DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) 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.
Applicant's response, filed on 04/09/2026, has been fully considered. 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 1-18 are canceled.
Claims 19, 26 and 35 are independent claims.
Claims 19-36 are pending and examined on the merits.
No claims are amended.
Claim set filed 10/06/2022 is examined below.
Priority
As detailed on the 06/01/2022 filing receipt, this application claims domestic priority to as early as 04/30/2010. This application is a CON of 15/928,202 filed 03/22/2018 which is a CON of 13/097,328 filed 04/29/2011 which claims benefit of 61/426,826 filed 12/23/2010 and claims benefit of 61/330,118 filed 04/30/2010.
Drawings
The drawings filed 03/21/2022 are accepted.
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 19-36 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Analysis of claims in Step 1.
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Independent claim 19 is directed to a 101 machine or manufacture, here a "system," with non-transitory elements such as "a nucleic acid sequencer; a memory; and a processor."
Independent claim 26 is directed to a 101 process, here a "method for identifying a fusion junction in a human transcriptome suspected of containing a gene fusion," with process steps such as "preparing…, detecting…"
Independent claim 35 is directed to a 101 machine or manufacture, here a "computer program product, non-transitory computer-readable storage medium."
[Step 1: claims 19-36: YES]
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Mental processes recited include:
Claims 19, 26 and 35 recite: "detect a plurality of signals during sequencing, the signals representative of nucleic acid sequences corresponding to the nucleic acid fragments…; generate the stored list of exon prefix sequences by comparing exons of the human genome to the read sequence and identifying the exons that have a prefix sequence mapping to a suffix sequence of the read sequence, generate the stored list of exon suffix sequences by comparing exons of the human genome to the read sequence and identifying the exons that have a suffix sequence mapping to a prefix sequence of the read sequence, select a pair of exon sequences from the stored lists of exon prefix sequences and exon suffix sequences, a first exon sequence of the pair being one of the exon suffix sequences and a second exon sequence of the pair being one of the exon prefix sequences, calculate a sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and a constant, and if the sum equals a length of the read sequence, identify a fusion junction between exons associated with the first exon sequence and second exon sequence in the human transcriptome, and identify a presence of a gene fusion in the human transcriptome based on the identified fusion junction, and if the sum does not equal a length of the read sequence, repeat the selecting of a pair of exon sequences and calculating of the sum for a different pair of exon sequences from the stored lists of exon prefix sequences and exon suffix sequences." The recited claim limitations are acts of evaluating, analyzing, observing and judging data that could be practically performed in the human mind and/or with pen and paper.
Claims 22 and 29 recite: "generate the stored list of exon prefix sequences by identifying the exons that have a prefix sequence mapping to a suffix sequence of the read sequence by at least a minimum number of sequence elements, and generate the stored list of exon suffix sequences by identifying the exons that have a suffix sequence mapping to a prefix sequence of the read sequence by at least the minimum number of sequence elements." Generating a list, mapping and identifying are acts of evaluating, analyzing, organizing and judging data that could be practically performed in the human mind and/or with pen and paper.
Claims 34 and 36 recite: "calculate a confidence value for the fusion junction based on a number of unique read sequences corresponding to the fusion junction." Calculating is an act of evaluating, analyzing and judging data that could be practically performed in the human mind and/or with pen and paper.
Mathematical concepts recited include:
Claims 19, 26 and 35 recite: "calculate a sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and a constant, and if the sum equals a length of the read sequence… calculating of the sum for a different pair of exon sequences from the stored lists of exon prefix sequences and exon suffix sequences." Calculating requires performing a series of mathematical calculations and are mathematical concepts and/or formulas.
Claims 34 and 36 recite: "calculate a confidence value for the fusion junction based on a number of unique read sequences corresponding to the fusion junction." Calculating requires performing a series of mathematical calculations and are mathematical concepts and/or formulas.
