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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 05/12/2026 has been entered.
Applicant Response
Applicant's response, filed 05/12/2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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.
Claim Status
Claim 27 is newly added.
Claim 1-27 are pending and under examination herein.
Claims 1-27 are rejected.
Priority
The instant application is the National Stage entry of PCT/EP2018/068523, International Filing Date: 07/09/2018, which claims the benefit of foreign priority to 17182324.8, filed 07/20/2017. As such, the effective filing date assigned to each of claims 1-27 is 07/20/2017. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Drawings
The drawings were accepted by the examiner in the office action mailed 01/16/2020.
Claim Rejections - 35 USC § 101
MAINTAINED REJECTIONS:
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 1-27 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Newly recited portions are necessitated by claim amendments.
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 and a law of nature or natural phenomenon:
Claim 1 recites (a) aligning nucleic acid sequencing reads obtained from massively parallel sequencing of one or more genomic regions of the sample to the reference sequence; (b) selecting nucleic acid sequencing reads which only partially map to the reference sequence, wherein each of the selected nucleic acid sequencing reads comprises a portion at the start or at the end of the nucleic acid sequencing read that remains unmapped and that comprises a soft-clipped region of at least 8 nucleotides, wherein one or more of the at least 8 nucleotides of the soft-clipped region do not correspond with respective nucleotides of the reference sequence; (c) creating groups of the nucleic acid sequencing reads with the soft-clipped regions wherein each group is defined by an identical start position of the soft-clipped region at the end of the nucleic acid sequencing reads in the group or an identical end position of the soft-clipped region at the start of the nucleic acid sequencing reads in the group; (d) generating a synthetic consensus sequence for each group as obtained in step (c) by selecting the most abundant nucleotide at each position of the soft-clipped regions within each group and obtaining synthetic consensus sequences for all the groups created in step (c); (e) generating combinations of positions between the groups of the nucleic acid sequencing reads comprising the soft-clipped region at the start of the nucleic acid sequence and the groups of nucleic acid sequencing reads comprising the soft- clipped region at the end of the nucleic acid sequence reads by repeatedly comparing the synthetic consensus sequences of step (d) with the reference sequence; (f) detecting the structural genomic rearrangement by detecting that both synthetic consensus sequences of the pair obtained in step (e) match at the respective positions in the reference sequence and comprise a distance between the soft-clipped region at the start of the synthetic consensus sequence and the soft-clipped region at the end of the synthetic consensus sequence relative to the reference sequence of less than 100 kilobases (kb).
Claim 2 recites wherein the structural genomic rearrangement is a deletion, a duplication or an inversion of a length between 10 basepairs and 100,000 basepairs.
Claim 3 recites wherein each of the soft-clipped regions is at least 8 to 15 nucleotides long.
Claim 4 recites wherein the aligning and the comparing are performed with a string matching algorithm.
Claim 5 recites wherein the nucleic acid sequencing reads obtained from massively parallel sequencing is provided in a format providing information on alignment and the soft-clipped regions.
Claim 6 recites where the nucleic acid sequencing reads have a length of about 50 nucleotides to 50 kb.
Claim 8 recites wherein, in step (c), the groups which comprise less than a predefined number of members are discarded.
Claim 9 recites wherein said predefined number of members is 1, 2, 3, 4, 5, 6, 7 or 8.
Claim 10 recites wherein each of the synthetic consensus sequence is identical to a predefined number of sequencing reads in the group of nucleic acid sequencing reads as defined in step (c).
Claim 11 recites wherein said predefined number of sequencing reads is 1, 2, 3, 4 or more.
Claim 12 recites wherein, in step (e), combinations of positions between groups of nucleic acid sequencing reads comprising repetitive consensus sequences and/or a distance between the soft-clipped positions of the nucleic acid sequencing reads with respect to the reference sequence of more than 35 kb are discarded from further analysis.
Claim 13 recites further comprising determining sequencing depth at a position of the detected structural genomic rearrangement in the nucleic acid molecule and/or determining a position of the detected structural genomic rearrangement with respect to an annotated functional information.
