DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Status of claims
Canceled:
3, 5, 17, 19-48, 50-63, 65-70
Pending:
1-2, 4, 6-16, 18, 49, 64 and 71-73
Withdrawn:
12, 49 and embodiments within particular claims per the 1/23/2026 election
Examined:
1-2, 4, 6-11, 13-16, 18, 64 and 71-73
Independent:
1 and 71
Allowable:
none
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
x
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
XXDATE
date format
Priority
As detailed on the 10/11/2022 filing receipt, this application claims priority to no earlier than 12/16/2019. All claims have been interpreted as being accorded this priority date.
Restriction/election
Applicant’s election with traverse in the 1/23/2026 reply is acknowledged.
Applicant timely traversed the restriction requirement. The traversal is on the ground(s) that "...the technical feature linking the groups makes a contribution over the art cited in the international search report" (applicant remarks). This assertion is not found persuasive because it is not clear what is the asserted technical feature. The requirements are deemed proper for the above reasons and as described in the 11/26/225 restriction requirement, and the requirements are made final.
Applicant may request an interview if it becomes clear during examination that examination would be advanced by relaxing the restriction requirement to re-join withdrawn subject matter, particularly with regard to a species election.
As listed above, claims are withdrawn as drawn to nonelected inventions pursuant to 37 CFR 1.142(b), and the remaining claims have been examined as listed above.
Objection to the specification: title
The title should be amended to more specifically reflect the claims, particularly referencing steps/elements: setting the context of the invention, particular to all claims, and distinguishing the instant application from any related applications, for example: multiplex polymerase chain reaction, ASCAT algorithm and homologous recombination repair deficiency score. The title should be "descriptive" and "as... specific as possible" (MPEP 606, 1st para. and 37 CFR 1.72; also MPEP 606.01 pertains).
Claim objections
Claim 1 is objected to because of the following informalities. Appropriate correction is required. In each objection the claims are definite with respect to the issues cited here because interpretation would have been sufficiently clear to PHOSITA, but nonetheless the claims are objected to for consistency among the claims or as otherwise indicated. With regard to any suggested amendment below to overcome an objection, in the subsequent examination it is assumed that each amendment is made. However, equivalent amendments also would be acceptable. Any amendments in response to the following objections should be applied throughout the claims, as appropriate.
The following issues are objected to:
Claim
Recitation
Comment
1
ASCAT
Each abbreviation should be defined once in the claims (instant specification at [42] pertains).
Claim rejections - 112/b
The following is a quotation of 35 USC 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 1-2, 4, 6-11, 13-16, 18, 64 and 71-73 are rejected under 112/b, as indefinite for failing to particularly point out and distinctly claim the subject matter which applicant 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. With regard to any suggested amendment below, for claim interpretation during the present examination it is assumed that each amendment suggested here is made. However equivalent amendments also would be acceptable.
The following issues cause the respective claims to be rejected under 112/b as indefinite:
Claim
Recitation
Comment (suggestions in bold)
1, 6, 13
the posterior probabilities
Requires but lacks clear antecedent; possibly "...[[the ]]posterior probabilites..." Claims 6 and 13 are rejected similarly concerning their differing instances of "posterior probability."
1, 71
ASCAT algorithm
Interpreted as an ""Allele-specific copy number analysis of tumors algorithm" with an objection above.
Indefinite under 112/b after invoking 112/f. Recites means (or an equivalent, nonce term, here "algorithm") and function and/or result (here "Allele-specific copy number analysis of tumors") without specifying steps or structure to prevent invoking, and it is not clear that the specification discloses sufficient structure, material, or acts rather than just function and results (e.g. [42]), noting that any disclosure must be clearly linked to the invoking recitation and that the above citation to the specification does not clearly disclose structure sufficient to satisfy 112/b. Incorporation by reference cannot support 112/f (MPEP 2181.III). MPEP 2181 pertains, and MPEP 2187, FP 7.34.23 lists options for overcoming the rejection. MPEP 2161.01.I "Determining Whether There Is Adequate Written Description For A Computer-Implemented Functional Claim Limitation" also pertains.
6, 10
, which have the same copy number
In claim 6,
(i) The comma is inappropriate since the clause is essential, i.e. the clause sets an essential condition. In this regard, claim 10 is rejected similarly.
(ii) It is unclear what is the antecedent of the "which" clause, e.g. "segments" vs. "amplicons." Possibly: "...[[,]] which amplicons have the..."
6, 8
posterior probability of a mixture component
In claim 6, the relationship is unclear between this "component" and those of claim 1. Claim 8 is rejected similarly.
