Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
DETAILED ACTION
Responsive to claim set of 5/20/2024
Claims pending 14-33
Claims currently under consideration 14-33
Priority
This application has a filing date of 10/16/2023 and is a CON of
18/065,567 12/13/2022 ABN
18/065,567 is a CON of 15/993,418 05/30/2018 ABN
15/993,418 is a CON of 15/136,780 04/22/2016 PAT 10023910
15/136,780 is a CON of 14/205,145 03/11/2014 PAT 9328382
14/205,145 has PRO 61/801,052 03/15/2013
Claim Rejections - 35 USC § 102
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.
Claims 14-17,19,24-26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by the Nextera® XT DNA Sample Preparation Guide from Illumina, October 2012 (referred to hereafter as Illumina).
Disclosed throughout the document and especially pp 1-5,8 including figure and table 1, is sample preparation of as little as 1 ng DNA, such as from a human genome, for sequencing on an Illumina nucleic acid sequencer that includes steps of: (A) combining a plurality of long DNA fragments of target nucleic acid with a population of tag-containing sequences, wherein the population comprises at least 1000 different tag sequence molecules (e.g. 2 primer sequences); (B) producing tagged long fragments, wherein each tagged long fragment comprises target nucleic acid sequences interspersed between multiple tag sequence(s), wherein the multiple interspersed tag sequences in an individual tagged long fragment may be the same or different;
(C) tagmenting, that is: both producing from each tagged long fragment a plurality of tagged subfragments, wherein the tagged subfragments each comprise additional tag sequences with a polymerase and primers and (D) obtaining sequence of individual tagged sub fragments, wherein the obtained sequence includes target nucleic acid sequence and additional tag sequence (e.g. comprising sequencing primer complements and sample indices (clonal barcodes); (E) combining sequences obtained in (D) to produce assembled sequence(s) of the target nucleic acid, wherein the combining comprises necessarily (1) determining that sequences obtained in (D) originated from the same long DNA fragment if said sequences comprise the same tag sequence and/or (2) identifying pairs of sequences as being adjacent sequences in the target nucleic acid if the pair comprise the same tag sequence (e.g. the upstream and downstream portions of the Sequencing-Ready Fragment depicted on the fifth page; and such that steps (A)-(C) are carried out in a mixture in a single vessel. The foregoing reads on claims 14,15,16,24,26 and inherently on claim 19. And moreover, such human genomic DNA sample has more than 5 copies and has segments well in excess for 50 kb like claim 17,25
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 14-17,19,24-26 and 18,20-23,28,30,31 are rejected under 35 U.S.C. 103 as being unpatentable over Illumina in view of Namsaraev (US AppPub 20110294689 ).
Illumina is relied on as above and claims 28 items (i) & (ii) polymerase at least of claim 29 as well as regarding claims 20,21,22 & 23 respectively, in so far as Illumina suggests 300 bp amplicons & human genomes are diploid in table 1. (Applicant is advised Illumina further appears disclose the subject matter of claims 32-33)
Illumina does not explicitly teach:10,000 barcodes of claims 30,31; RCA (rolling circle amplification) of monomers from 50 to 200 kb templates of claims 18 & claim 28 item (iv).
As in claim 28 items (iii) & (iv) and 30,31, Namsaraev teaches throughout the document and especially the abstract and paragraphs 0190-0194, and 0125, multiplexing techniques with 10,000 or more distinct barcodes such for as RCA (rolling circle amplification) that inherently generates concatemerized monomers. And in paragraph 0153, Namsaraev suggests 50 kb templates, in the range of claim 18. (Applicant is advised Namsaraev also appears to disclose the subject matter of claims 32-33).
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have employed the large number of barcodes for multiplexed RCA of monomers from long templates suggested by Namsaraev for sequencing in the manner of Illumina.
One of ordinary skill in the art would have been motivated to have employed the large number of barcodes for multiplexed RCA of monomers from long templates suggested by Namsaraev for sequencing in the manner of Illumina for the benefit of affording greater efficiency and lower cost toward large scale projects, as noted by Namsaraev in paragraph 0005.
One of ordinary skill in the art would have had a reasonable expectation of success in utilizing an Illumina sequencer for such concatenates of Namsaraev, since Illumina expressly specify concatenated amplicons are well suited therein at p 4 again in table 1.
Double Patenting
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claims 14,15,28 are provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claims 1,2, and 90 of copending Application No. 18/768640 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claim Rejections - 35 USC § 112
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 27,32-33 are 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 pre-AIA the applicant regards as the invention.
Claim 32 recites the limitation "the library members" in line 1. There is insufficient antecedent basis for this limitation in the claim, especially since claim 28 recites at least five libraries rendering the metes and bounds uncertain.
Claim 27 recites the phrase “any of claims 24” which is deemed grammatically incongruent: it is not clear if the claim depends from only claim 24 or alternatively plural other claims, therein rendering the metes and bounds unascertainable.
In accordance with MPEP 2173.02: If the language of the claim is such that a person of ordinary skill in the art could not interpret the metes and bounds of the claim so as to understand how to avoid infringement, a rejection of the claim under 35 U.S.C. 112, second paragraph, would be appropriate. See Morton Int ’l, Inc. v. Cardinal Chem. Co., 5 F.3d 1464, 1470, 28 USPQ2d 1190, 1195 (Fed. Cir. 1993).
In so far as the metes and bounds of the offending claim(s) may not be interpreted properly for the reasons above, all dependent claims therefrom claim 32 are rejected as being indefinite as well.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTOPHER M GROSS whose telephone number is (571)272-4446. The examiner can normally be reached M-F 10-6.
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, Heather Calamita can be reached on (571)272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CHRISTOPHER M GROSS/Primary Examiner, Art Unit 1684
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