DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Continued examination under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous office action has been withdrawn pursuant to 37 CFR 1.114. MPEP 706.07(h) pertains.
Status of claims
Canceled:
7-20
Pending:
1-6
Withdrawn:
none; however, the 1/23/2024 restriction requirement remains in effect
Examined:
1-6
Independent:
1
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
x
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
As detailed on the 12/5/2023 filing receipt, this application was filed 11/20/2023, and there is no claim to earlier priority.
Withdrawal / revision of objections and/or rejections
In view of the amendment and remarks:
The previous claim objection is withdrawn, however new objections are applied.
The previous 112/b rejections are withdrawn, except as noted below, and new rejections are applied.
The art rejections are withdrawn. No prior art is applied to claims 1-6. Close art, for example Zethelius as cited in the now withdrawn rejection, as well as other art found in the search histories and on the IDS, while teaching sample data patterns yielding biomarkers among case and non-case samples, does not teach the instant relationships and covariation among such biomarkers then yielding the recited relational biomarkers and their recited matrix analysis, and it is not clear that any combinable art of record would have rendered the claims obvious.
Rejections and/or objections not maintained from previous office actions are withdrawn. The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim objections
Claims 1, 3 and 7-20 are 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
;
wherein the biological material comprises...
The semi-colon preceding this "wherein" clause should be a comma.
3
non case
Should read "non-case"
7-20
The canceled claims should be listed without including their recitations and with an appropriate status identifier, "Claims 7-20 (canceled)." See MPEP 714.II.C, and see the instant 4/25/2025 and 10/6/2025 listings of claims.
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 1-6 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, 4
wherein the biological material
In claim 1, the relationship is unclear between this instance in the first "wherein" clause and the two instances in the preceding "defining" steps, i.e. "a first biological material" and "at least one additional biological material."
In claim 4, the same issue recurs.
1
for biological samples from subjects who have... ; and
generating a case covariation... and;
After the initial "comprising:...," a list of "-ing" steps follows, and that list should recite only one conjunction, i.e. the "and" before "applying." This "and" between the "for..., determining..." steps is inappropriate."
Similarly, the "and" between the "generating..." steps is inappropriate.
1, 3
for biological samples from subjects who do not have or will not develop
This "or" again appears illogical. This rejection already was applied and corrected in the 1/30/2025 action and 4/25/2025 claims. It is not clear why the claim has been amended back to the previously rejected recitation.
This issue should be addressed throughout the claims as needed.
1
the first conventional biomarker
Requires but lacks clear antecedent. It appears that deletion of "conventional" was omitted here.
1
generating a non-case... and non-case covarion...
The recited "covarion" renders the claim indefinite and possibly should read "covariation."
1
applying... a patient biological material..
The claim should not end with two periods
2
The method of claim 1, comprising:
generating an ensemble of the relational biomarker...
First, the relationship is unclear between this "generating" step and claim 1. It may suffice to amend to "...further comprising:..."
Second, the recited "the relational biomarker" requires but lacks clear antecedent. Instantiated in claim 1 was "at least one relational biomarker," which does not clearly provide antecedent. Possibly claim 2 should recite "generating an ensemble of the at least one relational biomarker."
2
...of additional biomarker...
First, a grammatical article would be needed before this singular noun.
Second, the relationship is unclear between this instance and the "at least one additional biomarker" of claim 1.
3
combinations of the case covariation and non case covariation of the at least one additional biomarker from the first and at least one additional biological material from subjects who have or will develop each additional disease or disorder, and from subjects who do not have or will not develop each
additional disease or disorder
First, each instance of "the..." requires clear antecedent, but it is not clear that there is clear antecedent in each instance, particularly not regarding "from the first and at least one additional biological material from subjects..." Clear antecedent would require each of these chained instances of "the..." having been previously recited, together, and this appears not to be present. Thus, this appears to be a new instantiation for which at least one of the instances of "the" here is inappropriate.
Second, the relationship is unclear between this instance of "the first and at least one additional biological material" versus the same element already instantiated in claim 1. Possibly, "the" should be recited here if referring to the same claim element. Or, if this is a new instantiation of "additional biological material," then possibly the various instances should be distinguished as "first," "second," "third," etc.
5
wherein the pattern and the additional pattern comprises
Not interpretable at least for lack of subject-verb agreement, i.e. "comprises" requires a singular subject, but the subject is plural.
5
representing a presence or absence or quantity or frequency or
proportion of the first and at least one additional biological material or a mathematical
transformation of the variable.
A list of elements follows "representing..." However, the use of multiple grammatical conjunctions (e.g. "or," "and," etc.) renders the list structure unclear and the claim indefinite. A simple grammatical list should include only one conjunction. If there are nested lists, then each should include one conjunction. The instant structure is unclear.
