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 .
DETAILED ACTION
1. election with traverse of Group I (claims 1-17) is acknowledged. The traversal is based on the arguments drawn to no serous search burden to examine all the groups together. The Applicant’s arguments were found unpersuasive because the International search report indicates anticipation/obviousness of the claimed invention over the prior art references and lack of unity is based on the lack of special technical feature. Further, the unity of invention is not dependent on search burden. For all the above the lack of unit is deemed proper.
Status of the Application
2. Claims 1-17 are considered for examination. Claims 28, 38 and 41 are withdrawn from further consideration as being drawn to nonelected group.
Priority
3. This application filed on April 28, 2024 is a 371 of PCT/IB2021/061892 filed on December 17, 2021, which claims priority benefit of US 63/168,119 filed on March 30, 2021 and US 63/129,248 filed on December 2020.
Informalities
4. The following informalities are noted:
(i) claims 1, 8 recite ‘i.’, ‘ii’ in step (a). Amending the claim to remove full stop before ‘i’, ‘ii’ is suggested.
(ii) claim 17 does not end with a full stop. Appropriate correction is required.
Claim Rejections - 35 USC § 102
5. 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 1-17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nolan et al. (WO2016/100976).
Nolan et al. teach a method of claim 1, for making a physical map of a population of barcoded particles, comprising: (a) producing a complex comprising: i. a population of barcoded particles, wherein the barcoded particles are uniquely barcoded by surface-tethered oligonucleotides that have unique particle identifier sequences (epitope specific barcode) (para 0096-0098, 0045-0058, 0005-0010); and ii. a population of bridging moieties that comprises oligonucleotide sequences (para 0096-0098, 0045-0058, 0005-0010); wherein the bridging moieties hybridize directly or indirectly via a splint to complementary sites in the surface-tethered oligonucleotides (para 0096-0098, 0045-0058, 0005-0010); (b) performing a ligation, polymerization, and/or a gap-fill/ligation reaction on the complex, thereby producing reaction products that comprise pairs of unique particle identifier sequences or from adjacent barcoded particles, or complements thereof (para 0096-0098, 0045-0058, 0005-0010); (c) sequencing the reaction products produced in step (b) (para 0096-0098, 0045-0058, 0005-0010); (d) analyzing the sequences to identify which pairs of unique particle identifier sequences or complements thereof have been copied and/or ligated together in step (b) (para 0096-0098, 0045-0058, 0005-0010); and (c) making one or more physical maps of the barcoded particles using the pairs of sequences identified in (d) ) (para 00112-00115, 00134-00135, 0096-0098, 0045-0058, 0005-0010).
With reference to Claims 2-3, Nolan et al. teach that step (b) is done by ligation or done by a polymerization or gap- fill/ligation reaction (para 0005-0010, 0047-0058).
With reference to Claim 4, Nolan et al. teach that the bridging moieties splint the surface-tethered oligonucleotides from two adjacent barcoded particles together and wherein: step (b) comprises performing a ligation on the complex, thereby producing reaction products that comprise pairs of unique particle identifier sequences from adjacent barcoded particles; and step (c) comprises sequencing the reaction products produced in step (b) (para 0005-0010, 0015-0017, 0047-0058).
With reference to Claim 5, Nolan et al. teach that the method comprises:(b) extending the bridging moieties that are hybridized to surface-tethered oligonucleotides of two barcoded particles to add the unique particle identifier sequences from the two barcoded particles or their complements to the bridging moieties; (c) sequencing the extended bridging moieties; (d) analyzing the sequences to identify which pairs of unique particle identifier sequences or complements thereof have been added onto the bridging moieties; and (e) making one or more physical maps of the barcoded particles using the pairs of sequences identified in (d) (para 00147, 0015-0017, 0056, 00124-00125).
With reference to Claim 6, Nolan et al. teach that hybridizing the population of bridging moieties and the population of barcoded particles, wherein either the bridging moieties or the barcoded particles are immobilized, and wherein: (i) the surface-tethered oligonucleotides of the barcoded particles each have a bridging moiety binding sequence in addition to a unique particle identifier sequence, and (ii) the bridging moieties each comprise a first terminal sequence that is complementary to a bridging moiety binding sequence and a second terminal sequence that is complementary to a bridging moiety binding sequence; and (iii) at least some of the bridging moieties hybridize to surface-tethered oligonucleotides two adjacent barcoded particles (para 0097-0098, 00114).
With reference to Claim 7, Nolan et al. teach that the extending comprises a polymerization, and/or, gap fill and/or ligation reaction, which adds the unique particle identifier sequences from the two adjacent barcoded particles, or their complements, onto the bridging moiety (para 0006, 0014-0024).
With reference to Claim 8, Nolan et al. teach that in step (a): (i) the population of barcoded particles comprises a first set of barcoded particles and a second set of barcoded particles, wherein i the surface-tethered oligonucleotides of the first set of barcoded particles further comprise a first bridging moiety binding sequence, and ii the surface-tethered oligonucleotides of the second set of barcoded particles further comprise a second bridging moiety binding sequence; (ii) the bridging moieties each comprise a first terminal sequence that is complementary to the first bridging moiety binding sequence and a second terminal sequence that is complementary to the second bridging moiety binding sequence; and (iii) at least some of the bridging moieties hybridize to surface-tethered oligonucleotides two adjacent barcoded particles (para 0006-0024).
With reference to Claim 9, Nolan et al. teach that the products of step (b) are amplified by PCR prior to sequencing (para 0006-0017).
With reference to Claims 10-14, Nolan et al. teach that the bridging moieties are immobilized and the barcoded particles are hybridized to the immobilized bridging moieties molecules, or wherein the barcoded particles are immobilized and the bridging moieties are hybridized to the immobilized barcoded particles wherein the bridging moieties are hybridized to sequences that are in or on a cell, prior to hybridization with the barcoded particles, and the bridging moieties are made in situ in or on a cell, prior to hybridization with the barcoded particles ((para 0018-0019).
With reference to Claims 15-16, Nolan et al. teach that the bridging moieties or the barcoded particles are immobilized via an antibody or the bridging moieties or the barcoded particles are immobilized via a nucleic acid probe (para 0018).
With reference to Claim 17, Nolan et al. teach that the bridging moieties or barcoded particles are immobilized on one or more surfaces (para 0091). For all the above the claims are anticipated.
Conclusion
No claims are allowable.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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