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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 17 September 2025 has been entered.
Status of the Claims
The claim set received 08 August 2025 has been entered into the application.
Claims 1 and 46 are amended.
Claim 48 is new.
Claims 2, 7, 13, 19-37, 40-41 and 43 are previously cancelled.
Claim(s) 1, 3-6, 8-12, 14-18, 38-39, 42, and 44-48 are pending.
Priority
Acknowledgment is made of applicant’s claim for priority as 371 of PCT/US2019/041447 filed 11 July 2018 which claims priority to US Provisional Application 62/696,783.
Claim Rejections - 35 USC § 101
The instant rejection is maintained for reason for record in the Office Action mailed 01 July 2025 and modified in view of the amendments filed 28 August 2025.
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, 3-6, 8-12, 14-18, 38-39, 42, and 44-47 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Following the flowchart of MPEP 2106
Step I - Process, Machine, Manufacture or Composition
Claims 1, 3-6, 8-12, 14-18, 38-39, 42, and 44-47 are directed towards a computer implemented method, so a process.
2A Prong I - Identification of an Abstract Idea
Claim 1 recites a computer-implemented method for determining whether two sample are associated with the same human patient while claim 48 was added to recite a method for performing diagnostic testing for pathogens in a human subject. Here, although claims 1 and 48 are drawn to different inventions, their claimed steps are the same. Thus, the claims are examined similarly.
Claims 1 and 48 recite:
Wherein the first sequencing library is an RNA sequencing library generated from a plurality of nucleic acid molecules of a first human patient sample and the second sequencing library is a DNA sequencing library generated from a plurality of nucleic acid molecules of a second human patient sample
This step is a description of the provided sequence libraries that will be sequenced to provide sequence data which will be processed by the abstract idea/mental processes.
(c) identifying one or more polymorphisms from the human nucleic acid sequences in the first sequencing library and one or more polymorphisms from the human nucleic acid sequences in the second sequencing library
This step can be performed in the human mind by observing and evaluating the polymorphism from the first and second sequencing libraries to identify polymorphisms and is therefore an abstract idea.
(d) assigning an index to each polymorphism of the one or more polymorphisms of the first sequencing library and the one or more polymorphisms of the second sequencing library using a particular hash function, such that the index assigned to a given polymorphism for the RNA sequencing library is the same as the index assigned to the same given polymorphism for the DNA sequencing library
This step can be performed in the human mind by following instructions to assign an index to each of the polymorphism of the first and second sequencing libraries using the same hash function such that the index assigned to the RNA sequencing library is the same as the DNA sequencing library and is therefore an abstract idea. This step encompasses using RNA and DNA sequence information (i.e., polymorphism data), manipulating the data using mathematical functions (i.e., particular hash function), and organizing the sequence data into a new form (i.e., indexes) which encompasses performing mathematical computations and is therefore an abstract idea. See MPEP 2106.04(a)(2)(A)(iv).
(e) comparing the one or more polymorphisms from the first sequencing library to the one or more polymorphisms from the second sequencing library by comparing the indexes representing the one or more polymorphisms of the RNA sequencing library and the indexes representing the one or more polymorphisms of the DNA sequencing library
This step can be performed in the human mind by observing and comparing polymorphisms from the first and second sequencing libraries by comparing the indexes representing polymorphisms of the RNA and DNA sequencing libraries and is therefore an abstract idea.
(f) determining if the first sample and the second sample are associated with the same human patient based on the comparison of the indexes
This step can be performed in the human mind by observing, comparing, evaluating the indexes to determine if the first and second sample are associated with the same human patient and is therefore an abstract idea.
Claims 3-6, 8, 10-11, 16-18, 38-39, and 44-47 are further drawn to limitations that describe the abstract ideas of claim 1 and are therefore also abstract ideas.
Claim 9 recites preparing the RNA and DNA sequencing libraries separately while claim 42 recites preparing the RNA and DNA sequencing libraries simultaneously. These claims are not interpreted as physical steps or physically preparing the sequencing libraries. The claims are interpreted as mere descriptions of how the data in the libraries was prepared. Therefore, the limitations of claims 9 and 42 merely provide descriptions of the sequencing libraries claim 1 step (a).
2A Prong II - Consideration of Practical Application
Claims 1 and 48 do not recite any additional elements which integrate the recited judicial exception into a practical application. Here, in the instant case the claims merely set forth methods of data analysis for comparing polymorphism data from a first sample and a second sample to determine if the first and second samples are associated with the same human patient. As such, practicing the claims merely results in determining if samples originate from the same patent based on assigned indexes encompassing and representing polymorphisms from RNA and DNA sequencing libraries. Such a result only produces information (i.e., polymorphism data) and does not provide for a practical application in the real-world realm of physical things and acts, i.e., the claims do not utilize the data generated by the judicial exception to affect any type of change. See MPEP 2106.04(a)(2)(A)(iv). Therefore, the provided sequencing libraries, sequenced libraries, identified polymorphisms, assigned indexes, and the abstract ideas do not construct a practical application such as treating a subject, transformation of matter, or improving upon an existing technology.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses 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.
