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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-2, 9-10, 12-13, 19-20, 31-31, 33, 35, 38-39, 41-43 and 75, in the reply filed on 3/4/2026 is acknowledged. Claims 22 and 23 are withdrawn from consideration as being drawn to a non-elected invention. Claims 3-8, 11, 14-18, 21, 24-29, 32, 34, 36-37, 40, 33-74, 76-80 have been canceled. Claims 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 are under examination.
Priority
This application is a CON of PCT/US2021/030295 filed 04/30/2021 which claims benefit of 63/018,363 filed 04/30/2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 8/8/2023 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings were received on 10/28/2022 is acknowledged. These drawings are found acceptable by the Examiner.
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 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception.
M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
The unpatentability of abstract ideas was recently confirmed by the U.S. Supreme Court. Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014); Bilski v. Kappos, 561 U.S. 593, 601 (2010).
The unpatentability of laws of nature was recently confirmed by the U.S. Supreme Court in Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 71 (2012). “[L]aws of nature, natural phenomena, and abstract ideas” are not patentable. Dia-mond v. Diehr, 450 U.S. 175, 185 (1981); see also Bilski v. Kappos, 561 U.S. at 601 (2010). The Supreme Court does acknowledge that it is possible “to transform an unpatentable law of nature,” but “one must do more than simply state the law of nature while adding the words ‘apply it.’” Mayo, 566 U.S. at 72 (quoting Gottschalk, 409 U.S. at 71–72). In Mayo, the Court found that “[i]f a law of nature is not patentable, the neither is a process reciting a law of nature, unless that process has additional features that provide practical assurance that the process is more than a drafting effort designed to monopolize the law of nature itself." 566 U.S. at 77. Additionally, “‘conventional or obvious’ ‘[pre]-solution activity’ is normally not sufficient to transform an unpatentable law of nature into a patent-eligible application of such a law.” Id. at 79 (quoting Flook, 437 U.S. at 590); see also Bilski, 561 U.S. at 593 (“[T]he prohibition against patenting abstract ideas ‘cannot be circumvented by’ . . . adding ‘insignificant post-solution activity’”) (quoting Diehr, 450 U.S. at 191–192).
The unpatentability of natural products was recently reconfirmed by the Supreme Court in Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2116, (2013).
In Alice Corp., the Supreme Court reiterated the two-step test it devised in Mayo to determine patent eligibility for claims: “First, we determine whether the claims at issue are directed to one of those patent-ineligible concepts. If so, we then ask, ‘[w]hat else is there in the claims before us?’ To answer that question, we consider the elements of each claim both individually and ‘as an ordered combination’ to determine whether the additional elements ‘transform the nature of the claim’ into a patent-eligible application.” 134 S. Ct. at 2355 (citing and quoting 566 U.S. at 72-73, 76-78).
The following inquiries are used to determine whether a claim is drawn to patent-eligible subject matter:
Step 1. Is the claim to a process, machine, manufacture, or composition of matter? Yes- The claims are directed to methods.
Concerning Step 1: YES. Claims 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 are directed to methods. Therefore, the claims are directed to a process, which is a statutory category.
Step 2. The step 2 analysis is a two-part analysis, step 2A and step 2B.
Step 2A, prong 1.
Step 2A, prong 1 requires a determination of whether the claims are directed towards a judicial exception, i.e. a law of nature, natural phenomenon, or an abstract idea, while step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical application if the claim recites a judicial exception under Prong 1.
The claims recite the judicial exception of an abstract idea. The claims 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 are directed towards a judicial exception, abstract ideas of analyzing a sample of DNA by obtaining a sequence reads, grouping sequence reads, determining sequences molecules from hypermethylated partitions and hypomethylated partition, calling plurality of bases. The claims further comprise a step of mapping sequence reads.
