DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Claim status identifier
Claims 67-196 status identifier should read "Cancelled" instead of "Original."
Status of claims
Canceled:
2-8, 13, 15-17, 20, 22, 24-27, 29-30, 32, 34-35, 37-38, 40, 42, 44-63, 67-196
Pending:
1, 9-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64-66
Withdrawn:
none
Examined:
1, 9-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64-66
Independent:
1 and 9
Allowable:
none
Rejections applied
Abbreviations
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 or column:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed on the 12/18/2023 filing receipt, this application claims priority to no earlier than 1/29/2021. All claims have been interpreted as being accorded this priority date.
Objection to the specification: title
The title should be amended to more specifically reflect the claims, particularly the independent claims and referencing steps/elements: setting the context of the invention, particular to all claims, and distinguishing the instant application from any related applications, for example a title including terms such as: machine learning. 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 interpretations
The following claim interpretations apply to all instances of the following terms throughout all claims:
Claim
Recitation
Comment
1 & 9
...model trained using...
In claim 1, the recited "...model trained using..." is interpreted as a product-by-process element, i.e. the recited "model" limited according to any structure clearly required by the recited product-by-process limitation of having been "trained..." as further recited. The recited process or step of having been "trained" is not itself directly claimed and is limiting only to the extent that the structure of the "model" 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). Claim 9 is interpreted similarly.
Claim 11 depends from claim 9 and countermands the above product-by-process interpretation of claim 9 by directly requiring the training.
64 & 66
A method...,
comprising:
obtaining a classification of a sample associated with the cancer as HCC-like or CCA-like, wherein the sample was classified using the method of claim 9; ...
In claim 64, the recited "...sample was classified..." is interpreted as a product-by-process element, i.e. the recited "sample" limited according to any structure clearly required by the recited product-by-process limitation of having been "classified using the method of claim 9." The recited process or step of having been "classified using the method of claim 9" is not itself directly claimed and is limiting only to the extent that the structure of the "sample" 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). Claim 66 is interpreted similarly.
Claim rejections - 35 USC 103
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 35 USC 103 which forms the basis for all obviousness rejections set forth in this office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102 of this title, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 USC 102(b)(2)(C) for any potential 35 USC 102(a)(2) prior art against the later invention.
Claims 1, 9-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64-66
Claims 1, 9-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64-66 are rejected under 35 USC 103 as unpatentable over Michuda (US PGPUB 2020-0365268 as cited on the 7/27/2023 IDS).
Regarding claim 1, the recited generating reads on "next-generation sequencing" and "ligation" (Michuda: [135]).
The recited hepatocellular cholangiocarcinoma (cHCC-CCA) machine-learning model and classifying read on "patient classification module" (Michuda: [111-112]; also [110, 114, 132]).
To the extent that the limitations within claim 1 are taught individually but are not explicitly taught with the recited relationships and sequencing among limitations -- as examples, separately teaching the recited sample preparation versus machine learning analysis, or separately teaching hepatocellular vs. cholangiocarcinoma, etc. -- then in the absence of a secondary consideration to the contrary, it would have been prima facie obvious to PHOSITA to try the recited combination of limitations as those limitations are taught individually as described above. Trying the recited combinations would have been examples of combining prior art elements, elements taught within the same reference, according to known methods to yield predictable results and choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success (MPEP 2143.I pertains).
The art is applied to claim 9 similarly to claim 1.
Regarding claim 10, the recited probabilistic classifier reads on "An entropy score may serve as a function that takes a probability vector and maps it to a single number characterizing how “uncertain” the result is" (Michuda: [231]).
The art is applied to claim 11 as described for claim 1.
Regarding claim 12, the recited bile duct cancer sample reads on "tumor samples" (Michuda: [73]) and "Bile Duct Cancer" (Michuda: [285]).
Regarding claim 14, the recited hepatocellular cholangiocarcinoma (cHCC-CCA) sample reads on "liver hepatocellular carcinoma" (Michuda: [328]) and "Cholangiocarcinoma" (Michuda: [285]).
Regarding claim 18, the recited tumor purity reads on "tumor purity" (Michuda: [129]).
Regarding claim 19, the recited aneuploidy status reads on "specialized database of chromosomal aberrations" (Michuda: [265]).
Regarding claim 21, the recited cancer cell fraction (CCF) reads on "relative proportion of tumor cells" (Michuda: [90]).
Regarding claim 23, the recited functional variant status reads on "functionality" (Michuda: [89]) and "functional genomics" (Michuda: [280]).
Regarding claim 28, the recited mutational burden reads on "mutational burden" (Michuda: [282]; also [322, 340, 395]).
Regarding claim 31, the recited microsatellite instability reads on "microsatellite instability" (Michuda: [153]; also [154, 156, 251, 269, 282, 322, 395]).
Regarding claim 33, the recited genome-wide loss of heterozygosity reads on "“het-SNP” refers to a heterozygous SNP, where the genome is at least diploid, and at least one but not all of the two or more homologous sequences exhibits the particular SNP" (Michuda: [84]).
Regarding claim 36, the recited ancestry status reads on "cell lineages" (Michuda: [294]).
Regarding claim 39, the recited hepatitis B virus (HBV) status reads on "identification of viral presence may include detection of Hepatitis B (HBV)" (Michuda: [303]).
Regarding claim 41, the recited clinicopathological feature reads on "leverage... pathology report data" (Michuda: [70]).
The art is applied to claim 43 as described for claim 1.
Regarding claims 64-66, the recited treatment selection and administration read on "provide tailored patient treatments" (Michuda: [7-8]; also [14]) and "the trained classification model further provides one or more treatment recommendations" (Michuda: [22]; also [24, 26, 68, 70, 103]).
