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 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 are pending and under examination.
Claims 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 are rejected.
Claims 45, 56, 63, 64, and 66 are objected to.
Claim 45 is independent.
Claims 45 and 61 are amended.
Claims 1-44, 48, 50-53, 59-60, 62, 65, 71-72, and 77-78 are canceled.
Office Action Overview
Rejections applied
Abbreviations
x
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
102, 103
JE
Judicial Exception
x
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
MM/DD/YYYY
date format
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, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosures of the prior-filed applications, U.S. Provisional Application No. 62/726,922, filed 09/04/2018, and U.S Provisional Application No. 62/810,625, filed 02/26/2019, fail to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application.
Claims 45 and 74 both recite the limitation "using a beta-binomial distribution". This limitation is not supported by the disclosures of U.S. Provisional Application No. 62/726,922, filed 09/04/2018, and U.S Provisional Application No. 62/810,625, filed 02/26/2019. All dependent claims ultimately depend from independent claim 45; accordingly, claims 46-47, 49, 54-58, 61, 63-70, and 72-76 are not entitled to the benefit of the prior application. Pending claims 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 are being examined with an effective filing date of 09/04/2019.
Overview of Withdrawal/Revision of Objections/Rejections
In view of the amendment and remarks received 06/10/2026:
• New claim objections are applied below.
• The 112(b) rejection is withdrawn; new 112(b) rejections are applied below.
• The 101 rejection is maintained with revision.
Specification
Applicant's 06/10/2026 remarks (p.8, ¶ 3) regarding cross reference to PCT Pat. App. No. PCT/US2018/052087 in the 06/10/2026 Specification amendment are acknowledged. However, the 06/10/2026 filed Petition was denied in the 07/08/2026 Petition decision. Therefore, the Specification is objected to for the amended-in phrase disclosing "PCT Pat. App. No. PCT/US2018/052087, filed Sep. 20, 2018." This phrase should be deleted in a future Specification amendment. Appropriate correction is required.
Claim Objections
Claims 45, 56, 63, 64, and 66 objected to because of the following informalities:
In claim 45 step (c) line 2, there should be a colon after the term "comprising."
In claim 45 step (c) line 3, there should be an "s" added at the end of the term "variant."
Claims 56, 63, 64, and 66 each recite "the group consisting of," in which each claim recites what its group consists of, such that it is clear how each group is interpreted. Nonetheless, there is no antecedent basis for each of "the group" in claims 56, 63, 64, and 66; each instance of "the group" should be amended to recite "a group."
Appropriate 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.
Claims 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate.
In claim 45 step (f) line 5-9, there appears to be a grammatical error which makes the connection unclear between "(i) detecting no germline variants" and "(ii) germline variants having" in the recited " (i) detecting no germline variant with an MAF of less than about 3% or (ii) germline variants having an MAF less than about 3% have a copy number mean in the same germline variant with an absolute value greater than a predetermined copy number mean threshold." The lack of the term "detecting" after "(ii)" makes the limitation starting with "(ii)" ambiguous. Possibly amending to recite "(ii) detecting germline variants having an MAF less than about 3% and [[have]]having a copy number mean in the same germline variant with an absolute value greater than a predetermined copy number mean threshold" might help overcome the rejection. Lines 2-4 of Specification [000128] were taken into consideration when making the suggestion. The claim will be interpreted as suggested to amend.
In claim 45 step (g) lines 3-4, the limitation "the presence or absence of the allelic imbalance" recites two terms which require but lack clear antecedent (bold emphasis added). Amending to recite "[[the]]a presence or absence of [[the]]a allelic imbalance" would likely overcome this rejection.
Also in claim 45 step (g) lines 3-4, the connection is unclear between "identifying" and "information, contamination and a second genome" in the recited "criterion identifying the presence or absence of the allelic imbalance of the sample and/or information, contamination and a second genome of the sample." It is unclear what is being identified with regard to the "and/or information, contamination and a second genome." Possibly amending to "criterion identifying the presence or absence of the allelic imbalance of the sample and/or identifying information[[,]] of contamination [[and]]or of a second genome of the sample" might help overcome the rejection. Lines 3-4 of Specification [00018], were taken into consideration when making the suggestion. The claim will be interpreted as suggested to amend.
In claim 46, the recited "the detecting in (e)" requires but lack clear antecedent. The term "detecting" has been deleted from claim 45 step (e). Possibly amending claim 46 to recite "wherein the determining in ([[e]]d) comprises determining" might help overcome the rejection. The claim will be interpreted as suggested to amend.
Claims 46 and 66 each recite "the predetermined criterion," which requires but lacks clear antecedent (bold emphasis added). Possibly amending to recite ""the first, second, and third criteria" might help overcome this rejection. The claim will be interpreted as suggested to amend.