Claim 14 recites wherein the structural genomic rearrangement detected in step (f) represent: (i) a duplication, when the nucleotide number in the reference sequence of the end position of the soft-clipped regions of at the start of the matched synthetic consensus sequences is smaller than the nucleotide number in the reference sequence of the start position of the soft-clipped regions at the end of the matched synthetic consensus sequences; (ii) a deletion, when the nucleotide number in the reference sequence of the end position of the soft-clipped regions at the start of the matched synthetic consensus sequences is larger than the start position of the soft-clipped regions at the end of the matched synthetic consensus sequences; or (iii) an inversion, when both members of the pair of said synthetic consensus sequences have the soft-clipped region at the start of the matched synthetic consensus sequences, or when both members of the pair have the soft- clipped region at the end of the matched synthetic consensus sequences.
Claim 15 further recites wherein the sample is from a patient with cancer.
Claim 19 recites wherein said cancer is breast cancer, prostate cancer, ovarian cancer, renal cancer, lung cancer, pancreas cancer, urinary bladder cancer, uterus cancer, kidney cancer, brain cancer, stomach cancer, colon cancer, melanoma, fibrosarcoma, gastrointestinal stromal tumor (GIST), glioblastoma or hematological leukemia and lymphomas, both from the myeloid and lymphatic lineage.
Claim 20 recites providing the report to a patient or to another person or entity, a caregiver, a physician, an oncologist, a hospital, clinic, third party payor, insurance company or government office.
Claim 21 recites wherein the report comprises one or more of (i) output from the method, comprising the identification of the structural genomic rearrangement or wild-type sequence associated with a tumor of the type of the sample; (ii) information on the role of a genomic alteration, or corresponding wild-type sequence, in a disease, wherein said information comprises information on prognosis, resistance, or potential or suggested therapeutic options; (iii) information on the likely effectiveness of a therapeutic option, the acceptability of the therapeutic option, or the advisability of applying the therapeutic option to a patient having a structural genomic rearrangement identified in the report; or (iv) information, or a recommendation on the administration of a drug, the administration at a preselected dosage, or in a preselected treatment regimen, in combination with other drugs, to the patient; (v) wherein not all structural genomic rearrangements identified in the method are specified in the report, and the report can be limited to alterations in genes of clinical relevance.
Claim 23 recites wherein the annotated functional information comprises a gene name or a location in an intron, exon, promoter, enhancer, telomere, pseudogene, or in a repetitive region.
Claim 24 recites wherein detecting the structural genomic rearrangement comprises detecting a breakpoint in the nucleic acid molecule relative to the reference sequence.
Claim 27 recites wherein the pair of the synthetic consensus sequences obtained in step (e) comprises soft-clipped regions that match at the respective positions in the reference sequence.
These recitations equate to steps of collecting information, analyzing data and making observations, evaluations and judgements that can be carried out in the human mind. Specifically, aligning reads obtained from massively parallel sequencing of genomic regions to reference sequences, selecting reads that only partially map to the reference sequence and comprises a soft-clipped region of at least 8 nucleotides long, creating groups of reads with the soft-clipped regions defined by the position of the soft-slipped read at the end of the nuclei acid sequencing or identical end positions of the soft-clipped regions at the start of the read, generating a synthetic consensus sequence for each group by selecting the most abundant nucleotide at each position of the soft-clipped regions within each group, obtaining synthetic consensus sequences for all groups, repeatedly comparing the synthetic consensus sequence to the reference sequence until a pair of the synthetic consensus sequences with soft-clipped regions which match at respective positions in the reference sequence is detected and generating combinations of positions between groups, detecting the structural genomic rearrangement when both synthetic consensus sequences of the pair match at respective positions in the reference sequence and comprise a distance between the soft-clipped region at the start of the synthetic consensus sequence and the soft-clipped region at the end of the synthetic consensus sequence relative to the reference sequence of less than 100 kilobases (kb), discarding groups with less than a predefined number of members discarding combinations of positions between groups with distance greater than 35kb to the reference sequence, and determining sequencing depth at the position of the detected structural genomic rearrangement or determining a position of the detected structural genomic rearrangement with respect to an annotated functional information can be practically performing the human mind as claimed and are similar to the concepts of collecting and comparing known information in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011) and collecting information, analyzing it, and reporting certain results of the collection and analysis in Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016) that the courts have identified as concepts that can be practically performed in the human mind. Therefore, each of the above recited limitations fall under the “Mental Processes” grouping of abstract ideas. Furthermore, the steps as claimed of providing a report to a patient or to another person or entity, a caregiver, a physician, an oncologist, a hospital, clinic, third party payor, insurance company or government office equate to the social activity of providing information to a person without interfering with the person’s primary activity as found in Interval Licensing LLC, v. AOL, Inc., 896 F.3d 1335, 127 USPQ2d 1553 (Fed. Cir. 2018), and therefore these limitations fall under the “Certain Methods Of Organizing Human Activity” grouping of abstract ideas. Claims 15-21 also recite a natural correlation between the presence of structural variants and response to a cancer therapy, and therefore fall under the “Laws of Nature or Natural Phenomena”. Claims 2-6, 9-11, 14, 19, 21, 23-24, and 27 further qualify the judicial exceptions. As such, claims 1-27 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). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere data gathering and outputting, and mere instructions to implement the abstract idea in a generic computing environment:
Claim 1 recites (h) reporting the structural genomic rearrangement of greater than 5 nucleotides, with exact location of breakpoint in the nucleic acid molecule, and comprising a deletion, a duplication, or an inversion in an electronic, web-based, or paper form.