Relatedly and as previously rejected, the relationship is unclear between the recited "or a mathematical transformation..." and the rest of the claim. First, in a recitation such as "X or Y", there should be no comma between "X" and "Y", e.g. not "X, or Y." It is unclear what is the first element in the recited "or" clause, e.g. "...comprise ..., or..." vs. "...representing ..., or...", etc.
Claim rejections - 112/a
The following is a quotation of 112/a:
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Regarding issues of written description support stemming even from the original claims and original disclosure, MPEP 2161.01.I (e.g. 6th para.), 2163.I and 2163.I.A pertain: "[O]riginal claims may lack written description when the claims define the invention in functional language specifying a desired result but the specification does not sufficiently describe how the function is performed or the result is achieved. For software, this can occur when the algorithm or steps/procedure for performing the computer function are not explained at all or are not explained in sufficient detail (simply restating the function recited in the claim is not necessarily sufficient). In other words, the algorithm or steps/procedure taken to perform the function must be described with sufficient detail so that one of ordinary skill in the art would understand how the inventor intended the function to be performed" (MPEP 2161.01.I,6th para.).
Written description
Claims 1-6 are rejected under 112/a as failing to comply with the written description requirement. The claims read on subject matter which is not described in the specification in such a way as to reasonably convey to PHOSITA that the inventors, at the time the application was filed, had possession of the claimed invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted. With regard to any suggested amendment(s) below to overcome a rejection, equivalent amendments also would be acceptable.
Claim 1, in the "generating" steps, recites "...entering the case covariation into a first matrix..." and "...entering the case covariation and non-case covarion into a second matrix..." The specification discloses "covariation" at [40 and 44], but written description support for the recited matrix entry and the recited relationships to "case" and "non-case" is unclear. The written description provided is not clearly commensurate with the recitation.
Although claims are interpreted in light of the specification, examples from the specification are not imported into the claims as limitations absent a clearly limiting definition in the specification. (MPEP 2145.VI pertains.)
As appropriate, these rejections may be overcome, for example, (i) by narrowing to clearly supported embodiments and/or (ii) by clarifying on the record where support can be found and how that support relates to the recitations.
In general, it is requested that any claim amendment in this regard be accompanied by citations to support in the original disclosure.
MPEP 2163 generally pertains.
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.
Response to arguments regarding Claim Rejections - 35 USC 101 -- Abstract idea
Applicant states (original emphasis removed, bold emphasis added, applicant remarks: p. 6-7):
...the proposed invention describes and claims a method of generating a relationship biomarker by applying a mathematical function to covariations that represent intra-biomarker relationships. This is an improved process that is not described, referenced, taught, or within the scope of the cited reference. This is an improvement that accomplishes what was no accomplished before, namely identifying biological samples as case or non-case by examining relationships between biomarkers (which would not be able to demonstrate covariance in a linear model). ... ...the proposed invention may identify such relationship by modeling relationship between these unconsidered biomarkers, thereby enabling clinicians to classify biological samples in a previously non-existent manner.
Applicant makes an argument under MPEP 2106, Step 2A, 2nd prong, 1st consideration regarding an improvement over the previous state of the technology field.
While the 102 rejection has been withdrawn, and it can be agreed that the instant claims are distinguishable from the previous state of the technology field, it remains unclear what is the improvement. A difference is necessary but is not alone sufficient. It may help to more clearly establish in the record what is the improvement. For example, having established "improvement" as the argument, it may help to further specify what is the improvement, including moving beyond use of just that term. Also, the purpose of the explanation of improvement is to demonstrate practical application, so it is helpful to describe how any improvement proceeds from the identified judicial exception to inform and deliver a practical application. Here, while "relational biomarkers" were not taught in the technology field, their importance is not clear. For example, it is not clear what practical application, benefit, etc. they provide.
Relatedly, the asserted "the proposed invention may identify such relationship by modeling relationship between these unconsidered biomarkers, thereby enabling clinicians to classify biological samples in a previously non-existent manner" is unclear at least due to what appear to be grammatical issues. It may help to revise and expand on this sentence.
Judicial exceptions (JE) to 101 patentability
Claims 1-6 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 1-6: 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 relating biological sample data to disease state including the JE elements of "defining..." (two instances), "...determining..." (two instances), "generating..." (two instances) and "applying...," 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.
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 the recited "mathematical function," as well as relationships inherent in recitations as the only supported embodiments.
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: claim 1: 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 3 are directed to a law relating sample data to diagnosis, including the JE element of "classifies an unknown biological sample as a case or noncase sample."
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, 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 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]). The above response to Applicant's remarks also pertains
[Step 2A, 2nd prong: claim 1: 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 claim 1 are part of one or more identified JEs (as described above).
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.
Suggestions regarding advancing examination by improvement argument versus non-conventional additional element argument are provided in the bullets at the end of this rejection.
[Step 2B: claim 1: NO]
Summary and conclusion regarding claims 1 and 3
Summing up the above analysis of claims 1 and 3, 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 and 4-6 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.
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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