Methods and Systems for Analyzing Nucleic Acid Molecules

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 the Claims Claims 2-14 are under examination. 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 2-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. Claims 2-14 are directed to method of identifying one or more cell-free DNA molecules that comprise a plurality of phased variants. 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 processing sequencing data to identify cell free DNA molecules with a plurality of phased variants and aligning reads of the cell-free DNA to the reference methylation status-containing reference sequence. These steps are drawn to mathematical algorithm or mental steps. Dependent claims 3-14 recite additional mathematical or mental steps or the data used in the judicial exception. 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 steps of obtaining sequence data, sequencing cell-free DNA, and contacting a biological sample from a subject with a bait set. However, these steps are extra solution data gathering steps. Extra solution data gathering steps 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 obtaining sequence data, sequencing cell-free DNA, and contacting a biological sample from a subject with a bait set. These elements are well-understood, conventional, and routine data gathering steps (MPEP §2106.05(d)(II)). Reciting such well-understood, routine, and conventional data gathering 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 gathering 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. Examiner’s Note: The closest prior art is Edelman et al (US 2018/0291427 A1). Edelman et al. teach that method that includes sequencing cell-free nucleic acids to detect phased variants (paragraphs [0089], [0095] and [0758]). The prior art does not teach aligning reads to the reference methylation status-containing reference sequence that is at least 10 kb in length and where at least 10% of the cell-free DNA molecules comprises a first phased variant and a second phased variant separated by at least one nucleotide. 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. 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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