In claim 63, the limitation "wherein the one or more quantitative measures indicative of the CNVs or the diploid genes" recites three terms which require but lack clear antecedent (bold emphasis added). Possibly amending claim 63 to "wherein [[the ]]one or more quantitative measures indicative of [[the ]]CNVs or [[the ]]diploid genes" might help overcome this rejection. The claim will be interpreted as suggested to amend.
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 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 details the following framework to analyze Subject Matter Eligibility:
• Step 1: Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter)? (see MPEP § 2106.03)
• Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP § 2106.04(a), 2106.04(a)(2), and 2106.04(b)).
• Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d))
• Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05)
Step 1:
Yes, the claims 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 are directed to a 101 machine, here a system, and therefore to a category of statutory subject matter. (See MPEP § 2106.03). (Step 1: Yes.)
Step 2A, Prong One:
The claims recite judicial exceptions of abstract ideas of mental processes and mathematical concepts as follows:
Independent claim 45 recites mental processes and mathematical concepts where noted):
• aligning reads to a reference sequence
• applying a first criterion to sequence reads
• identifying germline variants at an MAF (mutant allele fraction) using a beta binomial distribution (also considered a mathematical concept)
• detecting less than 2 germline SNPs below 15% MAF
• identifying a set of germline variants having MAF values
• determining a quantitative measure of the set of germline variants among discrete MAF ranges (also considered a mathematical concept)
• applying a second criterion by filtering the set of germline variants based on the quantitative measure among the discrete MAF ranges being greater than a threshold (also considered a mathematical concept)
• applying a third criterion comprising (i) detecting no germline variants at MAF less than 3%, and (ii) detecting no germline variants at MAF less than 3% and having a copy number mean with an absolute value greater than a threshold (also considered a mathematical concept)
• generating a report identifying allelic imbalance and/or information of contamination and of a second genome
The dependent claims recite mental processes (and mathematical concepts where noted) as follows:
• detecting quantitative measures from the reads indicative of copy number variations (CNVs) or diploid genes (claim 46)
• detecting a presence or absence of contamination or a second genome in the sample when the absence of the allelic imbalance is detected in the sample (claim 54)
• using a beta-binomial distribution; determining an estimate of μbin and ρ from the beta binomial distribution (also considered a mathematical concept) (claim 74)
• calculating a two-tailed p-value (also considered a mathematical concept) (claim 74)
Dependent claims that further limit the abstract idea of base claims:
Claims 55-58 further limit the set of germline variants of claim 45.
Claims 61, 63-64, 66, and 73 further limit the threshold and the quantitative measures of claim 45.
Claims 67-70 further limit the detecting of contamination of claim 54.
Claims 75 and 76 further limit the aligning of sequence reads to corresponding to obtained reads which correspond to a sample comprising at least 2xl010 polynucleotide molecules and a sample comprising at least 6xl010 polynucleotide molecules.
Step 2A Prong One Summary: The claims recite abstract ideas, characterized as mental processes and mathematical concepts. Considering the broadest reasonable interpretation (BRI) of the claims, there are mental processes and mathematical concepts recited in independent claim 45 (e.g., for aligning reads to a reference sequence; applying a first, second, and third criterion; identifying a germline variant(s) at an MAF, detecting less than 2 germline SNPs below 15% MAF, using beta-binomial distribution; determining a quantitative measure of the set of germline variants; filtering the set of germline variants, etc.). Under the BRI of the claims, these steps encompass mental observations or evaluations or calculations that can be practically performed in the human mind, or with pen and paper, because there are no limitations recited which would prevent the analysis and generating of results mentally. E.g., the aligning of reads recited in claim 45 is considered a mental process; the claims do not limit the size of the reference sequence, etc., and merely repeating a mental process a large number of times does not change the fact that it can be done mentally. The mathematical concepts recited in claims 45 and 74, for using a beta-binomial distribution, are discussed in Specification para. [000125], which points to the incorporated by reference application PCT/US2018/052087, filed September 20, 2018; this PCT app. discloses the specific math concepts at paragraph [011]. Further, under the BRI of the claims, the mathematical concepts encompass processes that can be performed mentally, or with pen and paper. While the recited mental processes and mathematical concepts (e.g., considering and aligning of sequence reads, detecting allelic imbalance based on criteria, using beta-binomial distributions, etc.) may take considerable time and effort, and although a general-purpose computer can perform these calculations and determinations at a rate and accuracy that can far exceed the mental performance of a skilled artisan, the nature of the activity is essentially the same, and therefore constitutes an abstract idea. Further, the MPEP at 2106.04(a)(2)(III)(C) points out that a claim that requires a computer may still recite a mental process, and presents three situations in which the claim is considered to recite a mental process, although the claim requires a computer: performing a mental process on a computer; performing a mental process in a computer environment; and using a computer as a tool to perform a mental process. In this case, e.g., regardless of the volume of sequence reads, and although the read analysis could be performed on a computer, the activity still represents an abstract idea. Therefore, the claims recite elements that constitute a judicial exception in the form of an abstract idea. (Step 2A, Prong One: Yes.)