The claim 1 recites a method of analyzing a sample of DNA, the method comprising: partitioning the DNA sample into a plurality of partitions, wherein the plurality of partitions comprises a hypermethylated partition and a hypomethylated partition; tagging the DNA in the hypermethylated and hypomethylated partitions to generate tagged nucleic acids, wherein the tagged nucleic acids comprise molecular barcodes; obtaining sequence reads of molecules from the hypermethylated partition and sequence reads of molecules from the hypomethylated partition, wherein the sequence reads comprise molecular barcode sequence and sample sequence; grouping sequence reads into families based on at least one of (a) the molecular barcode sequences and (b) genomic positions corresponding to the first and last nucleotides of the sample sequence, wherein the families comprise sequence reads derived from a single DNA molecule in the sample; determining a first set of sequences of molecules from the hypermethylated partition and a second set of sequences of molecules from the hypomethylated partition; and calling a plurality of bases based on the first and second sets of sequences, wherein: (i) calling a C to T or G to A transition mutation relative to a reference sequence based on sequences of molecules of the first set requires observation of the transition mutation in a greater number of molecules than calling a C to T or G to A transition mutation relative to the reference sequence based on sequences of molecules of the second set; or (ii) C to T or G to A transition mutations are not called relative to a reference sequence based on sequences of molecules of the first set, or C to T or G to A transition mutations are called relative to a reference sequence based on sequences of molecules of the second set without the use of sequences of molecules of the first set, or a C to T or G to A transition mutation is called relative to a reference sequence only if at least one sequence of a molecule of the second set comprises the C to T or G to A transition mutation. The claims 2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 embodies the limitations of the claim 1.
In the instant case, the claims are drawn to the method(s) recited above comprising steps of obtaining sequence reads, grouping sequence reads, determining set of sequences from hypermethylated and hypomethylated partitions, calling bases as transition mutations as compared to a reference sequence based on observations which are deemed sequence data analysis and comparisons methodologies that can be performed by general computer programs or performed as a mental process or with the aid of paper/pen.
The result of 2A analysis is that the claims are directed towards a judicial exception, i.e., abstract idea, specifically in the steps of grouping, determining, and calling base sequences as transition mutation relative to a reference sequence. These steps encompass limitations that can be performed with the use of a general computer, computer program, mathematical calculations or mental analyses in the mind or with the aid of paper/pen. The Court has made clear if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract ideas cannot be circumvented by attempting to limit the use [the idea] to a particular technological environment. See Alice Corp v. CLS Bank Int’l 573 U.S. (2014).
Additionally, in Fairwarming IP, LLC (decision, page 5, par. 2), the instant claims are also drawn to analyzing information according to rules to make determination and results in the providing of data or in information per se. Fairwarming IP, LLC (Decision, pages 5-6, connecting para.) and Elec. Power Grp. LLC v. Alstrom S.A. also set forth that the “realm of abstract ideas” includes “collecting information”, including when limited to a particular content” and “analyzing information by steps people go through in the minds or by mathematical algorithms, without more, as essentially mental processes within the abstract-idea category”. In this case, the claims comprise steps (absent the generic computer) that could be carried out as a mental process with the aid of paper/pen.
Concerning step 2A prong 1: YES. Claims 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 are directed towards a judicial exception of an abstract idea as discussed above.
Step 2A, Prong 2
Step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical application of the claim recites a judicial exception under Prong 1. MPEP 2106.04(d) states that a claim ca be said to integrate a judicial exception into a practical application when it applies, relies or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEPE 2106. 04(d).I; MPEP 2106.05(a-h)). If the claim contains no additional element beyond te judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d) III).
In the instant case, the claims comprise the additional elements of partitioning the DNA sample, tagging the DNA, obtaining sequence read. These steps are directed to data gathering steps or collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting are not sufficient to integrate the judicial exception into a practical application.
Concerning step 2A, prong 2: NO. None of the claims recite additional elements which would integrate a judicial exception into a practical application.
