DETAILED ACTION
Applicant's response, filed 07/06/2026, has been fully considered.
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 .
Priority
This application filed 12/13/2022 is a Continuation of 16395658, filed 04/26/2019, now U.S. Patent # 11560586, which is a Continuation of 15149045, filed 05/06/2016, now U.S. Patent # 10323268, which is a Divisional of 13669136, filed 11/05/2012, now U.S. Patent # 9367663, which is a Continuation of PCT/US2012/059123, filed 10/05/2012, which further claims priority from Provisional Application 61709899, filed 10/04/2012, from Provisional Application 61663477, filed 06/22/2012, and from Provisional Application 61544251, filed 10/06/2011. The claims are therefore examined as filed on 10/06/2011, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Election/Restrictions
Claims 10, 13 and 15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 07/06/2026.
Applicant’s election without traverse of claims 9, 12 and 14 in the reply filed on 07/06/2026 is acknowledged.
Claim Status
Claims 1-20 are pending.
Claims 10, 13 and 15 are withdrawn.
Claims 1-9, 11-12, 14, and 16-20 are directed to the elected invention.
Claims 1-9, 11-12, 14, and 16-20 are examined.
Claims 1-9, 11-12, 14, and 16-20 are rejected.
Information Disclosure Statement
The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered.
Specification
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because it consists of a single sentence rather than a paragraph within the range of 50 to 150 words in length . A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
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 1-9, 11-12, 14, and 16-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-9, 11-12, 14, and 16-20 are directed to a process (a method).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. The claims recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Determining a GC bias coefficient based on a fitted relation between the counts of the sequence reads mapped to portions of the reference genome and GC content for the portions (mental process/mathematical concept; the human mind is capable of determining a coefficient based on a fitted relationship between two variables; a mathematical relationship between variables is a mathematical concept; claim 1)
Determining a genomic section level for respective portions of the reference genome based on the counts of the GC bias coefficient and a fitted relation, for the respective portions of the reference genome, between the GC bias coefficient for each of multiple samples and counts of sequence reads mapped to the respective portions of the reference genome for the multiple samples, thereby providing calculated genomic section levels (mental process/mathematical concept; the human mind is capable of determining a value based on related variables, and doing so is equivalent to performing a calculation; claim 1)
Filtering one or more portions and removing counts associated with the filtered portions (mental process; the human mind is capable of filtering data; claims 8-9, 12)
Dependent claims 2-7, 11, and 14, further limit the abstract ideas recited in the independent claims, and do not change their characterization as abstract ideas.
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claim 1 and its dependents recite the additional element of “obtaining counts of sequence reads mapped to portions of a reference genome, which sequence reads are reads of circulating cell-free nucleic acid from a test sample,” and claims 16-20 further describe obtaining thousands to millions of reads using a massively parallel sequencing process.
While the claims recite the additional element of obtaining data using a massively parallel sequencing process, such steps that only amount to necessary data gathering for analysis, without any technical details of how the data is obtained that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims; further, the use of massively parallel sequencing for generating data, without further detail on this process, merely indicates a field of use or technological environment in which to apply a judicial exception (see MPEP 2106.05(g-h)). As a result, the judicial exception is not integrated into a practical application. Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). Non-particular instructions to gather or produce data do not provide an inventive concept, and are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, and “Amplifying and sequencing nucleic acid sequences”, from University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014) are recognized as conventional activities). Further, massively parallel sequencing of cell-free DNA in particular is also a well-known and conventional activity (see BIANCHI 2010 pg 748 section 2.4 as cited on the 892 form). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Claims Without an Art Rejection
No art rejection is applied to claims 1-9, 11-12, 14, and 16-20. Close art, for example FAN 2010 (cited on the IDS filed 2/13/2023), while teaching removal of GC bias in analysis of cell-free DNA within a sample, and ALKAN 2009 (also cited on the IDS filed 2/13/2023), while teaching normalization of read-depth based on the GC content to address GC bias within a sample, do not fully teach the claimed limitations of determining a genomic section level for respective portions of the reference genome based on the counts of sequence reads mapped to portions of a reference genome, the GC bias coefficient of the sample, and a fitted relation, for the respective portions of the reference genome, between the GC bias coefficient for each of multiple samples and counts of sequence reads mapped to the respective portions of the reference genome for the multiple samples, and no combinable art before the effective filing date could be found to render the claims as obvious.
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.
Claim Rejection over Patent No. 9367663
Claims 1-9, 11-12 and 17 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5, 7-8, and 10-12 of U.S. Patent No. 9367663. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the patent anticipate the claims of the present invention:
Claim 1 of the present invention is anticipated by claim 1 of Patent No. 9367663.
Claim 2 of the present invention is anticipated by claim 1 of the patent.
Claim 3 of the present invention is anticipated by claim 3 of the patent.
Claim 4 of the present invention is anticipated by claim 2 of the patent.
Claim 5 of the present invention is anticipated by claim 3 of the patent.
Claim 6 of the present invention is anticipated by claim 4 of the patent.
Claim 7 of the present invention is anticipated by claim 5 of the patent.
Claim 8 of the present invention is anticipated by claim 7 of the patent.
Claim 9 of the present invention is anticipated by claim 8 of the patent.
Claim 11 of the present invention is anticipated by claim 10 of the patent.
Claim 12 of the present invention is anticipated by claim 12 of the patent.
Claim 17 of the present invention is anticipated by claim 15 of the patent.
Claim Rejection over Patent No. 9984198
Claims 1-9, 11-12, and 17-18 are also rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 12-13, and 31-32 of U.S. Patent No. 9984198. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the patent anticipate the claims of the present invention:
Claim 1 of the present invention is anticipated by claim 1 of Patent No. 9984198.
Claim 2 of the present invention is anticipated by claim 1 of the patent.
Claim 3 of the present invention is anticipated by claim 2 of the patent.
Claim 4 of the present invention is anticipated by claim 4 of the patent.
Claim 5 of the present invention is anticipated by claim 5 of the patent.
Claim 6 of the present invention is anticipated by claim 6 of the patent.
Claim 7 of the present invention is anticipated by claim 7 of the patent.
Claim 8 of the present invention is anticipated by claim 8 of the patent.
Claim 9 of the present invention is anticipated by claim 10 of the patent.
Claim 11 of the present invention is anticipated by claim 12 of the patent.
Claim 12 of the present invention is anticipated by claim 13 of the patent.
Claim 17 of the present invention is anticipated by claim 31 of the patent.
Claim 18 of the present invention is anticipated by claim 32 of the patent.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
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, Karlheinz R. Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARY C LEVERETT/ Examiner, Art Unit 1687
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