Step 2A, Prong Two:
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs). Here at Step 2A, Prong Two, any remaining steps and/or elements not identified as JEs are therefore in addition to the identified JE(s) and are considered additional elements. Because the claims have been interpreted as being directed to judicial exceptions (abstract ideas in this instance) then Step 2A, Prong Two provides that the claims be examined further to determine whether the judicial exception is integrated into a practical application [see MPEP § 2106.04(d)]. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
MPEP § 2106.04(d)(I) lists the following five example considerations for evaluating whether a judicial exception is integrated into a practical application:
(1) An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a).
(2) Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2).
(3) Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b).
(4) Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c).
(5) Applying or using 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, as discussed in MPEP § 2106.05(e).
The claims recite the following additional elements:
Additional elements of data gathering, inputting, and outputting steps: Obtaining data (claim 45); and communicating the report to a third party (claim 49). These data gathering and outputting steps are additional elements which perform functions of inputting, collecting, and outputting the data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed, nor do they provide an improvement to technology [see MPEP § 2106.04(d)(I)].
Additional elements of computer components and a sequencer: A system, a controller, computer readable media, non-transitory computer-executable instructions, and processor (claim 45); a sequencer (claim 47); a non-transitory computer-executable instructions and processor (claims 49, 54, and 67-70). The claims require only generic computer components and a generic sequencer, which do not improve computer technology or sequencing technology, and do not integrate the recited judicial exception into a practical application (see MPEP§2106.04(d)(1) and MPEP§2106.05(f)).
Step 2A Prong Two summary: The claims have been further analyzed with respect to Step 2A, Prong Two, and no additional elements have been found, alone or in combination, that would integrate the judicial exception into a practical application. At this point in examination, it is not yet the case that any of the Step 2A Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of: (1) an improvement, (2) a treatment, (3) a particular machine, or (4) a transformation is clear in the record. For example, regarding the first consideration for improvement at MPEP 2106.04(d)(1), the record, including the Specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field, and the claims do not yet clearly result in such an improvement. (Step 2A, Prong Two: No).
Step 2B:
Because the additional claim elements do not integrate the judicial exception (JE) (here, abstract ideas) into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows:
Additional elements of data gathering, inputting, and outputting steps: Additional elements of obtaining data (claim 45), and communicating a report to a third party (claim 49), do not cause the claims to rise to the level of significantly more than the judicial exception. The courts have recognized receiving or transmitting data over a network; storing and retrieving information in memory; analyzing DNA to provide sequence information or detect allelic variants; and amplifying and sequencing nucleic acid sequences, [see MPEP§2106.05(d)(II)], as well-understood, routine, conventional activity when they are claimed in a merely generic manner (e.g., at a high level of generality) or as extra-solution activity. Thus, the data gathering steps are shown to be routine, well-understood, and conventional, and do not provide an inventive concept needed to amount to significantly more than the judicial exception.
Additional elements of computer components and a sequencer: Claims 45, 47, 49, 54, and 67-70 recite the additional elements of a system, a controller, computer readable media, non-transitory computer-executable instructions, a processor, and a sequencer. These are conventional computer components/sequencer, which are additionally shown to be conventional by the following references:
Shendure et al., (Nature biotechnology, vol. 30(11), pages 1084-1094 (2012)), presents a review on next generation sequencing (NGS), and lists sequencing instruments in table 2, p.1087.
Shu et al. shows sequencing using Illumina MiSeq or HiSeq4000 NGS platforms (Illumina) (p.9) and computational analysis of sequencing data using a customized bioinformatic pipeline (p.2; p.4, fig.2; and throughout document).
Therefore, the additional elements of computer components and a sequencer do not cause the claims to rise to the level of significantly more than the judicial exception as they do not provide an inventive concept.
Further regarding the conventionality of additional elements, the MPEP at 2106.05(b) and 2106.05(d) presents several points relevant to conventional computers and data gathering steps in regard to Step 2A Prong 2 and Step 2B, including:
• A general purpose computer that applies a judicial exception, such as an abstract idea, by use of conventional computer functions, does not qualify as a particular machine (see 2106.05(b)(I)), as in the case of claims 45, 47, 49, 54, and 67-70, which are interpreted to recite conventional computer components/sequencer.