Claims 19, 26 and 35 are involved with identifying, detecting, comparing, selecting, calculating and generating a list; claims 22 and 29 are involved with generating a list and identifying; claims 34 and 36 are involved with calculating. These claim elements are involved with acts of evaluating, analyzing, observing, organizing and judging data as indicated above. Acts of evaluating and analyzing data could be practically performed in the human mind and/or with pen and paper because they merely require making observations, evaluations, judgments, and opinions (See MPEP 2106.04(a)(2) subsection III). Although, claims 19, 22, 26, 29 and 34-35 recite a processor and performing the method as part of a method executed on a computer, there are no additional limitations to indicate that anything other than a generic computer is required. However, merely requiring that the steps are carried out with a generic computer does not negate the mental nature of these steps and equates rather to merely using a computer as a tool to perform the mental process. Therefore, under the broadest reasonable interpretation, the indicated claims above can be practically carried out in the human mind or with pen and paper as claimed, which falls under the "Mental processes" grouping of abstract ideas.
Claims 19, 26 and 34-36 recite mathematical concepts and formulas as discussed above. The process of calculating a sum and a confidence value requires performing a series of mathematical calculations and are mathematical concepts and/or formulas that falls under the “mathematical concepts” grouping of abstract ideas.
As such, claims 19-36 recite an abstract idea (Step 2A, Prong 1: YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The above indicated judicial exceptions are not integrated into a practical application because the claims do not recite an additional elements that apply, rely on or use the judicial exception in such a manner to amount to integration into a practical application. For example, there are no limitations that reflect an improvement to technology or applies or uses the recited judicial exception in some other meaningful way. Rather, the instant claims recite additional elements that equate to mere instructions to implement an abstract idea or insignificant extra solution activity. Specifically, the instant claims recite the following additional elements:
Claim 19 recites "receive a plurality of nucleic acid fragments of a fragment library, the fragment library comprising nucleic acid fragments created from the human transcriptome, provide reagents for sequencing the nucleic acid fragments," "memory comprising a stored list…," "processor," “obtain a plurality of read sequences based on the detected plurality of signals from the nucleic acid sequencer, the read sequences respectively corresponding to the nucleic acid sequences,” and “generate the stored list…”
Claim 22 recites “wherein the processor is further configured to, for each read sequence: generate the stored list…”
Claim 26 recites "preparing a fragment library from nucleic acids isolated from the human transcriptome; providing a plurality of nucleic acid fragments of the fragment library to a sequencing instrument," "processor to: obtain a plurality of read sequences based on the detected plurality of signals from the nucleic acid sequencer," and " generate the stored list…"
Claim 29 recites "wherein the processor is further configured to, for each read sequence: generate the stored list…"
Claim 34 recites “using the processor…”
Claim 35 recites " A computer program product, comprising a non-transitory computer-readable storage medium whose contents include a program with instructions being executed on a processor…," "…receive a plurality of nucleic acid fragments of a fragment library, the fragment library comprising nucleic acid fragments created from the human transcriptome, into a sequencing instrument," “…provide reagents for sequencing the nucleic acid fragments” and "…generate, for each read sequence, a list of exon suffix sequences…"
Claim 36 recites " The computer program product of claim 35, wherein the instructions…"
The elements of claims 19, 22, 26, 29, and 34-36 as indicated above equate to insignificant extra solutional activities of data gathering and outputting. For instance, limitations of receiving nucleic acid fragments and obtaining read sequences in claims 19, 26 and 35 are data gathering activities. Data gathering serves as input to the recited judicial exception in the claims. The limitation of generating a list in claims 19, 22, 26, 29 and 35 equates to outputting data. (See MPEP 2106.05(g)). Claims 19, 22, 29 and 34-36 also recite “memory,” “computer program product,” “a non-transitory computer readable storage medium" and "processor," which equate to generic computer components. These claims invoke the computer components merely as tools to execute the abstract idea. The use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application or provide significantly more. (see MPEP 2106.05(f)). Additionally, the listed additional elements are mere instructions to apply an exception because they recite no more than an idea of a solution or outcome and does not recite a technological solution to a technological problem. (See MPEP 2106.05(f)(1)). As such, as currently recited, the claims do not appear to recite an improvement to technology or apply or use the recited judicial exception in some other meaningful way. Therefore, claims 19-36 are directed to an abstract idea (Step 2A, Prong 2: NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to well-understood, routine and conventional activities, insignificant extra-solution activity or mere instructions to implement the abstract idea on a generic computer. The instant claims recite the following additional elements:
Claim 19 recites "receive a plurality of nucleic acid fragments of a fragment library, the fragment library comprising nucleic acid fragments created from the human transcriptome, provide reagents for sequencing the nucleic acid fragments," "memory comprising a stored list…," "processor," “obtain a plurality of read sequences based on the detected plurality of signals from the nucleic acid sequencer, the read sequences respectively corresponding to the nucleic acid sequences,” and “generate the stored list…”
Claim 22 recites “wherein the processor is further configured to, for each read sequence: generate the stored list…”
Claim 26 recites "preparing a fragment library from nucleic acids isolated from the human transcriptome; providing a plurality of nucleic acid fragments of the fragment library to a sequencing instrument," "processor to: obtain a plurality of read sequences based on the detected plurality of signals from the nucleic acid sequencer," and " generate the stored list…"
Claim 29 recites "wherein the processor is further configured to, for each read sequence: generate the stored list…"
Claim 34 recites “using the processor…”
Claim 35 recites " A computer program product, comprising a non-transitory computer-readable storage medium whose contents include a program with instructions being executed on a processor…," "…receive a plurality of nucleic acid fragments of a fragment library, the fragment library comprising nucleic acid fragments created from the human transcriptome, into a sequencing instrument," “…provide reagents for sequencing the nucleic acid fragments” and "…generate, for each read sequence, a list of exon suffix sequences…"
Claim 36 recites " The computer program product of claim 35, wherein the instructions…"
The additional elements indicated above do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. The limitations equate to mere data gathering activities, which are insignificant extra solutional activities. 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. (see MPEP 2106.05(g)). Also, limitations that equate to mere data gathering and outputting via generic computer components, such as receiving data at a computer or outputting data, amount to insignificant extra-solution activity as set forth by the courts in Mayo, 566 U.S. at 79, 101 USPQ2d at 1968 and OIP Techs., Inc, v, Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015). Also, the additional elements include storing and retrieving information in memory. Storing and retrieving information in memory were identified by the courts as well-understood, routine and conventional in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93. Also, the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application or provide significantly more as identified by the courts in Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Additionally, the claim limitations of preparing nucleic acid libraries and sequencing are well known and conventional as disclosed by Shendure (Next-generation DNA sequencing. Nat Biotechnol. 2008 Oct;26(10):1135-45. doi: 10.1038/nbt1486. PMID: 18846087.; as cited on the 05/25/2022 IDS Document and on the 01/09/2026 892 form). The courts have also recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity: Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546 and Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014) (See MPEP 2106.05(a)(II)). Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 19-36 are not patent eligible.
Response to 35 USC § 101 Arguments (Remarks filed 04/09/2026, pages 2-10)
It is noted that Applicant did not amend any claims.
Under Step 2A, Prong 1 of the 101 analysis, Applicant states that the human mind is not equipped to perform the actions of claim 1 at least because of the overwhelming volume of data being processed. Applicant refers to paragraph 33 of the Specification and cites that “if a million tests were executed each second, it would take about 76 thousand years to complete all the tests." Therefore, Applicant asserts that the steps of the claim are computation steps that cannot be performed in the human mind.
In response, Applicant’s arguments are not persuasive because there is no indication in the claims that the process or amount of data is too complicated or too large to be performed by the human mind and/or with pen and paper. As disclosed in MPEP 2111.01 (II), “Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment." Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).
It is also acknowledged that such computations performed mentally, or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.), 687 F.3d 1266,1278 (Fed. Cir. 2012) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations). Therefore, independent claim 1 recites mental process and mathematical concepts as discussed in the 101 rejection section above.
Under Step 2A, Prong 2 of the 101 analysis, Applicant's states that the claims are patent eligible for similar reasons that rendered the claims in McRO patent eligible as the claims, when considered as a whole, are directed toward a practical application and provide an improvement in the technological process of transcriptome fusion detection. Applicant states that the claimed subject matter goes beyond any abstract idea by enabling use of technological improvements for identification of fusion junctions and gene fusions with a high degree of efficiency and accuracy.