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, 9-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64-66 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, 9-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64-66: 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 analyzing and classifying including the JE elements of "analyzing...," "receiving..." (interpreted here as a process step internal to the method), "inputting..." (interpreted here as a process step internal to the method), "classifying...," 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 9 is interpreted 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 inputting into a combined hepatocellular cholangiocarcinoma (cHCC-CCA) machine-learning model to classify, in which the model is analogous to a mathematical function, as well as relationships inherent in recitations as the only supported embodiment.
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.
Regarding inherency of abstract ideas, MPEP 2106.04.II.A.1 includes: "the claims in Alice Corp. v. CLS Bank, 'described' the concept of intermediated settlement without ever explicitly using the words 'intermediated' or 'settlement'" (emphasis added, p. 1). Similarly, inherency can effectively be recitation, as in, for example, "By claiming simply 'crystalline paroxetine hydrochloride hemihydrate' with no reference to how it was produced, SKB effectively claimed 'crystalline paroxetine hydrochloride hemihydrate whether non-naturally occurring or arising through natural conversion.' Claim 1, as issued, therefore combines patentable and unpatentable subject matter, and is invalid under Section 101." (capitalization added, SmithKline Beecham Corp. v. Apotex Corp., 365 F.3d 1306, 1321-33, Fed. Cir. 2004).
In the instant type of data processing claims, the specification is not merely adding background explanation as to how a claimed process works, e.g. a physical process based on, involving or further explained by abstract ideas and natural laws. Rather, the specification is detailing the only disclosed way that a programmer may proceed from the recited inputs to the recited outputs, e.g. through actual performance of the disclosed judicial exceptions (JEs).
Regarding the "Meaning of 'Recites,'" MPEP 2106.04.II.A.1 states:
In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim. For instance, the claims in Diehr, 450 U.S. at 178 n. 2, 179 n.5, 191-92, 209 USPQ at 4-5 (1981), clearly stated a mathematical equation in the repetitively calculating step, and the claims in Mayo, 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012), clearly stated laws of nature in the wherein clause, such that the claims "set forth" an identifiable judicial exception. Alternatively, the claims in Alice Corp., 573 U.S. at 218, 110 USPQ2d at 1982, described the concept of intermediated settlement without ever explicitly using the words "intermediated" or "settlement."
While the "set forth" language approximates explicit recitation, it also is fundamental that all recitation must be interpreted and that to be patent eligible a claim must satisfy 101 according to its properly interpreted scope, e.g. for all embodiments on which the claim reads, e.g. according to any inherency pertinent to a given claim and disclosure accompanying that claim, i.e. consistent with the "described" meaning of "recites" as in the MPEP. Thus, within a BRI, the identified abstract idea elements read on one or more embodiments which only involve manipulation of data. It is not clear than any improvement argument clearly on the record causes a claim not to be directed to a JE for all embodiments within the scope of the claim.
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 and 9: 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? -- law of nature -- MPEP 2106.I and 2106.04
Preliminarily, at this 1st step of the analysis, elements of independent claim 1 are directed to a law relating sequence to disease classification, including the JE element of "classifying..."
Claim 9 is interpreted similarly to claim 1.
A BRI of the instant claims is analogous to a law of nature as found, for example, in Mayo (as cited in the MPEP above). It is not clear than any improvement argument clearly on the record causes a claim not to be directed to a JE for all embodiments within the scope of the claim. It is not clear that the above identified law of nature including the identified elements, taken together and within a BRI, must in all embodiments represent other than a law of nature according to any relevant analysis or case law. Therefore, in answer to the 1st Mayo/Alice question, the above elements are directed to a law of nature.
[Step 2A, 1st prong, natural law: claims 1 and 9: YES]
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: [3]).
[Step 2A, 2nd prong: claims 1 and 9: 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 9 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 providing, ligating, amplifying, capturing and sequencing are conventional elements of a laboratory and/or conventional data gathering/input/output elements, as exemplified in MPEP 2106.05(d).II and 2106.05(f-g), and as exemplified by Michuda (US PGPUB 2020-0365268 as cited on the 7/27/2023 IDS), and generally it is understood that the examples in the reference are well-known and routine.
Data gathering does not impose any meaningful limitation on the judicial exceptions or on how the judicial exceptions are performed. Data gathering is insufficient 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 9: NO]
Summary and conclusion regarding claims 1 and 9
Summing up the above analysis of claims 1 and 9, 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 10-12, 14, 18-19, 21, 23, 28, 31, 33, 36, 39, 41, 43 and 64 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.
Elements of the following claims are additional elements but nonetheless are conventional elements of a laboratory or computing environment, conventional data gathering elements or conventional post-processing elements, as in the following specific examples which also are understood to be well-known and routine:
claims 65-66: "administering..." is an additional element but is a conventional element of a laboratory and/or computing environment and/or conventional data gathering/input/output elements, as exemplified in MPEP 2106.05(d).II and 2106.05(f-g), and as exemplified by Michuda (US PGPUB 2020-0365268 as cited on the 7/27/2023 IDS), and generally it is understood that the examples in the reference are well-known and routine. Also, while the recited "administering..." is a treatment analogous to Step 2A, 2nd prong, 2nd consideration treatment (MPEP § 2106.04(d)(2)), the present recitation is interpreted as not necessarily requiring particular physical treatment in all claimed embodiments.
None of the dependent claim elements provides the something significantly more than the identified JE(s) necessary to satisfy 101.
Citations to art
In the above citations to documents in the art, rejections refer to the portions of each document cited as example portions 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
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