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 .
Status of Claims
Claims 1-20 are pending and examined on the merits.
Priority
The instant application filed on 11/21/2022 claims the benefit of priority to U.S. Provisional Patent Application No. 63/326,392 filed on 4/1/2022. Thus, the effective filing date of the claims is 4/1/2022.
The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing.
Information Disclosure Statement
The information disclosure statement (IDS) filed on 6/22/2023 has been entered and considered. A signed copy of the corresponding 1449 form has been included with this Office action.
Specification and Drawings
The disclosure is objected to because of the following informalities:
According to the specification at para.0084 "lines are drawn between windows of 8 SNPs" which is taken to mean 8 positions when associating this statement with Figure 5 (i.e. there are not 8 single nucleotide polymorphisms in each window, as there are homozygous positions that appear to count towards the total of 8). However, the first "full window" (from positions 31-39) contains 9 positions. The rest contain the expected 8.
The process of converting "a pair of bitmap sequences" into a "pair of sparse bitmap sequences" (i.e. a bitmap into a sparse bitmap) is not clear because the encoding in the sparse bitmap seems to pull positional data from the bitmap while (seemingly) randomly skipping others. For example, positions 39 and 43 in the bitmap are recorded as positions 8 and 9 in the sparse bitmap, while heterozygous positions 40-42 are skipped. Are heterozygous positions (double white blocks) meant to be "compressed" in the sparse bitmap (i.e. skipped over)? Or maybe they are meant to be compressed into a single position in the sparse bitmap as shown by the encoding of bitmap position 46 (or 44-50) to sparse bitmap position 10? However, if this were the case, then why are double white block positions 40-42 not included in the sparse bitmap? While this process is not explicitly in the claims, it should be clarified if Applicant plans on amending the claims with this second step of the encoding procedure.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 11-12 rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 11 rejected as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends. The claim recites "receiving a second input pair of encoded bitmap sequences of a second target individual; comparing the second input pair of encode bitmap sequences to the pairs of encoded bitmap sequences of the plurality of individuals that are sustained in the RAM of the plurality of servers", which does not further limit claim 1. The limitations of this claim are interpreted as simply running the same method of claim 1 on the same data type of a different individual, which is already covered by claim 1.
Claim 12 rejected as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends. The claim recites "the pairs of encoded bitmap sequences of the plurality of individuals are sustained in the RAM of the plurality of servers for comparisons for a plurality of targeted individuals without regenerating the pairs of encoded bitmap sequences from the genetic datasets stored on the one or more hard drives", which does not further limit claim 1 because claim 1 states "sustaining the pairs of encoded bitmap sequences of the plurality of individuals in the RAM of the plurality of servers".
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 5-15, and 17-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. 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:
Claim 1, 13, and 19: “encoding the genetic datasets of the plurality of individuals to generate pairs of encoded bitmap sequences based on an encoding scheme, wherein the genetic dataset of each individual is encoded to generate a pair of encoded bitmap sequences, the encoding scheme defining a sequence of values based on homozygosity of the genetic dataset of each individual” provides an evaluation (encoding the genetic datasets involves evaluating them based on the encoding scheme) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“determining matched segments between the target individual and the plurality of individuals, wherein determining matched segments comprises comparing the input pair of the target individual to the pairs that are stored in the RAM” provides a comparison (matching involves comparing input against reference segments) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“computing, for each server, a relationship between the target individual and an individual of the plurality of individuals” provides an evaluation (computing a relationship between individuals involves evaluating the matched segments) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 7 and 17: “comparing encoded data of the target individual that encodes a first type of homogeneous locations of the target individual to a second encoded data encoding a second type of homogeneous locations of another dataset; and identifying a common location that indicates the encoded data of the target individual and the other dataset in comparison are both homogeneous” provides a comparison (comparing encoded data to identify common locations) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Additionally, while claims 1, 13, and 19 recite performing some aspects of the analysis on “A computer-implemented method, comprising: storing genetic datasets [. . .] on one or more hard drives [and] in random-access memory (RAM) of a plurality of servers” (claim 1), “A non-transitory computer-readable storage medium comprising instructions” (claim 13), and “A system comprising: a database comprising one or more hard drives [and] a plurality of servers in communication with the database” (claim 19), there are no additional limitations that indicate that this requires anything other than carrying out the recited mental processes or mathematical concepts in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “Mental processes” grouping of abstract ideas. As such, claims 1-3, 5-15, and 17-20 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 judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements:
Claim 1, 13, and 19: “A computer-implemented method, comprising: storing genetic datasets [. . .] on one or more hard drives [and] in random-access memory (RAM) of a plurality of servers” (claim 1), “A non-transitory computer-readable storage medium comprising instructions” (claim 13), and “A system comprising: a database comprising one or more hard drives [and] a plurality of servers in communication with the database” (claim 19) provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application.