Step 2B
The second part, Step 2B of the two-step analysis is drawn to determining whether any element or combination of elements, in the instant claims is/are sufficient to ensure that the claims as a whole amount to significantly more than the judicial exception. In this case, the steps of partitioning the DNA samples, wherein the partitions comprise hypermethylated partition and hypomethylated partition, tagging in the partitions, wherein the tagged nucleic acid comprises molecular barcodes, and obtaining sequencing reads comprise of well-understood and routine and conventional activity already engaged in by the scientific community as evidence by Kennedy et al (WO 2018119452, June 2018, citation made of record on IDS filed 8/8/2023) teaches a method for analyzing a sample DNA ([00023]-[00028] and comprising partitioning the DNA into a plurality of partitions which comprises a hypermethylated and a hypomethylated partitions ([00069], [00074]), tagging each partitions with a molecular barcode ([00050]), sequencing each partitions, thereby obtaining groups of reads, analyzing base call frequency in each group at a base position relative to a reference sequence [00025], thereby identifying one or more sequence characteristic that can be cancer markers, such markers can be gene variation or epigenetic variations [00207]. See also [000101]-[000102], [000134], [000178]-[000180], [000186], {000211].
The additional limitations, which have been found to be known and routine in the art, do not transform the abstract idea into a patent eligible application of the abstract idea such that the claims amount to significantly more than the abstract idea. The Court has made clear that to transform an unpatentable law of nature into patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words “apply it”. Essentially, appending conventional steps or elements, specified at a high level of generality, to laws of nature, natural phenomena, and abstract ideas cannot make those laws, phenomena, and ideas patent-eligible. The Supreme Court also indicated that any additional steps that simply are routine and conventional in the art are insufficient to transform an otherwise patent-ineligible process.
Concerning step 2B: NO. The additional elements do not amount to significantly more than the above-identified judicial exception. Even when viewed as a combination, the additional elements fail to transform the exception into patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself.
In view of the foregoing, the claims are not drawn to patent eligible subject matter under 35 USC 101.
Claim Rejections - 35 USC § 112
8. 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.
9. Claims 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 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.
(a) Claims 1-2, 9-10, 12-13, 19-20, 30-31, 33, 35, 38-39, 41-43 and 75 are indefinite in the claims 1, 2, 22 and 23 at the recitation of “greater number” because neither the specification nor the claims provide a standard for measuring what is considered “greater” and thus one of ordinary skill in the art could nevertheless ascertain the scope of the claims.
(b) Claims 10 and 13 are indefinite and appear to lack proper antecedent basis at the recitation of “plurality of control samples are from individuals not suspected of having cancer” because the claim 1 from which the claims depend are not limited to “persons having cancer” or any specific condition. The claim 1 could also be utilized in a sample of a person not having cancer given rise to ambiguity between the test sample of claim 1 and the control sample(s) of the instant claims. Thus, a clear interpretation cannot be ascertained.
(c) Claim 12 is indefinite at the recitation of “higher than” because neither the specification nor the claims provide a standard for measuring what is considered “higher” and thus one of ordinary skill in the art could nevertheless ascertain the scope of the claim.
(d) Claims 20 and 31 are indefinite at the recitation of “less stringently” and “more stringently” because neither the specification nor the claims provide a limitation definition of the terms and thus the metes and bounds of the claimed limitations are unclear.
Closest prior art
10. The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Kennedy et al (WO 2018119452, June 2018, citation made of record on IDS filed 8/8/2023) teaches a method for analyzing a sample DNA ([00023]-[00028] and comprising partitioning the DNA into a plurality of partitions which comprises a hypermethylated and a hypomethylated partitions ([00069], [00074]), tagging each partitions with a molecular barcode ([00050]), sequencing each partitions, thereby obtaining groups of reads, analyzing base call frequency in each group at a base position relative to a reference sequence [00025], thereby identifying one or more sequence characteristic that can be cancer markers, such markers can be gene variation or epigenetic variations [00207]. See also [000101]-[000102], [000134], [000178]-[000180], [000186], {000211]. Kennedy, while teaching various aspects of the instant invention, the reference does not teach the specific combination steps recited in the method of claim 1 and those depending therefrom.
Conclusion
11. No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681
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