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.
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.
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.
Information Disclosure Statement
The Information Disclosure Statement filed on 05/25/2022 have been considered in part. The information disclosure statement fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. It has been placed in the application file, but the information referred to therein has not been considered. A signed copy of list of references cited from the IDS is included with this Office Action.
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 attached 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.
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 attached 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 attached 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.
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/K.K./ Examiner, Art Unit 1686
/LARRY D RIGGS II/ Supervisory Patent Examiner, Art Unit 1686