“storing genetic datasets of a plurality of individuals on one or more hard drives of a database”, “storing the pairs of encoded bitmap sequences in random-access memory (RAM) of a plurality of servers, each server's RAM storing the pairs of encoded bitmap sequences of a subset of individuals of the plurality of individuals, wherein the RAM is volatile and has a faster processing speed than the one or more hard drives”, and “sustaining the pairs of encoded bitmap sequences of the plurality of individuals in the RAM of the plurality of servers” provides insignificant extra-solution activities (storing data on generic computer components is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“receiving an input pair of encoded bitmap sequences of a target individual for determining relationships between the target individual and the plurality of individuals” provides insignificant extra-solution activities (receiving data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“each server operates in parallel with other servers for comparisons of different individuals” provides insignificant extra-solution activities (operating servers in parallel is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“collating the computed relationships” provides insignificant extra-solution activities (collating data is a post-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 6: “sustaining encoded data in the hash tables and storing [information]” provides insignificant extra-solution activities (storing data on generic computer components is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
The steps for storing, receiving, and collating data, and selecting and operating servers in parallel are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are pre- and post-solution activities involving data gathering, data manipulation, and sample manipulation steps (see MPEP 2106.04(d)(2)). Furthermore, the limitations regarding implementing program instructions do not indicate that they require anything other than mere instructions to implement the abstract idea in a generic way or in a generic computing environment. As such, this limitation equates 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. Therefore, claims 1-3, 5-15, and 17-20 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 are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment. As discussed above, there are no additional elements to indicate that the claimed “A computer-implemented method, comprising: storing genetic datasets [. . .] on one or more hard drives [and] in random-access memory (RAM) of a plurality of servers” (claim 1), “A non-transitory computer-readable storage medium comprising instructions” (claim 13), and “A system comprising: a database comprising one or more hard drives [and] a plurality of servers in communication with the database” (claim 19) requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. Additionally, the limitations for storing, receiving, and collating data, and selecting and operating servers in parallel are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are demonstrated to be well-understood, routine, and conventional, specifically:
storing and manipulating data on generic computer components (hard drives and RAM), as evidenced by Alnasir et al. (Briefings in bioinformatics 21.1 (2020): 96-105) on Page 2 col 2 paragraph 4 "Although Spark supports MapReduce programs, the main constraint Spark overcomes is Hadoop’s acyclic data flow model by allowing the re-usability of intermediate data in the form of a data structure that is central to Spark, the Resilient Distributed Dataset (RDD). The RDD serves as an abstraction for distributed memory that allows in-memory computations on large clusters in a fault-tolerant manner", and Lee et al. (Briefings in functional genomics 11.1 (2012): 12-24) on Page 3 col 1 paragraph 2 "Unlike Velvet, which requires substantial memory on a single large node, ABySS reduces the memory requirement by distribution across multiple smaller nodes, a more usual form of computer infrastructure".
