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 .
Claim Objections
2. The numbering of claims is not in accordance with 37 CFR 1.126 which requires the original numbering of the claims to be preserved throughout the prosecution. When claims are canceled, the remaining claims must not be renumbered. When new claims are presented, they must be numbered consecutively beginning with the number next following the highest numbered claims previously presented (whether entered or not).
Misnumbered claims 1-22 been renumbered 31-52.
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.
Claims 31-42 and 52 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Claims 31-42 and 52 are directed to a computer system that generates and stores the loss of heterozygosity class for the human leukocyte antigen gene. 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 steps of determining, using a three-class leukocyte antigen loss of heterozygosity model, a loss of heterozygosity class for a human leukocyte antigen gene. However, using a three-class leukocyte antigen loss of heterozygosity model is a mathematical algorithm (For example the model may be a logistic regression model (Specification, page 4, paragraph [16])) Dependent claims 32-42, recite additional mathematical steps or the data to be used in the mathematical algorithm. 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 computing system, processors, memory, and a non-transitory computer-readable medium. However, the instant claims do not recite structural limitations of these elements, and they do provide a particular machine. The claims also recite the steps of obtaining data, and generating and storing a report. However, these steps are extra solution data gathering steps and output steps. The instant claims 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 additional elements of computing system, processors, memory, and a non-transitory computer-readable medium. These elements are well-understood, conventional and routine components of a general computer (Specification, pages 41 and 42). The instant claims also recite the steps of obtaining data, and generating and storing a report. The steps of obtaining data, and generating and storing a report are well understood, conventional and routine data gathering steps and output steps (Specification, pages 41 and 42; page 53, paragraph [219]). Reciting such well-understood, routine, and conventional elements 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 the types of data for a data gathering step and a computer to implement the judicial exception. Thus, the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claim Rejections - 35 USC § 103
4. 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 31, 32, 41-43, and 52 are rejected under 35 U.S.C. 103 as being unpatentable over Swanton et al. (WO 2019/012296 A1) in view of Wang et al. (WO 2014/116729 A2).
Regarding claims 31 and 52, Swanton et al. teach a method of detecting loss of heterozygosity (LOH) of a human leukocyte antigen (HLA) gene (page 47, lines 14-15 and page 56, lines 11-17) that includes the steps of obtaining human leukocyte antigen coverage feature metrics of a biological sample (page 48, lines 14-18); determine the LOH class for the HLA gene using a three class HLA LOH model that includes a no LOH class (page 48, line 14 – page 49, line 11); and generating and storing a report of the determined LOH class for the HLA gene (page 54, line 37 – page 55, line 13).
While the method of Swanton et al. is drawn to a computation method of determining LOH in HLA genes, Swanton et al. do not explicitly disclose the use of a computer.
Wang et al. teach a method of determining mapped and unmapped reads and typing HLA (Abstract) which includes performing the method on a computer with memories and processors (page 16, paragraph [0078]-page 17, paragraph [0080]).
Regarding claim 32, Swanton et al. teach determining, by processing at least one of the HLA coverage feature metrics using the first LOH classifier model stage, a loss of heterozygosity of the biological sample (page 59, lines 1-23) and classifying, by processing at least one of the HLA coverage feature metrics using the second LOH classifier model stage, the LOH of the biological sample as a partial loss or a clonal loss (page 59, lines 1-23).
Regarding claims 41, Swanton et al. teach obtaining HLA coverage feature metrics of a biological sample from a next generation sequencing system (page 16, line 34-page 17, line 2). Wang et al. teach that the sequencing system may be communicatively coupled to the computing system through a communication network (page 13, paragraph [0064]; page 18, paragraph [0084])
Regarding claim 42, Wang et al. teach receiving sequencing data from a biological sample from a next generation sequencing system that is communicatively coupled to the computing system through a communication network (page 13, paragraph [0064]; page 18, paragraph [0084]). Swanton et al. teach determining HLA coverage feature metrics of the biological sample from the next generation sequencing data (page 16, line 34 – page 17, line 2; page 48, lines 14-18).
Regarding claim 43, Wang et al. teach a computer system that receives a next generation sequencing data generated from a biological sample (page 13, paragraph [0064]; page 18, paragraph [0084]); align the sequencing data against a reference genome to determine a mapped reads dataset and unmapped reads dataset (page 22, paragraph [0095]; page 24, paragraph [00103]); provide the unmapped reads dataset to a HLA typing process to identify at least one candidate HLA allele for the HLA gene (page 24, paragraph [00103]); identify the HLA sequence associated with each candidate HLA allele (page 24-25, paragraph [00104]); create a HLA reference genome using each identified HLA sequence (page 11, paragraph [0054]; page 16, paragraph [0075]); align the next generation sequencing data against HLA reference genome and adjust the HLA reference genome to account for a variant identified during the aligning (page 16, paragraphs [0076] and [0077]) ; align the next generation sequencing data against the HLA reference genome (page 5, paragraph [0020]); and determine the HLA coverage feature metrics associated with one or more identified candidate HLA alleles (page 5, paragraph [0020]).
It would have been obvious to one of ordinary skill in the art, at the time of filing, to combine the teachings of Swanton et al. and Wang et al. Wang et al teach a method of HLA typing of unmapped reads to take into account novel alleles. Thus, one of ordinary skill in the art would have been motivated to incorporate the method of Wang et al. into the method of Swanton et al. to gain the benefit of analyzing novel alleles. Furthermore, one of ordinary skill in the art would have a reasonable expectation of success because the computational steps are readily combinable.
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.
5. Claims 31-52 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,475,978. Although the claims at issue are not identical, they are not patentably distinct from each other.
The instant claims and the claims of the U.S. Patent are drawn to similar steps. The claims at issue differ in that the U.S. Patent is drawn to a computer-implemented method and the instant claims are drawn to a computer system. However, a computer system that implements that recited steps of the instant claims is a computer-implemented method. Thus, the instant claims are not patentably distinct.
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.
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, 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.
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.
/JERRY LIN/Primary Examiner, Art Unit 1685
Prosecution Insights