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 .
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and the fee set forth in 37 CFR 11.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 08/29/2025 has been entered.
Applicant's amendments and remarks, filed 08/29/2025, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1, 3-7, 9-11, 13, 15-19, 21-23, 25, 27, 29-31, 33-35, 37-48 are under examination. Claims 2, 8, 14, 20, 26, 28, and 32 are withdrawn. Claims 12, 24, 36 are cancelled.
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. Accordingly, the effective filing date of the instant application is 07/31/2020.
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 1, 3-7, 9-11, 13, 15-19, 21-23, 25, 27, 29-31, 33-35, 37-48 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1
Under the broadest reasonable interpretation, the claimed invention (claims 1, 13, 25 being representative) is directed to a system/method for performing a process. Therefore, the claims fall into one of the four statutory categories (Step 1: Yes).
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the claimed invention includes the following abstract idea steps:
(b) calculate, using a determined ratio of concentrations and a determined ratio of signals from the genetic sequencing results, at least one prediction band based on the multiple libraries, comprising:
determine, for each of the multiple libraries, a library signal value indicative of the number of reads based on an oligonucleotide signal value corresponding to concentrations…;
calculate a ratio of target concentrations for each pair of libraries in the multiple libraries by dividing a determined higher target concentration of the pair a determined lower target concentration of the pair;
calculate a ratio of signal values for each pair of libraries in the multiple libraries by dividing the signal value associated with the library with a determined higher target concentration of the pair by the signal value associated with the library with a determined lower target concentration of the pair, calculate a logarithm of each ratio of target concentration, calculate a logarithm of each ratio of signal values, and
calculate the at least one prediction band by generating a distribution of slopes based on a plurality of points each having an x value corresponding to the logarithm of the ratio of target concentration of two libraries and a y value corresponding to the logarithm of the ratio of signal values of the two libraries, wherein a prediction band represents a range of values within which at least one future measurement is expected to fall;
(c) repeat (a) and (b) for a plurality of preparations;
(d) output a final prediction band based on the prediction bands calculated at (b) for each of the plurality of preparations, the final prediction band comprising a pair of boundaries and representing a range of values within which at least one future measurement is expected to fall, and the final prediction band encompassing each prediction band calculated at (b) for the plurality of preparations at (c) such that a minimum value and a maximum value in each prediction band calculated for the plurality of preparations falls within the range of values represented by the final prediction band;
(e) evaluate a relative quality of an oligonucleotide library derived from a new preparation compared to the quality of the multiple libraries associated with the plurality of preparations used to generate the boundaries based on the final prediction band;
Mental Processes
Under the broadest reasonable interpretation, the claimed steps require analyzing data (via calculations), outputting the results, and making decisions based on said results. The courts are clear that an invention directed to the “collection, manipulation, and display of data” is an abstract process. See Intellectual Ventures, 850 F.3d at 1340. In addition, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data analysis methods [pages 12-16]. Accordingly, but for the recitation of a computer processor, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
Mathematical Concept
In this case, the claimed step (and sub-steps) explicitly requires performing calculations and therefore, by definition, also amounts to a mathematical concept. Similarly, the step for “outputting a final prediction” also broadly encompasses a mathematical calculation (since it is essentially another calculation based on repeated previous ratio calculations). Applicant is reminded that a mathematical calculation is a mathematical operation or an act of calculating using mathematical methods to determine a variable or number, e.g., a prediction band. There is no particular word or set of words that indicates a claim recites a mathematical calculation. See MPEP 2106.04(a)(2). This position is further support by applicant’s own specification, which teaches calculating prediction bands using mathematical operations, e.g. ratios and logarithms [0017]. Therefore, when read in light of applicant’s own specification, the claims are directed to manipulating information through a mathematical relationship/correlation. See MPEP 2106.04 and 2106.05(II). For these reasons, the claims are directed to one or more judicial exceptions. [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim includes any additional elements that integrate the recited judicial exception into a practical application of the exception. In this case, the additional steps/elements that are not part of the abstract idea are as follows:
(a) receive genetic sequencing results for multiple libraries each associated with a target concentration of a plurality of oligonucleotides, wherein the genetic sequencing results for each of the multiple libraries is indicative of a number of reads corresponding to each oligonucleotide of the plurality of oligonucleotides, wherein the number of reads comprises a corresponding concentration and signal value;
(f) determine, using a sequencing device, sequence information for a sample which comprises the oligonucleotide library derived from the new preparation to determine whether the sequencing device properly identifies the oligonucleotide library derived from the new preparation comprising at least metrics of the final prediction band to be presented to a user
With regards to step (a), this step requires obtaining information for use by the abstract idea. Accordingly, this step amounts to “insignificant extra-solution activity”, i.e. activities incidental to the primary process or product that are merely a nominal or tangential addition to the claim. See MPEP 2106.05 (g).