Claim 7 recites wherein, in the nucleic acid sequencing reads comprising the soft- clipped sequencing reads obtained in step (b), information on the position of mapped portion of said reads is stored electronically.
Claim 16 recites comprising a preparation step for the nucleic acid molecule, which precedes step (a), comprising a hybrid-capture based nucleic acid enrichment for a genomic region of interest.
Claim 17 recites wherein said genomic region of interest is a gene or region known to be relevant in cancer.
Claim 18 recites wherein said sample comprises one or more premalignant or malignant cells; cells from a solid tumor, soft-tissue tumor or a metastatic lesion; tissue or cells from a surgical margin; a histologically normal tissue obtained in a biopsy; one or more circulating tumor cells (CTC); a normal, adjacent tissue (NAT) from a subject having a tumor or being at risk of having a tumor; or a blood, plasma or serum sample from a subject having a tumor or being at risk of having a tumor; or an paraffin or formalin-fixed paraffin-embedded (FFPE) tumor sample.
Claim 22 recites wherein the format comprises Binary Alignment Map (BAM) or Compressed Columnar File Format (CRAM).
Claim 25 recites wherein the format comprises Sequence Alignment Map (SAM).
Claim 26 recites wherein the string matching algorithm is Burrows-Wheeler Aligner (BWA).
Claims 2-6, 8-15, 19-21, 23-24, and 27 do not recite any elements in addition to the recited judicial exception. Claim 16 recites limitations of how data is gathered and claims 17-18, 22 and 25-26 further recite limitations on the type of data gathered. These limitations equate to selecting a particular data source or type of data to be manipulated to perform the mental evaluations and judgements (see MPEP 2106.05(g)). Claim 1 recites limitations on data outputting. There is no indication that any of these additional elements provide a practical application of the recited judicial exception outside of the judicial exception itself. Claims 7, 22 and 25 also merely recite storing data electronically and using digital data formats and claim 26 recites using a computer program to perform abstract ideas, which equate to using a generic computing systems and computer program products to carry out instructions to implement an abstract idea on a computer. The computer program product as claimed fails to recite details of how a solution to a problem is accomplished and only recites the idea of a solution or outcome. There are no limitations that indicate that the claimed steps require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. Furthermore, 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. See 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).As such, claims 1-27 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). Further analyzing the additional elements under step 2B, the additional elements as described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims under the 2B analysis, the instant specification discloses that a hybrid-capture based nucleic acid enrichment for a genomic region of interest as a preparation step for nucleic acid molecules for sequencing is well-known and conventional in the art (p 32, line 4-28). Furthermore, the prior art to Zhongwu Lai et al. (01/17/202 IDS, NPL ref #11; previously cited; hereafter referred to as Zhongwu) and Holland et al. (Forensic Science International: Genetics 2017, 28, 90-98; previously cited; hereafter referred to as Holland) disclose obtaining massively parallel sequencing information is a data gathering element that is routine, well-understood and conventional in the art (Zhongwu, abstract and p 2, col 1, para 1-2; Holland, abstract). Holland further discloses performing massively parallel nucleic acid sequencing and saving the output electronically (p 91, col 1, para 2-col 2, para 4). Guan and Sung (Methods 2016, 102, pp.36-49; previously cited) reviews structural variation detection using next-generation sequencing data and discloses that storing sequencing reads in SAM/BAM format and aligning reads with generic read mappers such as BWA is conventional in the art (title; p 40, col 1, para 4-5; p 40, col 2, para 5). The instant specification discloses BWA is well-understood, routine and conventional in the art (p 17, lines 26-28). Zhongwu further discloses receiving the data as a BAM file and using their program to detect tumor DNA for PCR-based targeted sequencing in diagnostic settings (abstract; p 2, col 1, para 1-2). Furthermore, Zhongwu and Holland both disclose outputting data on the structural genomic rearrangement (Zhongwu, fig 4 and table 2; Holland fig 5). As such, activities such as data gathering and outputting do not provide a non-conventional or unconventional step. Rather, the data gathering and outputting steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Furthermore, the computer system limitations of claims 7 and 22 are generically recited and are well-understood, routine, conventional activities, as evidenced by Zhongwu and Holland. Zhongwu’s and Holland’s methods are inherently computer implemented as they utilize computer software and computer file formats (Zhongwu, abstract and p 2, col 1, para 2; Holland, abstract). Furthermore, 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 provide significantly more. See 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).