In response, Applicant’s arguments are not persuasive because any improved accuracy is due to the recited abstract idea. The asserted improvement in transcriptome fusion detection, which is in itself an improvement to the abstract idea. The claimed subject matter does not improve the operation of a polynucleotide sequencer or a computer. Instead, any improvement is due to an improved abstract idea.
Under Step 2B of the 101 analysis, Applicant's states the Office Action fails to provide any factual evidence or other citations noted above for supporting an assertion of the claims being well-understood, routine or conventional. Applicant mentions that the Office Action acknowledges that "[n]o prior art is applied to claims 19-36" and that "it is not clear that any combinable art of record would have rendered the claims obvious." Office Action at p. 11. Applicant states that based on this language and the lack of any factual evidence provide to support the assertions regarding the various claim elements being well-understood, routine, or conventional, Applicant submits that the claims as a whole cannot be considered to recite well-understood, routine or conventional activity subject matter.
In response, Applicant’s arguments are not persuasive. According to MPEP 2106.07(a), when the examiner has concluded that certain claim elements recite well understood, routine, conventional activities in the relevant field, the examiner must expressly support the rejection in writing with one of the four options specified in Subsection III of MPEP 2106.07(a). One of the listed supports that could be utilized is a citation to one or more of the court decisions discussed in MPEP § 2106.05(d), subsection II, as noting the well-understood, routine, conventional nature of the additional element(s). As disclosed in the 101 rejection section above and in the previous office action, limitations that equate to mere data gathering and outputting via generic computer components, such as receiving data at a computer or outputting data, amount to insignificant extra-solution activity as set forth by the courts in Mayo, 566 U.S. at 79, 101 USPQ2d at 1968 and OIP Techs., Inc, v, Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015). Also, storing and retrieving information in memory were identified by the courts as well-understood, routine and conventional in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93. Shendure was also cited for disclosing preparing nucleic acid libraries and sequencing, which are well known and conventional. The courts have also recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity: Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546 and amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014) (See MPEP 2106.05(a)(II)). Therefore, the burden of establishing the conventionality of the additional elements under Step 2B of the 101 analysis was adequately established.
Although there are no current art rejections, the courts mentioned that 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 Iv. Symantec Corp., 838 F.3d 1307, 1315, 120 USPQ2d 1353, 1358 (Fed. Cir. 2016) (quoting Diamond v. Diehr, 450 U.S. at 188-89, 209 USPQ at 9). (See MPEP 2106.05).
Regarding 35 USC 102/103 -- no art and no rejection applied
No prior art is applied to claims 19-36. Closest art, for example are Maher (“Transcriptome sequencing to detect gene fusions in cancer.” Nature vol. 458,7234 (2009): 97-101.; as cited on the 05/25/2022 IDS Document and on the 01/09/2026 892 form) and Berger ("Integrative analysis of the melanoma transcriptome." Genome research 20.4 (February 23, 2010): 413-427.; as cited on the 05/25/2022 IDS Document and on the 01/09/2026 892 form). While the art teaches methods for detecting gene fusions, it does not teach the limitation of "calculate a sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and a constant, and if the sum equals a length of the read sequence, identify a fusion junction between exons associated with the first exon sequence and second exon sequence in the human transcriptome, and identify a presence of a gene fusion in the human transcriptome based on the identified fusion junction, and if the sum does not equal a length of the read sequence, repeat the selecting of a pair of exon sequences and calculating of the sum for a different pair of exon sequences from the stored lists of exon prefix sequences and exon suffix sequences" in independent claims 19, 26 and 35 and it is not clear that any combinable art of record would have rendered the claims obvious.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KETTIP KRIANGCHAIVECH whose telephone number is (571)272-1735. The examiner can normally be reached 8:30am-5:00pm EDT.
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/K.K./ Examiner, Art Unit 1686
/LARRY D RIGGS II/ Supervisory Patent Examiner, Art Unit 1686
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