DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
Election/Restrictions
2. Applicant’s election with traverse of Group II (claims 62-70) in the reply filed on 4/3/2026 is acknowledged. The traversal is based on applicant’s following argument(s)/assertion(s): (1) “even if the Office deems claims of Groups I and II to be independent or distinct, examination should be extended to both Groups in the absence of a serious search burden”; (2) “[t]he fact that both claims 1 and 22 were granted in the ‘127 patent demonstrates that the Office found no serious burden in examining both in the same application”. This is not found persuasive because: (1) search and examination of both of the two patently distinct methods as recited in the claims of Groups I and II would constitute a serious burden because each of Groups I and II requires different and distinctive feature(s) to be searched; (2) each case is decided on its own facts, and how the other case is examined/handled, based on different facts, is not evidence on how the instant case should be examined. Accordingly, the restriction requirement is still deemed proper and is therefore made FINAL.
3. Claims 39-70 are pending in the application. Claims 39-61 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 62-70 are currently under examination.
Priority
4. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e), 120, 121, or 365(c) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994)
Claims 62-70 of the instant application were first presented on 9/1/2021 via a preliminary amendment. The disclosure of each of the prior-filed applications fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for claims 62-70 of this application. Specifically, none of the prior-filed applications provides support for the following features as recited in independent claim 62: (i) the use of “partially single-stranded cypher polynucleotides comprising bar codes” in the “attaching” step to generate a library of double-stranded cypher-target nucleic acid complexes, and (ii) the feature of “comparing the error-corrected sequences to a reference sequence” as used in step (d). In fact, such features were also not described in the specification as filed on 9/1/2021. Accordingly, instant claims 62-70 are not entitled to the benefit of any of the prior-filed applications, and therefore the instant filing date of 9/1/2021 (when instant claims 62-70 were first presented via preliminary amendment) is the effective filing date for instant claims 62-70.
Claim Rejections - 35 USC § 102
5. The following is a quotation of the appropriate paragraphs of pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(e) the invention was described in (1) an application for patent, published under section 122(b), by another filed in the United States before the invention by the applicant for patent or (2) a patent granted on an application for patent by another filed in the United States before the invention by the applicant for patent, except that an international application filed under the treaty defined in section 351(a) shall have the effects for purposes of this subsection of an application filed in the United States only if the international application designated the United States and was published under Article 21(2) of such treaty in the English language.
6. Claims 62-70 are rejected under pre-AIA 35 U.S.C. 102(a) and 102(e) as being anticipated by Salk et al. (US 10,760,127 B2).
Regarding claim 62
Salk et al. teach a method of sequencing DNA, the method comprising: (a) attaching partially single-stranded cypher polynucleotides (e.g., partially single-stranded adapters) comprising bar codes (e.g., barcodes) selected from a plurality of distinct bar code sequences to double-stranded DNA fragments obtained from a patient sample (e.g., bodily sample from a human subject having a tumor cell population), wherein attachment of the adapters to the double-stranded DNA fragments generates a library of double-stranded cypher-target nucleic acid complexes; (b) amplifying the cypher-target nucleic acid complexes in the library to produce a plurality of cypher-target amplification products from first strands and complementary second strands of the cypher-target nucleic acid complexes; (c) sequencing the cypher-target amplification products to produce a plurality of sequencing reads comprising a bar code sequence and DNA fragment-specific sequence; and (d) for at least some of the cypher-target nucleic acid complexes: (i) grouping the sequencing reads based on the bar code sequence and the DNA fragment-specific sequence; (ii) comparing sequencing reads within the groups to generate an error-corrected sequence (e.g., consensus sequence) for each of a plurality of the double-stranded DNA fragments; (iii) comparing the error-corrected sequences to a reference sequence; and (iv) analyzing one or more sequence correspondences between the error-corrected sequence and the reference sequence to identify a true mutation (e.g., a true sequence variation identified by analyzing one or more correspondences between the consensus sequence and the reference sequence), wherein the true mutation is a mutation present in both the first strand and complementary second strand of the cypher-target nucleic acid complex (see claims 22 and 25).
Regarding claim 63
The method according to Salk et al., wherein the patient sample comprises tissue obtained from the patient (see claims 23-24).
Regarding claim 64
The method according to Salk et al., wherein at least some of the double-stranded DNA fragments are derived from a tumor or circulating tumor cells (see claim 24).
Regarding claim 65
The method according to Salk et al., wherein the patient sample is derived from a patient having tumor cells, wherein the true mutation is a mutation that confers resistance to therapy, and wherein the true mutation is present in an error-corrected sequence derived from one of the double-stranded DNA fragments in the patient sample (see claim 25).
Regarding claim 66
The method according to Salk et al., wherein the double-stranded DNA fragments in the patient sample comprise double-stranded DNA fragments obtained from the tumor cells (see claims 24-25).
Regarding claim 67
The method according to Salk et al., wherein (i) at least two of the bar codes are identical in sequence and are attached to different double-stranded DNA fragments, thereby non-uniquely tagging the different double-stranded DNA fragments; and (ii) the different double-stranded DNA fragments that are non-uniquely tagged comprise distinguishable end sequences (see claim 26).
Regarding claim 68
The method according to Salk et al., further comprising purifying a plurality of cypher-target nucleic acid complexes, wherein the purified cypher-target nucleic acid complexes comprise nucleic acid molecules that map to specific genomic region (see claims 27-28).
Regarding claim 69
The method according to Salk et al., wherein (a) prior to sequencing, the cypher-target nucleic acid complexes or amplification products thereof are selectively enriched by hybridization to substrate bound oligonucleotides; and (b) the sequencing produces sequencing reads for the molecules that map to the specific genomic regions (see claim 28).
Regarding claim 70
The method according to Salk et al., wherein the bar code sequences are 6 nucleotides in length (see claim 29).
Conclusion
7. 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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