2B Analysis - Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea.
The additional element of providing sequencing libraries of claim 1 step (a) and claim 48 step (a) does not add more to the recited judicial exception because providing sequencing libraries that are further sequenced to provide a source of DNA and/or RNA data that is subsequently analyzed by the abstract is deemed well-known and conventional. Seep MPEP 2106.05(d)(II)(v) and (vii).
The additional element of data gathering of claim 1 step (b) and claim 48 step (b) does not add more than the recited judicial exception because sequencing DNA and RNA to provide nucleic acid data that is subsequently analyzed by the abstract is deemed well-known and conventional. Seep MPEP 2106.05(d)(II)(v) and (vii).
The additional element of generating sequencing libraries of claim 6 does not add more than the recited judicial exception because generating sequencing libraries that are further sequenced to provide a source of DNA and/or RNA data that is subsequently analyzed by the abstract is deemed well-known and conventional.
The recited additional element of utilizing synthesis or nanopore sequencing of claim 10 does not add significantly more to the judicial exception because using nanopore sequencing to obtain sequencing data that is subsequently analyzed by the abstract idea is deemed well-known and conventional. Seep MPEP 2106.05(d)(II)(v) and (vii).
The recited additional element of utilizing reverse transcribing of RNA molecules of claim 11 does not add significantly more to the judicial exception because reverse transcribing RNA sequence data to obtain complementary DNA (cDNA) data that is subsequently analyzed by the abstract idea is deemed well-known and conventional. Seep MPEP 2106.05(d)(II)(v) and (vii).
The additional element of using cell of claim 12 does not add more than the recited judicial exception because using cells and lysing cells to obtain nucleic acids that are subsequently analyzed by the abstract idea is deemed well-known and conventional. See MPEP 2106.05(d)(II).
The additional element of using body fluids of claims 14 and 15 does not add more than the recited judicial exception because using body fluids to provide samples of nucleic acids that are subsequently analyzed by the abstract idea is deemed well-known and conventional. Seep MPEP 2106.05(d)(II).
In conclusion, and when viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments and amendments, filed 28 August 2025, have been fully considered but the rejection is maintained.
The Applicant states “claim 1 can still be patent-eligible if it improves an existing technical field. Even if the method of claim 1 gathers and analyzes information using allegedly conventional techniques and does not improve over these allegedly conventional techniques, claim 1 can still provide an improvement to an existing technical field-in particular, the field of diagnostic testing, and therefore be patentable subject matter. As stated in Applicant's previous argument, claim 1 involves a specific method of determining whether two samples are associated with the same human patient. This specific method is a specific improvement in the field of diagnostic testing over prior systems. This is indicative that an additional element has integrated the alleged exception into a practical application, even though claim 1 does not explicitly recite an improvement to diagnostic testing.” [remarks, page 8]. The Applicant points to MPEP 2106.04(d) and 2106.04(d)(I) for guidance [remarks, page 7].
In response, the claims are drawn to merely gathering and analyzing information (i.e., RNA and DNA sequencing library data) using conventional techniques (i.e., providing nucleic acid libraires and sequencing the nucleic libraries) and displaying the result (i.e., determining if the first and second sample are from the same human patient). See MPEP 2106.05(a)(II)(iii). Additionally, claim 1 does not contain or recite any additional elements other than additional elements for providing nucleic acid sequencing libraries and sequencing the nucleic acids which is not indicative that an additional element has integrated the recited judicial exception into a practical application. Moreover, the claims are entirely drawn to nucleic acid sequence data analysis that can be performed by the human mind or math, or with the aid of a generic computer merely for programming efficiency. The steps are not applied to any additional elements so as to result in a practical application or an improvement to technology. Here, it appears that the claims are drawn to an abstract idea that results in a computational process that is more efficient than others known in the art. However, novel or improved abstract idea steps alone are not deemed to be “an improvement to technology.” Therefore, under Step 2A Prong II of the 101 analyses, the claims are not patent eligible.
The Applicant states “the Examiner has not established whether or not Claim 1 as a whole, or even each of steps (c)-(f), is well-known and conventional.” The Applicant points to the MPEP 2106.05 for guidance. The Applicant states “claim 1, when viewed as a whole is not a conventional method. For example, the Examiner has withdrawn the 35 U.S.C. § 103 rejection to the claims (See Office Action at pp. 13-15), indicating that the claims are not obvious variants from the prior art. When reviewing claim 1, as a whole, the method involves sequencing a first RNA sequencing library and a second DNA sequencing library, identifying one or more polymorphisms in those libraries, assigning an index to each polymorphism in the libraries using the particular hash function, such that the index assigned to a given polymorphism for the RNA sequencing library is the same as the index assigned to the same polymorphism for the DNA sequencing library, comparing polymorphisms and determining if the first sample and the second sample are associated with the same human patient based on the comparison of the indexes. This overall method is not conventional nor well known. Thus, claim 1 as a whole possesses an inventive concept that as a whole is sufficient to ensure that the claim as a whole amounts to significantly more than the alleged judicial exception under the Step 2B analysis.” [remarks, page 9].
