DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. 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 the Claims
Claims 1-20 are under examination.
Claim Rejections - 35 USC § 112
2. The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 6-11 and 17-19 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Instant claims 6-8 and 17-19 recite steps of “regarding” or “regard”. It is unclear what is meant by this step or what processes are required to perform this step. Claims 9-11 are also rejected for depending from claim 8.
Claim Rejections - 35 USC § 101
3. 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.
4. Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Claims 1-20 are directed to method and device drawn to extracting somatic mutations from single-cell transcriptome sequencing data. As described in Alice Corp. Pty. Ltd. V. CLS Bank Int’l, 573 U.S._, 134 S. Cr. 2347, 110 U.S.P.Q.2d 1976 (2014), a two-step analysis is required in considering the patent eligibility of the claimed subject matter. The first step requires determining if the claimed subject matter is directed to a judicial exception. The instant claims require the processing single-cell transcriptome raw sequencing data with a first comparison and identification method to obtain a plurality of first somatic mutations sites; processing the single-cell transcriptome raw sequencing data with a second comparison and identification method to obtain a plurality of second somatic mutation sites, integrating the plurality of first somatic mutations sites and the plurality of second somatic mutation sites to obtain a plurality of candidate somatic mutation sites; and performing mutation screening on the plurality of candidate somatic mutation sites to obtain final somatic mutation sites. These steps are mathematical steps or mental steps. Dependent claims 2-11 and 13-19 are drawn to additional mental steps or mathematical steps. Mental steps are a judicial exception. The courts have found mathematical algorithms to be drawn to the judicial exception of an abstract idea (In re Grams, 888 F.2d 835, 12 U.S.P.Q.2d 1824 (Fed. Cir. 1989)). Thus, the instant claims are drawn to a judicial exception.
This judicial exception is not integrated into a practical application. The instant claims do not recite an element that reflects an improvement in the functioning of a computer or other technology, an element that applies the judicial exception to effect a particular treatment, an element that implements the judicial exception with a particular machine, or an element that effects a transformation of a particular article to a different state or thing. The instant claims recite the elements of a device, memory, processor, and computer readable storage medium. The instant claims do not recite any structural limitations of these elements. Thus, the instant claims are not drawn to a particular machine and do not integrate the judicial exception into a practical application.
The second part of the analysis requires determining if the claims include additional elements that are sufficient to amount to significantly more than the judicial exception. The instant claims recite the elements of a device, memory, processor, and computer readable storage medium. These elements are well-understood, conventional, and routine computer components (Specification, pages 21 and 22). Reciting such well-understood, routine, and conventional computer components do not transform a judicial exception into patent eligible subject matter. In addition, the recitation of the specific types of data to be used in the judicial exception does not transform the abstract idea into a non-abstract idea. (See buySAFE, Inc. v Google, Inc. 765 F.3d 1350, 112 U.S.P.Q.2d 1093 (Fed.Cir.2014)). Furthermore, the elements taken as a combination are also well-understood, routine, and conventional, since the elements are merely specifying a general computer and data for the judicial exception. Thus, the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
5. Claim 20 rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Instant claim 20 is drawn to a computer readable storage medium. A computer readable storage medium encompasses carrier waves. Carrier waves are non-statutory per se. Thus, the instant claim is drawn to non-statutory subject matter.
Claim Rejections - 35 USC § 102
6. 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-4, 12-15, and 20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Enge et al. (“Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutations Patterns” (2017) Cell volume 171, pages 321-330).
Regarding claims 1, 12, and 20, Enge et al. teach processing single-cell raw sequencing data (page e3) with a first comparison and identification method (page 324, right column; page e4) to obtain a plurality of first somatic mutations sites (pages e5-e6); processing single-cell raw sequencing data (page 324; page e3) with a second comparison and identification method (page e4) to obtain a plurality of second somatic mutations sites (pages e5-e6); integrating the plurality of first somatic mutation sites and plurality of second somatic mutation sites to obtain a plurality of candidate somatic mutation sites (page 323, right column; pages e5-e6); performing mutation screening on the plurality of candidate somatic mutation sites to obtain final somatic mutation sites (pages e5-e6). Furthermore, Enge et al. teach that the method is performed with software which would require a device with memory, processor and a computer readable storage medium (page e4).
Regarding claims 2 and 13, Enge et al.t each comparing the single-cell transcriptome raw sequencing data with reference genome data using a comparison mode to obtain a comparison information record file (page e4); labeling the comparison information record file (pages e4-e6); performing correction and annotation the comparison information record file that has been labeled to obtain the plurality of first somatic mutation sites (pages e4-e5); and where the correction includes sequence correction and base quality correction, and the annotation includes annotation of functional effects on encoded proteins and annotation of a database for germline mutations and RNA editing (page 324, Figure 3; pages e4-e6).
Regarding claims 3 and 14, Enge et al. teach comparing single-cell transcriptome raw sequencing data with reference genome data (page e4); obtaining the plurality of second somatic mutation sites with an identification mode from the comparison results (pages e4-e5).
Regarding claims 4 and 15, filtering the plurality of the first somatic mutations sites to obtain a plurality of filtered first somatic sites (pages e4-e5); comparing the plurality of filtered first somatic mutation sites with a plurality of second somatic mutation sites to obtain the plurality of candidate somatic mutation sites (pages e4-e5).
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JERRY LIN/Primary Examiner, Art Unit 1685
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