Therefore, the additional elements 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, and the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-27 are not patent eligible.
Response to applicant’s arguments
Applicant states the claims do no recite mental process, as the human mind, even with the use of pencil, paper or a computer as a tool, is unequipped to perform an alignment of numerous nucleic acid sequencing reads from massively parallel sequencing of one or more genomic regions of a sample to a reference sample to detect and identify those with soft-clipped regions, select and create groups of reads based on these having identical start or end positions of soft-clipped regions, generate synthetic consensus sequences and align these back to the reference sequence, and repeat these steps until a pair of synthetic consensus sequences with soft-clipped regions which match at the respect respective positions int the reference sequence is detected to accurately report on the structural genomic arrangement, and further that as the reads are provided in specialized electronic file formats, such as BAM or CRAM, which are compressed binary data for computer-to-computer communication and the use of a sting matching algorithm in claims 4 and 26, and as the method steps are performed using specialized computer programs for multi-step manipulation of data and are inherently computer implemented, and that recognition of Zhongwu’s and Holland’s methods as inherently computer implemented that utilize computer software and computer file formats is an acknowledgment that the method steps recited by the instant claims could not be performed in the human mind as they are computer implemented (Applicant’s Arguments, p 20, para 1-p 22, para 2).
It is respectfully submitted that this is not persuasive, as under the broadest reasonable interpretation of the claim limitations, the data set size is not inherently large. Even if the data consisted of millions of data points, it is noted that such computations performed mentally, or with paper and pencil, may 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). There is nothing in the instant claims to suggest the use of specialized bioinformatics instruments versus software that can be implemented on a generic computer. As discussed in MPEP 2106(I), the programmed computer or "special purpose computer" test of In re Alappat, 33 F.3d 1526, 31 USPQ2d 1545 (Fed. Cir. 1994) (i.e., the rationale that an otherwise ineligible algorithm or software could be made patent-eligible by merely adding a generic computer to the claim for the "special purpose" of executing the algorithm or software) was also superseded by the Supreme Court’s Bilski and Alice Corp. decisions. Eon Corp. IP Holdings LLC v. AT&T Mobility LLC, 785 F.3d 616, 623, 114 USPQ2d 1711, 1715 (Fed. Cir. 2015) ("[W]e note that Alappat has been superseded by Bilski, 561 U.S. at 605–06, and Alice Corp. v. CLS Bank Int’l, 573 U.S. 208, 110 USPQ2d 1976 (2014)"). And as discussed in the MPEP 2406.04(a)(2)(III), the courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer, and therefore, the argument that the steps are inherently computer implemented similar to Zhongwu’s and Holland’s method and is not a mental process is not persuasive. Therefore, the recited limitation fall under the “Mental Processes” grouping of abstract ideas.
The argument that claims 1 and 22 do not recite mental processes because the method steps (a)-(f) require the use of the BAM or CRAM formats is not commensurate with the claim as claims 5, 22 and 26 only require the nucleic acid sequencing reads are provided in a file format, and there is no requirement that steps (b)-(g) use the file. However, the examiner agrees that the limitations of using of specific file formats as recited in claims 22 and 26 are not mental processes, and therefore these limitations was analyzed as an additional element. The use of string matching algorithm in claim 4 was considered an abstract idea, as discussed above. The examiner also agrees that the use of BWA cited in claim 26 are not mental processes, and therefore it was also analyzed above as an additional element.
