likelihood function, which is a mathematical concept.
Claim 88 recites additional information about the alignment, which is interpreted as directed to the mental processes described above, and segmentation by circular binary segmentation, which is a mathematical algorithm for dividing the genome, which is interpreted as a mathematical concept.
Claim 89 recites additional information about the data obtained by the computer.
Claim 90 recites additional information about estimate tumor fraction, which is interpreted as a mathematical concept.
Claim 91 recites determining number of representations and a mutant allele fraction, which are interpreted as mathematical concepts.
Claim 92 recites segmenting based on the mutant allele fraction, where segmenting is interpreted as a mental process of conceptualizing the off-target reference as bins.
Claim 93 recites an alternative segmentation process, where segmenting is interpreted as a mental process of conceptualizing the off-target reference as bins.
Hence, the claims explicitly recite numerous elements that, individually and in combination,
constitute abstract ideas. The claims must therefore be examined further to determine whether they
integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Additional elements that are not abstract ideas recited in the claims include a computer system having memory and processors (claim 70) and obtaining sequence data (claims 70 and 76). Obtaining sequence data is interpreted as data gathering and thus insignificant extra-solution activity (MPEP 2106.05(g)) while implementing the method using a general purpose computer is interpreted as applying the abstract idea using a computer (MPEP 2106.05(f)), neither of which integrate the abstract idea into a practical application.
None of the dependent claims recite any additional non-abstract elements; they are all directed
to further aspects of the information being analyzed, the manner in which that analysis is performed, or
the mathematical operations performed on the information. [Step 2A Prong Two: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself. Step 2B of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05).
Additional elements that are not abstract ideas recited in the claims include a computer system having memory and processors (claim 70) and obtaining sequence data (claim 70). The claims recite a computer, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions, which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)). Storing data on a computer is a conventional computer function (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; MPEP 2106.05(d)). Receiving data using a computer is also a conventional computer task (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014)).
Therefore, the recited additional elements, alone or in combination with the judicial exceptions, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Claim Subject Matter Free of the Prior Art
The claims are interpreted as free of the prior art. Claim 70 recites second quantitative measures for individual second segments based on the first normalized quantitative measures and the second normalized quantitative measures of the respective plurality of individual first segments included in the individual second segment. Close art, such as Talevich (Plos Computational Biology 12(4): 1-18, 2016; newly cited) teaches determining copy number variation from on-target and off-target alignments. However, Talevich does not teach segmenting only off-target regions or applying a second metric based on a second segmentation method in which the quantitative data is normalized based on a first segmentation. Kuilman (Genome Biology 16(49): 1-15, 2015; newly cited) teaches multiple segmentation methods but not normalizing between them. Therefore, the claims are considered free of the prior art.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia M. Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685