With regards to the claimed determining (step f), this limitation is generically recited and not limited to any particular acts or operations. As such, under the BRI, this step is broadly interpreted as performing sequencing to obtain additional information (as intended use recitations are not given patentable weight). In addition, to the extent that applicant is testing a sequencer device, it is noted with particularity that examples of activities that the courts have found to be insignificant extra-solution activity include testing a system for a response, the response being used to determine system malfunction, In re Meyers, 688 F.2d 789, 794; 215 USPQ 193, 196-97 (CCPA 1982). MPEP 2106.05(g). Accordingly, this step amounts to adding insignificant post-solution activity to the judicial exception, as discussed in MPEP § 2106.05(g); and/or generally linking the use of a judicial exception to a particular technological environment or field of use, as discussed in MPEP § 2106.05(h).
With regards to the recited hardware processor and “libraries” (i.e. databases), these are recited at a high level of generality and thus can be viewed as nothing more than an attempt to generally link the use of the judicial exception to the technological environment of a computer. Applicant is reminded that “generic computer components such as a computer and database do not satisfy the inventive concept requirement.” See MPEP 2106.05(h).
In summary, the additional elements discussed above (i) do not constitute a particular machine or manufacture that is integral to the claim (and instead merely add insignificant pre-solution activity), (ii) do not improve the functioning of a computer or other technology, (iii) do not effect sufficiently a transformation or reduction of a particular article to a different state or thing, and (iv) are not applied in any meaningful way to do more than link the judicial exception to a particular technological environment to carry out the abstract idea. See MPEP §§ 2106.05(a), (b), (c), (e), (f), and (h). Consequently, the claimed invention does not integrate the abstract idea into a “practical application.”
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the above non-abstract steps (including the full limitations and not just the verbs) amount to nothing more than insignificant extra-solution activity and/or instructions to “apply” the exception in a generic way. As explained by the Supreme Court, the addition of insignificant extra-solution activity does not amount to an inventive concept, particularly when the activity is well-understood or conventional. Parker v. Flook, 437 U.S. 584, 588-89, 198 USPQ 193, 196 (1978). See MPEP 2106.05(g). In this case, the specification teaches routine and conventional libraries, sequencing devices, and computer hardware for carrying out the above non-abstract steps [0044-0058]. Moreover, Brettschneider et al. (TECHNOMETRICS, AUGUST 2008, VOL. 50, NO. 3, pp.241-264) teaches methods of quality assessment for short oligonucleotide microarray data, including receiving oligonucleotide data obtained from microarrays and outputting statistical reports relating to the quality of said data [See Figures A2, A3, B1, B3]. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract steps and elements being claimed. See MPEP 2106.05(d)(Part II).
In addition, with regards to the claimed hardware processor, as explained with respect to Step 2A Prong Two, the courts have also explained that the use of generic computer elements do not alone transform an otherwise abstract idea into patent-eligible subject matter. See DDR Holdings (Fed. Cir. 2014). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception, i.e. the additional components/steps of the claim add nothing that is not already present when the steps are considered separately. Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
The dependent claims 3-7, 9-11, 15-19, 21-23, 27, 29-31, 33-35, 37-48 have been considered under the two-part analysis, but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception. Regarding claim(s) 3-7, 9-12, 15-19, 21-24, 27, 29-31, and 33-36, all of these claims also further limit the nature of the data used by the abstract idea and/or specificity of the abstract idea set forth above. As such, the claimed subject matter is not patent eligible for reasons set forth above in the Step 2A (prong 1) analysis or the Step 2A (prong 2)/Step 2B analysis. Regarding claim(s) newly added claims 37-45, all of these claims also further limit the nature of the data used by the abstract idea and/or specificity of the abstract idea set forth above. As such, the claimed subject matter is also not patent eligible for reasons set forth above in the Step 2A (prong 1) analysis or the Step 2A (prong 2)/Step 2B analysis. Regarding claim(s) 46-48, these claims further comprise sequencing the oligo library or using the library as a control (i.e. necessary data collection). As such, the claimed subject matter is not patent eligible for reasons set forth above in the Step 2A (prong 1) analysis or the Step 2A (prong 2)/Step 2B analysis.