Applicant further states that the claims recite a specific use of a specific type of data (i.e. soft-clipped regions), as a claimed combination that provides a specific improvement in a technological field which is not directed to a judicial exceptions, and further states it is similar to Enfish, LLC v. Microsoft Corp., 822 F.3d 1327 (Fed. Cir. 2016) and that the office did not consider the synthetic consensus sequences as the additional element that together with the claimed method steps which provides the claimed improvement of reporting the structural genomic rearrangement, which is an improvement in structural variant calling (Applicant’s Arguments, p 23, para 1-p 26, para 2). Applicant also asserts the office failed to explain why it does not consider the soft-clipped regions and the synthetic consensus sequences as additional elements since these elements are not mathematical concepts, certain methods of organizing human activity or mental processes, and the result of analysis steps does not necessary itself become a judicial exception (p 23, para 3- p 24, para 1). Applicant further states the Office acknowledged that the claimed methods is novel and non-obvious over the methods of the prior art, and therefore, the claimed method steps recite the additional element of synthetic consensus sequences, which, in combination with the alleged judicial exception, incorporates the judicial exception into a practical application. Applicant also states the soft-clipped regions are an additional element that is significant and that the soft-clipped regions and the synthetic consensus sequences, in combination with the alleged judicial exception, provide the claimed improvement of reporting the structural genomic rearrangement, and that prior to the earliest filing date of the application, the art was unable to accurately detect and report structural genomic rearrangements as claimed (Applicant’s Arguments, p 26, para 3-p 32, para 1).
It is respectfully submitted that this is not persuasive. As discussed in MPEP 2106.05, 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., 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 also Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1151, 120 USPQ2d 1473, 1483 (Fed. Cir. 2016) ("a claim for a new abstract idea is still an abstract idea. The search for a § 101 inventive concept is thus distinct from demonstrating § 102 novelty.").
The synthetic consensus sequence is part of the abstract idea itself and an result of the analysis steps, and is not considered to be an element in addition to the recited judicial exceptions. Furthermore, the soft-clipped regions were a part of the nucleic acid sequence reads, and are simply the region of the sequence that remains unmapped after aligning the nucleic acid sequence read to a reference read, and performing steps such as creating groups with identical positions for these soft-clipped regions at the start or end of the sequence read, and subsequent steps of comparison based on these regions can be performed mentally. The presence of a soft-clipped region or a synthetic consensus sequence with a step that is a mental process or obtained as a result of a mental process is considered an abstract idea itself because it is simply data that is used and produced by the mental process, as opposed to a limitation in addition to the recited judicial exceptions. Therefore, the use of the soft-clipped regions and generation of the synthetic consensus sequences are part of the abstract idea itself.
Furthermore, the instant claims are not analogous those in the cited case, as the claims in Enfish, LLC v. Microsoft Corp. were found patent eligible because specific type of data structure (i.e. the self-referential table) improved the functioning of a computer itself through the way it stores and retrieves data in memory. In contract, the instant claims do not provide an improvement to computer or other technology, through the reporting of the structural genomic rearrangements. Rather, the improvements appear to the judicial exceptions themselves (i.e. the steps of identifying and determining on of the structural genomic rearrangements), in which the soft-clipped regions were part of the data used in the identification and determination. There is nothing in this specific region of data that precludes it from being analyzed mentally. As discussed in MPEP 2106.05(a), the improvement cannot be to the judicial exception itself.
And as discussed above, the additional elements of the claim amount to mere data gathering and outputting, and mere instructions to implement the abstract idea in a generic computing environment. Therefore, there is no indication that any of these additional elements provide a practical application of the recited judicial exception outside of the judicial exception itself.
Applicant also states that under Step 2B, the soft-clipped regions, the synthetic consensus sequences, and step (g) of claim 1 do not generally link the alleged judicial exception to a technological environment, but are significant features that impose meaningful limits on the claims and do not amount to "mere data gathering and outputting", and that under the Step 2B analysis, the additional elements in combination with the judicial exception provide an improvement in detecting structural genomic rearrangements in samples of interest, and request withdrawal of the rejection (Applicant’s Arguments, p 32, para 2-p 34, para 3).