• Integral use of a machine to achieve performance of a method may integrate the recited judicial exception into a practical application or provide significantly more, in contrast to where the machine is merely an object on which the method operates, which does not integrate the exception into a practical application or provide significantly more (see 2106.05(b)(II). In the instant claims, the recited conventional computer components/sequencer are used in are used in sequence data analysis to determine allelic imbalance and generate a report; as such, the conventional computer components and experimental system act only as a tool to perform the steps of data analysis, and do not integrate the exception into a practical application or provide significantly more.
• Use of a machine that contributes only nominally or insignificantly to the execution of the claimed method (e.g., in a data gathering step or in a field-of-use limitation) would not integrate a judicial exception or provide significantly more (see 2106.05(b)(III). The conventional computer components/sequencer of the claims do not impose meaningful limitations on the claims.
• The courts have recognized "receiving or transmitting data over a network", "performing repetitive calculations", and "storing and retrieving information in memory", as well-understood, routine, and conventional functions when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)(II)). The obtaining and outputting of data in the claims is recited in a generic manner.
All the limitations of claims 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76 have been analyzed with respect to Step 2B, and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception, and thus do not transform the judicial exception into a patent eligible application of the exceptions. Step2B: NO.
Therefore, claims 45-47, 49, 54-58, 61, 63-64, 66-70, and 73-76, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as reciting non-patent eligible subject matter.
Response to Applicant Arguments - 35 USC § 101
Applicant's arguments filed 06/10/2026 have been fully considered but they are not yet persuasive.
Referring to 101 analysis as organized in MPEP 2106, Applicant's remarks are understood to address Step 2A, Prong Two, 1st consideration explanation of improvement over the previous state of the technology field (MPEP 2106.04).
Applicant asserts, at p.10 of Applicant's remarks (bold emphasis added):
• "Applicants have previously highlighted that the improvement is at least by elimination of nebulous human manual review with an erroneous overcalling rate of 20%. See Page 15, second paragraph of Applicant Response dated September 19, 2025, referring to para. 136 of the Specification." (Instant remarks, p.10, ¶ 1.)
• ..."the presently amended claims provide a further specific improvement in
functioning of a computer by reciting use of a decision tree...This includes, more particularly, the three-criterion decision-tree structure recited in steps (c), (e), and (f) for specific use in cell-free DNA (cfDNA) allelic imbalance (AI) applications, hereto unachieved by others in the field." (Instant remarks, p.10, ¶ 2.)
• "The Inventors' creation and design of the of the particularly claimed three-criterion decision-tree structure achieves efficient memory use, computational cycle reduction and ultimately, massive scalability...Use of this approach in cfDNA application for AI determination provides a compact structure in memory that radically reduces computational cycles necessary to make such comparisons. Together, this allows for scalability, as computational and memory load is greatly reduced allowing for massive sample analysis.... Moreover, the Inventors' generation of the specifically defined and specifically claimed three criterion decision-tree fully provides embodiments achieving the improvement, as shown by use of this specific data structure processing a wide number of samples with flawless 100% sensitivity. (Instant remarks, p.10, ¶ 3.)
The arguments are not yet persuasive because it is not yet clear which assays are being compared in determining overcalling being reduced by 20%, nor is it known if all embodiments of the claim would result in a reduction in overcalling, nor is it clear if the overcalling reduction distinguishes the instant claims from the previous state of the technology.
Further, the argument is not yet persuasive because the three-criterion decision-tree (which is characterized as reciting abstract ideas of mental processes and mathematical concepts at Step 2A Prong One of the 101 analysis) may provide an improvement to the abstract idea of data analysis, however, there is no nexus between the output of the data analysis and a real world practical application. The claims do not integrate the judicial exceptions into a practical application, and as such do not provide an improvement to computer technology or another practical application at Step 2A Prong Two of the 101 analysis. .
Additionally, Applicant claims efficient memory use and radical computational cycle reduction, however, without comparison data, it is not clear that the claims recite an improvement to computer technology.
Overall, the arguments are not yet persuasive because the improvement appears to be to the abstract idea, even when considering the claim as a whole, and a nexus between the abstract idea informing a practical application is lacking. However, a detailed explanation of a technical improvement may help to overcome a 101 rejection, as discussed at Step 2A/2nd Prong, 1st consideration of the 101 analysis in MPEP 2106.04(d) and (d)(1). The explanation might include a concise statement of the improvement, including improvement over the previous state of the technology field; identification of the technology field; explanation of how the claims deliver the improvement and that reasonably all embodiments within the claim scope also will result in the asserted improvement, and extension of the explanation to persuasively demonstrate the nexus of integration of the judicial exceptions into a practical application.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/M.A.V./Examiner, Art Unit 1687
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