6, 8, 13
which was determined by mixture modeling...
In claim 6, it is unclear whether the recited "was determined" is a required step of the instant "method" or part of a product-by-process (PbP) recitation not directly claimed as part of the instant "method." If PbP, then the recited process or step is not itself claimed and is limiting only to the extent that the structure of the product is clearly required to be limited by that process or step. Regarding product-by-process limitations within a claim, MPEP 2113 pertains, as well as, for example, Biogen MA, Inc. v. EMD Serono, Inc. (Fed. Cir. 9-28-2020, precedential). Claims 8 and 13 are rejected similarly.
9
wherein breakpoint count per unit-length
The relationship is unclear to the previous "breakpoint count per unit-length" at least for lack of a grammatical article, e.g. "the" preceding "breakpoint."
Claim interpretations
The following claim interpretations apply to all instances of the following terms throughout all claims:
Claim
Recitation
Comment
64
a human subject who has been diagnosed with an HRRD based on the method of claim 1
The recited "...subject... diagnosed... based on the method of claim 1" is interpreted as a product-by-process (PbP) element, i.e. the recited "subject" limited according to any structure clearly required by the recited product-by-process limitation of having been "diagnosed..." The recited process or step of having been "diagnosed..." is not itself claimed and is limiting only to the extent that the structure of the "subject" is clearly required to be limited by that process or step. Regarding product-by-process limitations within a claim, MPEP 2113 pertains, as well as, for example, Biogen MA, Inc. v. EMD Serono, Inc. (Fed. Cir. 9-28-2020, precedential).
Thus, in a BRI, the "subject" must have an HRRD, but the steps of claim 1 do not limit claim 64.
No prior art has been applied to the following claims
No prior art is applied to claims 1-2, 4, 6-11, 13-16, 18 and 71-73. Close art, for example WO2014-165785, WO2015-086473, WO2017-191076 and WO2014-018080 (each as cited on the 6/14/2022 IDS), does not teach the instant combination of posterior probabilities determined from components comprising segment size, breakpoint count per unit-length and copy number and used to calculate a homologous recombination repair deficiency score, and it is not clear that any combinable art of record would have rendered the claims obvious.
Claim rejections - 102
In the event the determination of the status of the application as subject to AIA 35 USC 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claims 18 and 64
Claims 18 and 64 are rejected under 35 USC 102(a)(1) as anticipated by WO2014-165785 (as cited on the 6/14/2022 IDS).
In claim 64, as interpreted above, claim 1 is interpreted as part of a product-by-process (PbP) recitation, and the particular method of claim 1 does not clearly limit claim 64. WO2014-165785 teaches the treatment of claims 64 and 18 (WO2014-165785: [58]; and entire document).
Claim rejections - 101
35 USC 101 reads:
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.
For each rejection below, dependent claims are rejected similarly as not remedying the rejection, unless otherwise noted.
Judicial exceptions (JE) to 101 patentability
Claims 1-2, 4, 6-11, 13-16, 18 and 71-73 are rejected under 35 USC 101 because the claimed inventions are not directed to patent eligible subject matter. After consideration of relevant factors with respect to each claim as a whole, each claim is directed to one or more JEs (i.e. an abstract idea, a natural phenomenon, a law of nature and/or a product of nature), as identified below. Any elements or combination of elements beyond the JE(s) (i.e. "additional elements") are conventional and do not constitute significantly more than the JE(s). Thus, no claim includes additional elements amounting to significantly more than the JE(s), as explained below.
In Alice, citing Mayo and Bilski, two Mayo/Alice questions determine eligibility under 101: First, is a claim directed to a JE? And second, if so, does the claim recite significantly more than the JE?
MPEP 2106 organizes JE analysis into Steps 1, 2A (1st & 2nd prongs) and 2B as follows below.
MPEP 2106 and the following USPTO website provide further explanation and case law citations: www.uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter? -- MPEP 2106.I and 2106.03
[Step 1: claims 1-2, 4, 6-11, 13-16, 18, 64 and 71-73: YES]
Step 2A, 1st prong: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea? -- abstract idea -- MPEP 2106.I and 2106.04
Preliminarily, in a 1st prong of Step 2A, elements of independent claim 1 are interpreted as directed to the abstract idea of predicting homologous recombination repair deficiency (HRRD) including the JE elements of "b) determining...," "c) identifying...," "d) determining..." and "e) calculating...," each of which, including all recitation within each listed element, in at least some embodiments within a BRI, involves only manipulation of data. While manipulation of data is not per se directed to an abstract idea, in this instance the above-identified elements are directed to the abstract ideas identified below.
