DETAILED ACTION
This application is being examined under AIA first-to-file provisions.
Continued examination under 37 CFR 1.114
A 7/29/2025 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous office action has been withdrawn pursuant to 37 CFR 1.114.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.
Applicant's 12/13/2024 claims amendment and 10/15/2025 remarks have been considered. The 6/27/2025 claims amendment and remarks were not entered.
Status of claims
Canceled:
2 and 4-128
Pending:
1 and 3
Withdrawn:
none; however the 11/24/2023 and 6/21/2024 restriction requirements and associated elections remain in effect
Examined:
1 and 3
Independent:
1
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
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 3/17/2023 filing receipt, this application claims priority to as early as 8/30/2017. At this point in examination, all claims have been interpreted as being accorded this priority date.
Withdrawal / revision of objections and/or rejections
Rejections and/or objections not maintained from previous office actions are withdrawn.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
Claim 3 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
3
(ii)... based on the inter-motif distances determined in the step (e), and the inter-motif distance probability plot.
The comma in this two-element list appears inappropriate, e.g. "X and Y" not "X, and Y."
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.
Claim 3 is 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)
3
a probability value that the second transposase is significantly different from the first transposase
The relationship is unclear between this instance of "a probability..." and the same recitation in claim 1, step (f). Possibly this instance in claim 3 should recite "[[a]]the probability..."
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
It is not clear what particular 101 argument is being put forth. While the claims have been amended, the logical path from that amendment to patent eligibility is not explained and is not clear on its face.
It is noted that while "patent eligibility" is the ultimate goal of the 101 argument, its direct assertion typically will not be a persuasive argument. Similarly, "practical application" can be an intermediate goal toward patent eligibility, but, as the MPEP details, practical application may be demonstrated by recourse to one of several "considerations" listed in the MPEP and at the start of Step 2A, 2nd prong of the below 101 rejection.
MPEP 2106 puts forth various possible paths to patent eligibility among its analysis steps 1-2B as cited in the rejection. No specific argument with respect to any of those particular paths, e.g. the above considerations in Step 2A, 2nd prong, has been presented.
If, for example at Step 2A, 2nd prong, what is intended is argument by the consideration of an explanation of improvement over the previous state of the technology field, then this is not clear.
It is clear that the claimed method differs from the previous state of the technology field in that, for example, the claims satisfy 102 and 103. However, a difference is a necessary but not a sufficient condition for improvement over the previous state of the technology field. It also must be clear that the difference results in an improvement, and, here, it is not clear what is that improvement, let alone that it must necessarily result from the claims.
The 10/15/2025 remarks conclude with "It is submitted that the inventive concept lies... in the non-obvious combination of a specific, new distance algorithm and a novel, engineered statistical interpretation method (bootstrapping / interpolation on simulated data), which collectively enable the practical, high-throughput screening of potentially millions of mutant transposases" (emphasis added, p. 5). From these remarks, an asserted improvement over the previous state of the technology field possibly would appear to be, implicitly, one of: (i) previous methods were relatively impractical, (ii) previous methods were not "high-throughput" or (iii) previous methods did not screen "millions" of mutant transposes. It is not clear either which if any of these assertions is intended to demonstrate improvement, nor is it clear that any is true. An improvement cannot be simply a positive feature of the claims on their face. An improvement must be in comparison to the previous state of the technology field.
Relatedly, Applicant's remarks cite extensively to the instant specification, which is valuable. However, it is noted that arguments and evidence are not limited to what was disclosed in the original specification and alternatively may be extrinsic to the original disclosure, including references available after the priority date, as long as it is clear that an argument applies to all embodiments of a properly supported claim.
The rejection is maintained.
Possibly an interview would help to select and explain a path to patent eligibility, e.g. relying on an explanation of improvement over the previous state of the technology field consistent with MPEP §§ 2106.04(d)(1) and 2106.05(a).
Judicial exceptions (JE) to 101 patentability
Claims 1 and 3 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
Claim 1 is directed to a 101 process, here a "method," with process steps such as "contacting..."
[Step 1: 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? -- 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 sequence comparison including the JE elements of "(e) determining an inter-motif distance...," "calculating..." (three instances: (i) through (iii)), "(iv) averaging..." and "(f)... determining a probability...," 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 determining an inter-motif distance and determining a probability, 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.
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: claim 1: 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: [82, 126, 141, 153, etc.]), as further discussed in the above response to Applicant remarks.
[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), except for elements identified here as conventional elements in addition to the above judicial exceptions:
The recited "contacting..." and "sequencing..." 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) and as exemplified by Green, Kia, Zhou and Naumann (each as cited on the 3/2/2020 IDS), and generally it is understood that the examples in the reference are well-known and routine.
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: claim 1: NO]
Summary and conclusion regarding claim 1
Summing up the above analysis of claim 1, 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
Claim 3 adds 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.
Inquiries
Information regarding the filing, management and status of patent applications which are published (available to all users) or unpublished (available to registered users) may be obtained from the Patent Center: https://patentcenter.uspto.gov. Further information is available at https://www.uspto.gov/patents/apply/patent-center, and information about filing in DOCX format is available at https://www.uspto.gov/patents/docx.
The Electronic Business Center (EBC) at 866-217-9197 (toll-free) is available for additional questions, and assistance from a Customer Service Representative is available at 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
The examiner for this Office action, G. Steven Vanni, may be contacted at:
(571) 272-3855 Tu-F 8-7 (ET).
An interview may be requested and is suggested via the Automated Interview Request (AIR) tool available at:
https://www.uspto.gov/patents/laws/interview-practice
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 (previously 1672)
Prosecution Insights