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 .
Election/Restrictions
2. Applicant’s election without traverse of Species B, claims 5-9, in the reply filed on May 7, 2026 is acknowledged.
Claims 2-4 and 10-11 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Status of the Claims
Claims 1, 5-9, and 12-22 are under examination.
Claims 2-4 and 10-11 are withdrawn.
Specification
3. The disclosure is objected to because of the following informalities:
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. (See pages 9-10, paragraph [74]) Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
4. 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 1, 5-9, and 12-22 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.
Claim 1 recites the limitation "the HLA type data" in line 4. There is insufficient antecedent basis for this limitation in the claim. This term was not recited previously in the instant claim. It is unclear to what it refers. Dependent claims 5-9 and 12-22 are also rejected for depending from claim 1.
Claim 1 recites the limitation "the filtered aligned read data" in line 11. There is insufficient antecedent basis for this limitation in the claim. This term was not recited previously in the instant claim. It is unclear to what it refers.
The term “low mapping quality score” in claim 1 is a relative term which renders the claim indefinite. The term “low” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim 13 recites the limitation "the event based filter rule" in line 2. There is insufficient antecedent basis for this limitation in the claim. This term was not recited previously in the instant claim. It is unclear to what it refers.
Claim Rejections - 35 USC § 101
5. 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, 5-9, and 12-22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Claims 1, 5-9, and 12-22 are directed to method identifying somatic variants in an HLA gene in a subject. 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 aligning the HLA sequence read data for the normal samples and the HLA sequence data for the tumor sample to the patient specific HLA reference genome, adjusting a mapping quality score associated with each read having a low mapping quality score indicated of multiple-mapping, and performing a variant calling process on the filtered aligned read data and determining the somatic variants of the HLA class. These steps are mental steps.. Dependent claims 5-9 and 12-22 are drawn to additional mental steps or the data used in the steps. 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 steps of obtaining a patient specific HLA reference genome, receiving HLA sequence read data, generating and storing a report, and outputting data. These steps are extra solution data gathering steps. Extra solution data gathering steps do not integrate a 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 obtaining a patient specific HLA reference genome, receiving HLA sequence read data, generating and storing a report, and outputting data. The steps of receiving data and outputting data are well-understood, routine, and conventional data gathering and outputting steps. (MPEP §2106.05(d) and §2106.05(g)). Reciting such well-understood, routine, and conventional data gathering and outputting steps 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. Thus, the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Examiner’s Note:
6. The closest prior art is Yelensky et al. (US 2017/0199961 A1). Yelensky et al teach method of performing variant calling of HLA class (paragraph [0271]). However, Yelensky et al. does not teach aligning the HLA sequence read data from the normal samples and tumor samples to a patient specific HLA reference genome from the HLA type data.
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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/JERRY LIN/Primary Examiner, Art Unit 1685
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