operating servers in parallel, as evidenced by Fjukstad et al. (Data Science and Engineering 2.3 (2017): 245-251) on Page 3 col 2 paragraph 1 "GATK provides multiple approaches to parallelize tasks: multi-threading and scatter–gather", Page 3 col 2 paragraph 3 "ADAM uses Spark to scale out parallel processing", Page 4 col 1 paragraph 4 "The pipeline [GESALL] can run unmodified analysis tools by wrapping these using their genome data parallel toolkit. The tools access their data using the standard file system interface, but GESALL optimizes data access patterns and enables correct distributed execution", and Page 4 col 2 last paragraph "Containers can be orchestrated for parallel execution using, for example, Kubernetes (https://kubernetes.io/) or Docker Swarm (https://github.com/docker/swarm), and there are now multiple pipelining tools that use Docker or provide Docker container support including Nextflow [26], Toil [22], Pachyderm (http://www.pachyderm.io/), Luigi (https://github.com/spotify/luigi) [27], Rabix/bunny [28], and our own walrus system (http://github.com/fjukstad/walrus)"
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. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-3, 5-15, and 17-20 are not patent eligible.
Claim Rejections - 35 USC § 103
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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-2, 7, 10-13, 17, and 19 rejected under 35 U.S.C. 103 as being unpatentable over Lunter (EP-3430551).
Regarding claim 1, 11-13, and 19, Lunter teaches storing genetic datasets of a plurality of individuals on one or more hard drives of a database; and storing the pairs of encoded bitmap sequences in random-access memory (RAM) of a plurality of servers, each server's RAM storing the pairs of encoded bitmap sequences of a subset of individuals of the plurality of individuals, wherein the RAM is volatile and has a faster processing speed than the one or more hard drives (Claim 15 "a memory device storing a reference database comprising a plurality of reference lists of genetic variants from other individuals" and para.0029 "The encoding may form a data stream for example, which may be written into a memory or transmitted to another device for example" suggests storage of the encoded data in RAM).
Lunter also teaches encoding the genetic datasets of the plurality of individuals to generate pairs of encoded bitmap sequences based on an encoding scheme, wherein the genetic dataset of each individual is encoded to generate a pair of encoded bitmap sequences, the encoding scheme defining a sequence of values based on homozygosity of the genetic dataset of each individual (Para.0049 "the algorithm achieves this speedup relative to the standard implementation of the Li and Stephens model in two ways. First, the algorithm does not consider single states (representing pairs of haplotypes to copy from), but instead considers groups of states representing pairs of haplotypes each of which sharing a particular substring").
Lunter also teaches receiving an input pair of encoded bitmap sequences of a target individual for determining relationships between the target individual and the plurality of individuals (Para.0020 "the method could also be applied to the case where the input file comprises phased information").
Lunter also teaches determining matched segments between the target individual and the plurality of individuals, wherein determining matched segments comprises comparing the input pair of the target individual to the pairs that are stored in the RAM, wherein each server operates in parallel with other servers for comparisons of different individuals; computing, for each server, a relationship between the target individual and an individual of the plurality of individuals and collating the computed relationships (Para.0047 "The method may for example comprise obtaining an exact or approximate solution to the diploid Li and Stephens model (see N Li and M Stephens, Genetics 2003, 165(4):2213-33), which is itself an approximation of the coalescent model describing the relationship of genomes in a population").
Finally, sustaining data in the RAM is widely used by computationally expensive software, particularly bioinformatics programs as evidenced by Alnasir et al. (Page 2 col 2 paragraph 4 "Although Spark supports MapReduce programs, the main constraint Spark overcomes is Hadoop’s acyclic data flow model by allowing the re-usability of intermediate data in the form of a data structure that is central to Spark, the Resilient Distributed Dataset (RDD). The RDD serves as an abstraction for distributed memory that allows in-memory computations on large clusters in a fault-tolerant manner") and Lee et al. (Page 3 col 1 paragraph 2 "Unlike Velvet, which requires substantial memory on a single large node, ABySS reduces the memory requirement by distribution across multiple smaller nodes, a more usual form of computer infrastructure").