Therefore, based on the two-part analysis, the instantly rejected claims as a whole are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. For additional guidance, applicant is directed generally to the October 2019 Revised Patent Subject Matter Eligibility Guidance.
Response to Arguments
Applicant’s arguments, filed 08/29/2025, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the amended claims integrate the judicial exception into a practical application, citing steps (e) and (f). In response, this argument is not persuasive for reasons set forth above. In particular, step (e) has been interpreted as part of the abstract idea and Applicant is reminded that the claimed invention’s use of the ineligible concept to which it is directed (i.e. the abstract idea) cannot supply the inventive concept that renders the invention ‘significantly more’ than that ineligible concept.” BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018). With regards to step (f), this limitation is generically recited and not limited to any particular acts or operations. As such, under the BRI, this step is broadly interpreted as performing sequencing to obtain additional information (as intended use recitations are not given patentable weight). In addition, to the extent that applicant intends for the claim to be testing a sequencer device, it is noted with particularity that examples of activities that the courts have found to be insignificant extra-solution activity include testing a system for a response, the response being used to determine system malfunction, In re Meyers, 688 F.2d 789, 794; 215 USPQ 193, 196-97 (CCPA 1982). MPEP 2106.05(g). Accordingly, this step amounts to adding insignificant post-solution activity to the judicial exception, as discussed in MPEP § 2106.05(g); and/or generally linking the use of a judicial exception to a particular technological environment or field of use, as discussed in MPEP § 2106.05(h). For these reasons, and absent any evidence to the contrary, the rejection is maintained.
Claim rejections - 35 USC § 112, 2nd Paragraph
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-7, 9-11, 13, 15-19, 21-23, 25, 27, 29-31, 33-35, 37-48 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1, 13, 25 is/are also rejected due to said dependency.
Claims 1, 13, 25 recite “(b) calculate, using a determined ratio of concentrations and a determined ratio of signals from the genetic sequencing results, at least one prediction band based on the multiple libraries…”. There is lack of antecedent basis for “a determined ratio of concentrations and a determined ratio of signals”, as there are no previous steps for actually determining these ratios. Stated differently, the claim appears to be “using” information that has not been previously obtained. There is support for receiving read information that “comprises a corresponding concentration and signal value”. However, this does not inherently provide support for a “ratio of concentration” and a “ratio of signals”, and this position is supported by Applicant’s own specification (which teaches that these features must be calculated [0017]). Clarification is requested via amendment.
Claims 1, 13, 25 recite “evaluate a relative quality of an oligonucleotide library…based on the final prediction band.” It is unclear in what way the evaluation step is “based on the final prediction band”. Such generic functional claim language amounts to descriptions of problems to be solved and a review of the specification does not provide any guidance on this issue (mathematical, computationally, or otherwise). Therefore, the claim(s) is/are indefinite for failing to point out the requisite computational techniques that are included or excluded by the claim language, such that the artisan would know how to avoid infringement. Clarification is requested via amendment.
Claims 1, 13, 25 recite “(f) determine, using a sequencing device, sequence information for a sample which comprises the oligonucleotide library derived from the new preparation to determine whether the sequencing device properly identifies the oligonucleotide library derived from the new preparation comprising at least metrics of the final prediction band to be presented to a user”. It is unclear what positive process limitation is intended by the above “determine” step for the following reasons. (1) In particular, it is unclear what limiting effects is/are intended by a “sample which comprises the oligonucleotide library derived from the new preparation to determine whether the sequencing device properly identifies the oligonucleotide library derived from the new preparation comprising at least metrics of the final prediction band to be presented to a user”. This phrase confusingly describes the environment in which the sample/library was obtained (at a previous time period) in combination with additional intended use limitations and conditional limitations. Applicant is reminded that claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed. MPEP 2111.04. (2) In addition, the term “properly” is relative and the specification does not provide any limiting definitions, specific properties, or scoring criteria indicating the scope of this term, i.e. the result is subjective and imperceptible. As a result, the claim is also indefinite for failing to point out the requisite computational techniques that are included or excluded by the claim language, such that the artisan would know how to avoid infringement, i.e. in what way is the oligonucleotide library “properly identified.” A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. Clarification is requested via amendment.
Cited Prior Art
The following prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Trivedi et al. (Front. Genet., May 2014, Vol. 5, Article 111, pp.1-13), which teaches methods for evaluating quality control of next-generation sequencing data without a reference.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619