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.
Claim 20 is 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 20 is indefinite for reciting a group selected from ”blood, serum, plasma and urine.” The claim is indefinite because it is not clear if the third embodiment is plasma or a combination of plasma and urine. The rejection would be overcome by insertion of a comma after the term plasma.
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 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 of determining of a chromosome aneuploidy, microduplication or microdeletion in a test sample is from a cancer cell or a non-cancer cell nucleic acid. 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 normalizing counts of nucleotide sequence reads mapped to a segment comprising aneuploidy, microduplication, or microdeletion where the nucleotide sequence reads are circulating cell-free nucleic acid from nucleic acid fragments having lengths less than or equal to a first selected fragment length, normalizing counts of nucleotide sequence reads mapped to a segment comprising aneuploidy, microduplication, or microdeletion where the nucleotide sequence reads are circulating cell-free nucleic acid from nucleic acid fragments having lengths less than or equal to a second selected fragment length, determining a first fraction of the cancer cell nucleic acid based on normalized counts, determining a second fraction of cancer cell nucleic acid based on the normalized counts, and determining whether the chromosome aneuploidy, microduplication, or microdeletion is from a cancer cell nucleic acid or non-cancer cell nucleic acid according to the difference between the first fraction of cancer cell nucleic acid and the second fraction of the cancer cell nucleic acid. These steps are drawn to mathematical or mental steps. Dependent claims 2-17 and 20 recite additional mathematical steps, the data used in the mathematical algorithm, or the source of data. 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 sequencing nucleic acid to generate sequence reads by a paired end nucleotide sequencing process. However, this is an extra solution data gathering step. Extra solution data gathering steps are not sufficient to 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 sequencing nucleic acid to generate sequence reads by a paired end nucleotide sequencing process. However, this element is well-understood, conventional and routine data gathering process (Specification, pages 281-282). 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 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.
Claim Rejections - 35 USC § 102
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 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)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 2, 4, 13, 14, and 18-20 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Lo et al. ( US 2013/0237431).
The subject matter of claims 1, 2, and 4 is a process of determining whether a chromosome aneuploidy, microduplication, or microdeletion present in cell-free nucleic acids are derived from either a cancer cell or a non-cancer cell. Counts of sequence reads that map to a segment comprising the chromosome aneuploidy, microduplication, or microdeletion are normalized. Fractions of fragment size classes in the analyzed cell-free nucleic sample are determined and used to determine if the chromosome aneuploidy, microduplication, or microdeletion is derived from a cancer cell or a non-cancer cell. In the embodiment of claim 13 a fragment size of between about 20bp to about 499bp is a lower fragment length threshold. In the embodiment of claim 14 a fragment size between about 100bp to about 199bp is a lower fragment length threshold. In the embodiment of claim 18 the process includes sequencing the nucleic acids. In the process of claim 19 the process includes paired end sequencing of nucleic acids. In the process of claim 20 the sample is derived from blood, serum, plasma, and urine.
Lo et al. shows in the abstract and throughout a process of correlating proportions of tumor DNA of a particular size with the presence of cancer cells in a subject. Fragment sizes of a cell-free sample are analyzed in Figures 15A-16B, as discussed in paragraphs 34-37. Analysis of size ratios of size classes are shown in Figures 17-20 as discussed in paragraphs 38-43. A lower size class of 100bp to 150bp is shown in Figure 17. Determination of the presence of cancer cells is shown in the flowchart in Figure 21. Paragraph 63 discusses correlating the size of fragments of tumor DNA with the percentage of tumor DNA fragments in a sample, and is further discussed in paragraphs 153-161. Sequencing of samples is shown in paragraph 141. Analysis of regions with a duplication or mutation are shown in paragraphs 142-143. Normalization of sequence read counts is shown in paragraph 71. Use of paired end sequencing is shown in paragraph 48. Samples derived from plasma, serum, and urine are shown in paragraph 47.
Double Patenting
5. 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.
6. Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of U.S. Patent No. 11,783,911. 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 recite similar limitations. The claims differ in that the claims of the U.S. Patent recite a first and second minority nucleic acid species whereas the instant claims recite a cancer cell and non-cancer cell. However, the claims of the U.S. Patent recite in claim 7 that the minority species may be a cancer cell or non-cancer cell. Thus, the instant claims recite overlapping subject matter and 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.
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/JERRY LIN/ Primary Examiner, Art Unit 1685
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