It is recognized that the citations and evidence provided above are derived from potentially different embodiments of a single reference. Nevertheless, it would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains to employ combinations and sub-combinations of these complementary embodiments in order to efficiently implement phase information (para.0012 "The inventors have discovered that efficient implementation is in fact possible and also that significant improvements in compression can be achieved by building in this phase information"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with efficient representation of phased genotype data. Additionally, doing so merely combines prior art elements according to known methods to yield predictable results.
Regarding claims 2 and 14, Lunter teaches the methods of Claims 1 and 13 on which this claim depends/these claims depend, respectively. Lunter also teaches the genetic datasets comprise phased genotype datasets or genotype datasets (Para.0020 "the method could also be applied to the case where the input file comprises phased information").
Regarding claims 7 and 17, Lunter teaches the methods of Claims 1 and 13 on which this claim depends/these claims depend, respectively. Lunter also teaches comparing encoded data of the target individual that encodes a first type of homogeneous locations of the target individual to a second encoded data encoding a second type of homogeneous locations of another dataset; and identifying a common location that indicates the encoded data of the target individual and the other dataset in comparison are both homogeneous (Para.0020 "In this case, for each variant it may be stated whether the genotype is homozygous and matching to the reference genome, heterozygous, or homozygous and different to the reference genome" suggests any comparison would yield information regarding homogeneity and location).
Regarding claim 10, Lunter teaches the methods of Claims 1 and 13 on which this claim depends/these claims depend, respectively. The limitation of claim 10 (data being sustained in the RAM of the plurality of servers until power off of a server) is the default for volatile memory (RAM) as evidenced by Vaidyanathan (page 1 first paragraph "When a computer is switched off, the data in Volatile memory like RAM is wiped clean, because RAM needs constant power to hold its contents. Non-volatile memory, such as ROM, hard drives, SSDs, and USB flash drives, keeps the data intact by storing it as magnetic patterns or trapped electric charges that survive without any power").
Claims 3-4, 15-16, and 20 rejected under 35 U.S.C. 103 as being unpatentable over Lunter (EP-3430551) as applied to claims 1-2, 7, 10-13, 17, and 19 above, and further in view of Denton et al. (US-7058517).
Lunter is applied to claims 1-2, 7, 10-13, 17, and 19.
Regarding claims 3-4, 15-16, and 20, Lunter teaches the method of Claims 1, 13, and 19 on which this claim depends/these claims depend.
Lunter does not explicitly teach: the encoded bitmap sequences of the subset of individuals stored in one of the servers comprises the encoded bitmap sequences of a reference panel of a genetic community; determining that the target individual belongs to the genetic community; selecting the one of the servers that stores the encoded bitmap sequences of the reference panel; nor using the one of the servers to determine relationships between the target individual and the reference panel.
However, Denton teaches determining groups of individuals by haplotype-pair by their observed variation and assign population groups (Page 124 col 1 line 20 "We can use the ANOVA calculation to see whether grouping individuals by haplotype-pair (or sub-haplotype-pair) helps explain the observed variation in response in a statistically significant way").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Lunter as taught by Denton in order to administer drugs to the appropriate population (page 66 col 1 line 12 "The invention relates to the field of genomics, and genetics, including genome analysis and the study of DNA variation. In particular, the invention relates to the fields of pharmacogenetics and pharmacogenenomics and the use of genetic haplotype information to predict an individual's susceptibility to disease and/or their response to a particular drug or drugs, so that drugs tailored to genetic differences of population groups may be developed and/or administered to the appropriate population"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with processing and matching haplotype data.