Claim 64, as interpreted above, reads on embodiments requiring only treatment of an HRRD patient and therefore does not recite a JE.
Claim 71 is analyzed similarly to claim 1.
BRIs of the claims are analogous to an abstract idea in the form of at least a mental process, at least equivalent to a computer-implemented process, including obtaining and comparing intangible data (e.g. Cybersource, Synopsys and Electric Power Group). In a BRI, it is not clear that the claim embodiments are limited so as to require complexity precluding analogy to a mental process.
BRIs of the claims also are analogous to an abstract idea in the form of a mathematical concept, including mathematical relationships and calculations, as found in the following case law, as cited and discussed above: collecting information, analyzing it, and displaying certain results of the collection and analysis (Electric Power Group) and/or obtaining and comparing intangible data (e.g. Cybersource, Ambry and Myriad CAFC) and/or execution of an algorithm to implement mathematical relationships and/or formulas, including image processing (e.g. TLI, Digitech, Benson, Flook, Diehr, FuzzySharp, In re Grams and In re Abele all as cited in MPEP 2106).
Instant examples of math concepts include parameter and probability determination and score calculation.
The preceding case law examples are cited for the basic form of their identified abstract ideas, and analogy to these example abstract ideas need not be within the same technology field, 101 analysis generally being assumed to be neutral with respect to technology field.
As in Alice (at 306, as cited in the MPEP above) and Bilski (as cited in Alice, id), an abstract idea may comprise multiple abstract elements or steps (i.e. from Alice: "a series of steps" at 306) and need not be a single equation, relationship or principle.
It is not clear that the identified elements must represent other than an abstract idea according to any relevant analysis or case law.
[Step 2A, 1st prong, abstract idea: claims 1-2, 4, 6-11, 13-16, and 71-73: YES; claim 18 and 64: NO]
Step 2A, 2nd prong: If the claims recite a judicial exception under the 1st prong, then is the judicial exception integrated into a practical application? -- MPEP 2106.I and 2106.04(d)
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
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);
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);
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);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
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).
In Step 2A, 1st prong above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In Step 2B below, any remaining steps and/or elements are therefore in addition to the identified JE(s). Any such additional steps and additional elements are further discussed in Step 2B.
Here in Step 2A, 2nd prong, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, 2nd prong 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. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement (e.g. specification: [4]).
[Step 2A, 2nd prong: claims 1-2, 4, 6-11, 13-16 and 71-73: NO]
Step 2B: Do the claims recite a non-conventional arrangement of additional elements in addition to the identified JEs? -- MPEP 2106.I and 2106.05
Addressing the second Mayo/Alice question, all elements of claims 1 and 71 are part of one or more identified JEs (as described above), except for elements identified here as conventional elements in addition to the above judicial exceptions:
The recited "PCR... assay," "processors" and "receiving" are conventional elements of a laboratory and/or computing environment and/or conventional data gathering/input elements, as exemplified in MPEP 2106.05(d).II and 2106.05(f-g). Data gathering does not impose any meaningful limitation on the judicial exceptions or on how the judicial exceptions are performed. Data gathering are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
It is emphasized that, outside of an improvement argument, analysis of what is conventional generally pertains to the above-identified additional elements and not to elements identified as part of a JE.
[Step 2B: claims 1 and 71: NO]
Summary and conclusion regarding claims 1 and 71
Summing up the above analysis of claims 1 and 71, each viewed as a whole and considering all elements individually and in combination, no claim recites limitations that transform the claim, finally interpreted as directed to the identified JE(s), into patent eligible subject matter, and it is not clear that any claim is sufficiently analogous to controlling case law identifying an example of an eligible claim.
Remaining claims
Claims 2, 4, 6-11, 13-16 and 72-73 add elements which also are part of the identified JEs for the same reasons described above regarding the independent claims and therefore do not provide the something significantly more necessary to satisfy 101.
None of the dependent claim elements provides the something significantly more than the identified JE(s) necessary to satisfy 101.
Citations to art
In citations to documents in the art, rejections refer to cited portions of each document as well as to the entirety of each document, unless otherwise noted in the situation of lengthy, multi-subject documents. Other passages not specifically cited within a document may apply as well.
Conclusion
No claim is allowed.
A shortened statutory period for reply is set to expire THREE MONTHS from the mailing date of this communication.
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The examiner for this Office action, G. Steven Vanni, may be contacted at:
(571) 272-3855 Tu-F 8-7 (ET).
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D. Riggs, II, may be reached at (571) 270-3062.
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686