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 .
Information Disclosure Statement
The IDS filed 6/29/2022, 3/20/2023 and 7/23/2024 have been considered by the Examiner.
Priority
Priority of PCT/CN/2019/130731 filed 12/31/2019 is acknowledged.
Status of Claims
Claims 1-14 are under consideration.
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 1-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-8, 10, 11, and 13 are drawn to a method.
Claims 9, 12 and 14 are drawn to a non-transitory computer readable medium.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s):
1. aligning genome sequence data of individuals to reference genome data to obtain a mutation result of the genome sequence relative to the reference genome data.
This step requires comparing nucleic acid sequence data which can be performed by the human mind and is therefore an abstract idea.
2. partitioning a genome of the species into a plurality of unit regions of biological significance.
This step reads on a mental process of identifying biological significance and determining partition points. The step is therefore an abstract idea.
3. generating a plurality of mutant patterns of the plurality of individuals in each unit region by statistically analyzing mutant status for each region based on the mutation result and numbering the mutant patterns to obtain the mutation dictionary..
This step recites math by statistically analyzing mutant status. As recited the analyzing can also be performed by the human mind. Numbering can also be performed by the human mind. The step is therefore an abstract idea.
4. wherein the gene mutation dictionary comprises the plurality of unit region of biological significance and a unique index number associated with the regions, each unit region comprising mutant patterns and each mutant pattern having a unique index number.
This limitation is drawn to describing how information is organized in the mutation dictionary. Organizing information by mutant region and unique index number can be performed by the human mind and is therefore an abstract idea.
Dependent claims 2-8, 10, 11, and 13 are further drawn to describing the abstract idea and quantifying the number of regions as being in the tens of thousands. However, the amount of data being analyzed does not takes the process steps themselves outside the realm of being abstract ideas. Computations on a lot of data performed mentally, or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.), 687 F.3d 1266,1278 (Fed. Cir. 2012) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations).
Step 2A Prong Two: Consideration of Practical Application
The claims result in obtaining a gene mutation dictionary which is a result of outputted organized information. The claims do not recite any additional elements that integrate the abstract idea into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Dependent claims 1-8, 10, 11, and 14 are further drawn to describing the data in the database which is organized by the abstract idea steps and further abstract idea steps describing organizing and analyzing the information.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
Obtaining genome sequence data of a plurality of individuals of a species and reference genome data of the species.
This step reads on extra solution activity of data gathering, as described in MPEP 2106.05(g).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because receiving genomic data as process of data transmission is well known, routine and conventional.
Other elements of the method include a non-transitory computer readable storage medium (claims 9, 12 and 14) which is a recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
Claims 1-6 and 9-14 are rejected under 35 U.S.C. 103(a) as being unpatentable over Kimura (US 2017/0017717; IDS filed 3/20/2023) in view of Trakadis (US 2014/0310215).
Kimura teaches mapping DNA fragments of a subject to genome DNA of a reference to detect mutations (par. 0005) and detecting SNPs when positions of a sample DNA fragment differs from a genome DNA (par. 0056)(i.e. aligning genome sequence data of individuals to the reference genome data to obtain mutation result of the genome sequence data), as in claim 1.
Kimura teaches genome mapping to a genome DNA by determining a position from which the mate sequence of the sample DNA (i.e. of an individual) is derived. The mapped regions read on units of biological significance (par. 0060)(i.e. partitioning a genome into unit regions because the mapped regions of biological significance), as in claim 1.
Kimura teaches determining whether the sample DNA fragment of the mate sequence includes the mutation indication by analysis information according to the success or failure in mapping of the mate sequence (par. 0061); result of the analysis information outputs the number of sample DNA fragments where SNP is detected (par 0121)(i.e. generating a plurality of mutant patterns in each unit region based on mutation result)m as in claim 1.
Kimura teaches a detection number counter value of the SNP information (par. 0119) and associates the SNP information with the detection number counter value (par. 0120-0122)(i.e. numbering the mutant patterns), as in claim 1.
Kimura teaches outputting a report with the detection number counter (par. 0121-0122)(i.e. the gene mutation dictionary with unit regions of biological significance) with the number of read fragments that are the mutated base detection number and the position (i.e. a unique index number associated with each of the plurality of unit regions of biological significance)(i.e. par. 0122 and Figure 7D, see Based Position Coordinate which reads on a unique index), as in claim 1.
Kimura does not teach that the genome sequence data is of a plurality of individuals and that the mutant patterns are of a plurality of individuals, as in claim 1.
Trakadis teaches a subjects database (Abstract) for searching a subject with respect to identified mutations (par. 0005, 0009); Trakadis teaches that the subjects database is searched for genetic changes (par. 0119)(i.e. enome sequence data is of a plurality of individuals and that the mutant patterns are of a plurality of individuals), as in claim 1.
It would be obvious to one of ordinary skill in the art at the time the invention was made to have combined that mutation dictionary taught by Kimura for at least one subject with the teaching of Trakadis for a subjects database which can be queried for a specific individual. Trakadis provides motivation (Abstract) by teaching that a database (i.e. dictionary) of a plurality of subjects can be used to determine genetic conditions based on matches between a searched subject and the subjects in the database. One of skill in the art would have had a reasonable expectation of success at combining the teachings of Kimura and Trakadis because both teach computerized storage of genetic mutation data.
Regarding dependent claims 2-6 and 9-14
Regarding claim 2, Trakadis teaches a subjects database (Abstract) where the subjects database is searched for genetic changes (par. 0119); Trakadis does not specifically teach that the database comprises 1000 or more human individuals. However Trakadis suggests a database of a 1000 or more individuals by teaching similar databases which are the Human Gene Mutation Database (HGMD), Mutation Database (DMuDB), MutatDatabase and the ClinVar (par. 0248). Trakadis also teaches that the databases can be updated, for example by a doctor, to include more subjects as needed.
Regarding claims 3-6, Kimura et al. do not explicitly teach coding and non-coding regions, unit regions from thousands to tens of thousands, at least 60,000 unit region and 30,000 coding and 30,000 non-coding regions. However, Kimura et al. teach sequencing 1 billion pieces of sample DNA fragments (par. 0045) and suggest that the sequences have introns and exons (par. 0047)(i.e. non-coding and coding regions); Kimura et al. teach that 5 billion kinds of identifiers for sequences are required (par. 0146) which suggests billions of regions, as in claims 3-6.
Kimura et al. teach creating a read sequence dictionary (Abstract) and searching the reads sequence dictionary to reconstruct a sample (par. 0022-0023)(i.e. aligning genome sequencing data to the gene mutation dictionary to obtain a mutant pattern consistent with a mutant status of unit regions in the dictionary), as in claim 10.
Kimura et al. teach adding to the read sequence dictionary (par. 0087), as in claim 11.
Kimura et al. teach a concatenation character that connects a pair of a sample DNA fragment in the read dictionary (par. 0143)(i.e. obtaining compressed genomic data generated by compression using gene mutation dictionary, comprising index numbers of mutant patterns), as in claim 13.
Kimura et al. teach reconstructing the mate sequence based on the concatenation character embedded in the read sequence dictionary (par. 0144)(i.e. finding the index number of the mutant pattern for each of the plurality of unit regions in the dictionary and extracting the mutation pattern), as in claim 13.
Kimura et al. teach implementing their process in a computer (par. 0039) which suggests a non-transitory computer readable medium, as in claims 9, 12 and 14.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
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/Anna Skibinsky/
Primary Examiner, AU 1635