Claims 5-6 and 9 rejected under 35 U.S.C. 103 as being unpatentable over Lunter (EP-3430551) as applied to claims 1-2, 7, 10-13, 17, and 19 above, and further in view of Duncan (US-20170213127).
Lunter is applied to claims 1-2, 7, 10-13, 17, and 19.
Regarding claims 5 and 6, Lunter teaches the method of Claim 1 on which this claim depends/these claims depend.
Lunter does not explicitly teach creating a hash table to store a hash of a user's account name, a hash of a user's name, a hash of a user's date of birth, a hash of a user's location of birth, or a hash of a combination of a user's information.
However, Duncan describes in para.1074 user information contained in a hash table including name, date of birth, location, etc., and para.0198 explicitly mentions accounts which would reasonably associate with each user in such a table.
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Lunter as taught by Duncan in order to track all available user data (abstract "employing all available data regarding the genome-matching results of Users associated to those trees, and all available historical data influencing the subjects in the trees"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with matching sequence segments between target and reference genetic data.
Regarding claim 9, Lunter teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Duncan also teaches the relationships between the target individual and the plurality of individuals correspond to identity by descent (IBD) relationships (Para.0060 "From these SNP's, participating members' resulting genomic data are compared SNP by SNP to discover contiguously matched sequences (segments), and where identical along a segment length greater than a threshold, an ‘Inherited By Descent’ (IBD) match is considered probable, with confidence proportional to the length of the segment, or count and length of multiple segments").
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-20 rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-20 of US-20220382730 in view of Lunter (EP-3430551). Although the claims at issue are not identical, they are not patentably distinct from each other because both involve encoding datasets, comparing the encoded datasets, and identifying matches (including identity by descent).
While US-20220382730 does not explicitly teach storing the datasets in RAM or computing the relationship between segments, it would have been obvious to one of ordinary skill in the art to modify these methods, with those taught by Lunter as described above for claims 1, 13, and 19 of the instant application, in order to efficiently implement phase information (para.0012 "The inventors have discovered that efficient implementation is in fact possible and also that significant improvements in compression can be achieved by building in this phase information"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with efficient representation of phased genotype data.
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Band et al. "BGEN: a binary file format for imputed genotype and haplotype data." BioRxiv (2018): 308296
Encoding haplotypes
Kawam et al. "Fast and efficient genotype encoding using sparse 2D bitmaps for database-driven genomics applications." 2018 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI). IEEE, 2018
Bitmap encoding
EXAMINER NOTE
Claims 8 and 18 objected to as being dependent upon a rejected base claim, but are otherwise free of the art. The closest prior art is considered to be Lunter, as discussed above relating to the rejection of independent claims 1, 13, and 19 under 35 U.S.C. 103. As discussed above, Lunter teaches encoding and storing genetic datasets, comparing the encoded datasets, identifying matches, and computing the relationship between segments. However, there is no teaching or motivation present for the specific paired haplotype encoding schema detailed in claims 8 and 18.
While claims 4 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Lunter (EP-3430551) in view of Denton et al. (US-7058517), the additional elements of “selecting the one of the servers that stores the encoded bitmap sequences of the reference panel; using the one of the servers to determine relationships between the target individual and the reference panel” are not considered insignificant extra-solution activities. While selecting a specific server for computation is a well-understood, routine, or conventional approach for the field, the decision is typically based on computational resource differences between the severs. Because claims 4 and 16 are selecting a specific server for segment matching and relationship computations based on genetic community identity, these additional elements serve to integrate the judicial exceptions of claim 4 (“determining that the target individual belongs to the genetic community” provides an evaluation (making a genetic community assignment determination involves evaluating and comparing the encoded data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea) and independent claims 1 and 13 into a practical application and thus are patent eligible subject matter.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert A. Player whose telephone number is 571-272-6350. The examiner can normally be reached Mon-Fri, 8am-5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R. Skowronek can be reached at 571-272-9047. 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.
/R.A.P./Examiner, Art Unit 1686
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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