With respect to Step 2B, as discussed in MPEP 2106.05, an "inventive concept" is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and an inventive concept "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself. The limitations using soft-clipped regions, which are abstract ideas, appears to solely provide the improvement, and therefore these limitations cannot provide the inventive concept. Furthermore, as discussed above, the steps for detecting genomic structural rearrangements using the soft-clipped regions of the reads are also judicial exceptions, and therefore these limitations are not analyzed under Step 2B, and therefore cannot provide the inventive concept. The rejections are maintained.
Claim Rejections - 35 USC § 103
The rejection of claims 1-15, 18-24 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Zhongwu Lai et al. (01/17/202 IDS, NPL ref #11; previously cited; hereafter referred to as Lai) as evidenced by Eberle et al. (Genome research 2016, 27(1), pp. 1-9; previously; hereafter referred to as Eberle) , and further in view of Jung et al. (US20150142328A1; previously cited; hereafter referred to as Jung) and Bartenhagen et al. (Briefings in Bioinformatics 2016, Volume 17, Issue 1, pp. 51–62; previously cited; hereafter referred to as Bartenhagen) is withdrawn in view Applicant’s Argument filed 05/12/2026, as the argument that the cited art does not appear to teach or suggest generating a synthetic consensus sequence for each group by selecting the most abundant nucleotide at each position and accurately detect and report structural genomic rearrangements as recited in the instant claims, and the argument that it would not have been obvious to combine the cited methods to arrive at the methods of the instant application is found to be persuasive. Claim 26 also appear to be free from prior art for the reasons discussed above.
The rejections of claims 16-17 under 35 U.S.C. 103 as being unpatentable over Zhongwu Lai et al. (01/17/202 IDS, NPL ref #11; previously cited; hereafter referred to as Lai) as evidenced by Eberle et al. (Genome research 2016, 27(1), pp. 1-9; previously cited; hereafter referred to as Eberle), in view of Jung et al. (US20150142328A1; previously cited; hereafter referred to as Jung) and Bartenhagen et al. (Briefings in Bioinformatics 2016, Volume 17, Issue 1, pp. 51–62; previously cited; hereafter referred to as Bartenhagen) as applied to claims 1 and 15, and further in view of Erwin L. van Dijk et al. (01/17/202 IDS, NPL ref #12; previously cited; hereafter referred to as Erwin L. van Dijk), is withdrawn in view Applicant’s Argument filed 05/12/2026, as the argument that the cited art does not appear to teach or suggest generating a synthetic consensus sequence for each group by selecting the most abundant nucleotide at each position and accurately detect and report structural genomic rearrangements as recited in the instant claims, and the argument that it would not have been obvious to combine the cited methods to arrive at the methods of the instant application is found to be persuasive.
The rejection of claim 25 under 35 U.S.C. 103 as being unpatentable over Zhongwu Lai et al. (01/17/202 IDS, NPL ref #11; previously cited; hereafter referred to as Lai) as evidenced by Eberle et al. (Genome research 2016, 27(1), pp. 1-9; previously cited; hereafter referred to as Eberle), in view of Jung et al. (US20150142328A1; previously cited; hereafter referred to as Jung) and Bartenhagen et al. (Briefings in Bioinformatics 2016, Volume 17, Issue 1, pp. 51–62; previously cited; hereafter referred to as Bartenhagen) as applied to claims 1 and 5, and further in view of Li et al. (01/17/202 IDS, NPL ref #19; previously cited; hereafter referred to as Li) is withdrawn in view Applicant’s Argument filed 05/12/2026, as the argument that the cited art does not appear to teach or suggest generating a synthetic consensus sequence for each group by selecting the most abundant nucleotide at each position and accurately detect and report structural genomic rearrangements as recited in the instant claims, and the argument that it would not have been obvious to combine the cited methods to arrive at the methods of the instant application is found to be persuasive
Conclusion
No claims allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to NIDHI DHARITHREESAN whose telephone number is (571)272-5486. The examiner can normally be reached Monday - Friday 9:00 - 5:00.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs II can be reached on (571) 270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/N.D./ Examiner, Art Unit 1686
/Karlheinz R. Skowronek/ Supervisory Patent Examiner, Art Unit 1687
Prosecution Insights