In response, and with respect to the withdrawal of the 35 U.S.C § 103 rejection, it is noted in the MPEP 2106.05(I) states “Although the courts often evaluate considerations such as the conventionality of an additional element in the eligibility analysis, the search for an inventive concept should not be confused with a novelty or non-obviousness determination. See Mayo, 566 U.S. at 91, 101 USPQ2d at 1973. As made clear by the courts, the "‘novelty’ of any element or steps in a process, or even of the process itself, is of no relevance in determining whether the subject matter of a claim falls within the § 101 categories of possibly patentable subject matter." Intellectual Ventures I v. Symantec Corp. In addition, the search for an inventive concept is different from an obviousness analysis under 35 U.S.C § 103. Specifically, lack of novelty under 35 U.S.C § 102 or obviousness under 35 U.S.C § 103 of a claimed invention does not necessarily indicate that additional elements are well-understood, routine, conventional elements. Because they are separate and distinct requirements from eligibility, patentability of the claimed invention under 35 U.S.C § 102 and 103 with respect to the prior art is neither required for, nor a guarantee of, patent eligibility under 35 U.S.C § 101”.
Furthermore, and with respect to claim 1 step (c)-(f), the claimed steps are not drawn to well-known and conventional additional elements because the claimed steps are abstract ideas/mental processes/mathematical concepts performed in the human mind as noted in the 35 U.S.C § 101 rejection above. Here, the ordered combination of steps encompasses providing sequencing libraries and sequencing the libraries for gathering sequencing data that is subsequently analyzed by the abstract ideas (i.e., identifying polymorphisms, assigning an index, comparing polymorphisms, and determining if samples are associated with the same human patient). Furthermore, the claims further recite abstract ideas because the claims are drawn to "collecting information (i.e., sequencing data), analyzing it, and displaying certain results of the collection and analysis where, here, the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind”, "comparing RNA and DNA nucleic acid sequences and determining the existence of alterations to determine if the first and second sample are associated with the same human patient where, here, the claims cover any way of comparing nucleic acid sequences such that the comparison steps can practically be performed in the human mind”, and “collecting and comparing known information (nucleic acid data) which are steps that can be practically performed in the human mind” which reads on abstract ideas. See MPEP 2106.04(a)(2)(III)(A). Thus, claim 1 is drawn to abstract ideas that are evaluated under Step 2A Prong I of the 101 analyses and not evaluated under Step 2B of the101 analyses.
Additionally, the claims are drawn to amplifying and sequencing nucleic acids to provide sequence information (i.e., DNA/RNA data) to detect allelic variants to determine if the first and second samples are from the same human patient which does not provide unconventional and not well-known methods for analyzing nucleic acid data. See MPEP 2106.05(d)(II) (i-iii, v, vii). Thus, the claimed steps are drawn to abstract ideas, and the claims utilize well-known, routine, and conventional additional elements for analyzing nucleic acid data for determining allelic variants in order to determine if a first and second sample are associated with the same human patient which does not provide significantly more than the recited judicial exception. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
The Applicant states “Claim 48 uses the alleged judicial exception in a manner that imposes a meaningful limit on the alleged exception, such that the claim is more than a drafting effort designed to monopolize the alleged exception. Claim 48 provides an improvement to the technical field of diagnostic testing, which is indicative that an additional element has integrated the alleged exception into a practical application. Thus, claim 48 is patent-eligible under 35 U.S.C. § 101.
In response, claim 48 does not integrate the recited judicial exception into a practical application because the claim does not encompass any additional elements that integrate the result of determining if the first and the second samples are associated with the same human patient. Here, the result is not applied to administering a particular treatment, a transformation of matter, and/or applied with or by use of a particular machine. Additionally, claim 48 is drawn to gathering and analyzing information (i.e., DNA and RNA sequence data) using conventional techniques (i.e., providing nucleic acid sequencing libraries and sequencing of the nucleic acid libraries) and displaying the results (i.e., determination if the first and second sample are associated with the human patient) which is insufficient to show an improvement to technology. See MPEP 2106.05(a)(II)(iii).
Conclusion
Claims 1-6, 8-12, 14-19, 38-39, 42, and 44-47 are rejected.
No claims are allowed.
Finality
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH C PULLIAM whose telephone number is (571)272-8696. The examiner can normally be reached 0730-1700 M-F.
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/J.C.P./ Examiner, Art Unit 1687
/Anna Skibinsky/
Primary Examiner, AU 1635