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. Claim 53 is objected to because of the following informalities: “KRAS-G13D, KRAS-G13C, KRAS-G13R, KRAS-G13D, KRAS-G13C, KRAS-G13R, KRAS-G13S, KRAS-G12V, KRAS-G12A, KRAS-G12D, KRAS-G12D, KRAS-G12C” in lines 6-8 should be changed to “KRAS-G13D, KRAS-G13C, KRAS-G13R, . Appropriate correction is required.
Claim Rejections - 35 USC § 102
3. 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 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.
4. 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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(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.
5. Claims 41-54 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Cann et al. (US 2016/0017396 A1).
Regarding claim 41
Cann et al. teach, throughout the whole document, a method for analyzing the genome of a cancer patient, comprising: providing an endonuclease system that comprises a plurality of crRNAs, or derivatives thereof, and a plurality of Cas proteins, or variants thereof, wherein each crRNA comprises a targeting sequence, and wherein each Cas protein is capable of binding to a PAM site on a target nucleic acid (see paragraphs [0028]-[0029], [0136] and 0148]); contacting a patient sample, obtained from the cancer patient and comprising a plurality of target nucleic acids, with the endonuclease system to obtain a pool of target nucleic acid fragments associated with the patient sample, wherein each target nucleic acid fragment of the pool of target nucleic acid fragments is a DNA fragment of cell-free DNA (cfDNA) (see paragraphs [0054], [0156] and [0165]); sequencing the pool of target nucleic acid fragments to obtain first sequencing data from the cancer patient (see paragraphs [0054] and [0214]); and comparing the first sequencing data from the cancer patient with second sequencing data from a reference genome fragmented by the endonuclease system to detect structural rearrangements and mutations in the genome of the cancer patient (see paragraphs [0165]-[0166] and [0183]. When the method is used to “monitor tumor progression”, it involves comparing a first sequencing data from the cancer patient at a later time point with a second sequencing data from the cancer patient at an earlier time point, where the second sequencing data may be interpreted as sequencing data from a reference genome (i.e., the cancer patient’s genome at an earlier time point) fragmented by the same endonuclease system.).
Regarding claim 42
The method according to Cann et al., wherein comparing the sequencing data comprises: comparing a first fragmentation pattern of the pool of target nucleic acids fragments associated with the patient sample with a second fragmentation pattern of a pool of target nucleic acids fragments from the reference genome (see paragraphs [0165]-[0166] and [0183]. When the method is used to “monitor tumor progression”, comparing the sequencing data comprises: comparing a first fragmentation pattern of the pool of target nucleic acids fragments associated with the patient sample [at a later time point] with a second fragmentation pattern of a pool of target nucleic acids fragments from the reference genome (i.e., the cancer patient’s genome at an earlier time point).).
Regarding claim 43
The method according to Cann et al., further comprising: contacting a control sample, obtained from a control subject and comprising a plurality of target nucleic acids, with the endonuclease system to obtain the pool of target nucleic acid fragments from the reference genome and associated with the control sample; and sequencing the pool of target nucleic acid fragments associated with the control sample to obtain the second sequencing data from the reference genome (see paragraphs [0165]-[0166] and [0183]. When the method is used to “monitor tumor progression”, the control sample (which is obtained from the cancer patient at an earlier time point) is contacted with the same endonuclease system, and sequenced in the same way as the patient sample [at a later time point].).
Regarding claims 44-45
The method according to Cann et al., wherein the endonuclease system cleaves target nucleic acids in the control sample at a predetermined interval, wherein the predetermined interval is about 300 bp (see paragraph [0194]).
Regarding claims 46-47
The method according to Cann et al., wherein the plurality of Cas proteins comprises Cas9 or a variant thereof, wherein the Cas9 or variant thereof is derived from Streptococcus pyogenes (see paragraphs [0015], [0026], [0054] and [0149]).
Regarding claim 48
The method according to Cann et al., wherein the patient sample comprises a blood sample, a serum sample, a plasma sample, a urine sample, or a cerebrospinal fluid sample (see paragraphs [0028] and [0156]).
Regarding claim 49
The method according to Cann et al., wherein a sequence in the plurality of target nucleic acids in the patient sample comprises a mutant allele sequence (e.g., B-Raf V600E) selected from a group consisting of: AKT1, BRAF, EGFR, KRAS, MAP2K1, NRAS, PI3KCA and PTEN (see paragraph [0167]).
Regarding claim 50
The method according to Cann et al., wherein a sequence in the plurality of target nucleic acids in the patient sample comprises a point mutation of at least one base pair (see paragraphs [0165]-[0166]).
Regarding claim 51
The method according to Cann et al., wherein the cfDNA comprises circulating tumor DNA (ctDNA) that includes a mutation selected from a group consisting of: a single nucleotide mutation, an insertion, and a deletion (see paragraphs [0165]-[0166]).
Regarding claim 52
The method according to Cann et al., wherein a target nucleic acid fragment of the pool of target nucleic acid fragments has either a blunt end or a staggered end (see paragraph [0204]).
Regarding claims 53-54
The method according to Cann et al., wherein a sequence in the plurality of target nucleic acids in the patient sample comprises BRAF-V600E (i.e., B-Raf V600E) (see paragraph [0167]).
Conclusion
6. No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAIJIANG ZHANG whose telephone number is (571)272-5207. The examiner can normally be reached Monday - Friday, 8:30 am - 5 pm.
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/KAIJIANG ZHANG/Primary Examiner, Art Unit 1684
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