Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
DETAILED ACTION
1. The Applicant’s response to the office action filed on September 26, 2025 is acknowledged. The Applicant is herein informed about a change in the Examiner on the record.
Status of the Application
2. Claims 112-117 and 119-130 are pending under examination. Claims 1-111 and 118 are canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive for the following reasons.
Claim Rejections - 35 USC § 102-Withdrawn
3. The rejection of claims under 35 USC 102(e) as being anticipated by Samuels et al. has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 103-Withdrawn
4. The rejection of claims under 35 USC 103(a) as being obvious over Samuels et al. in view of Park et al. has been withdrawn in view of the amendment.
Double Patenting-Withdrawn
5. The rejection of claims under obviousness type of double patenting over the claims in US pat 11,001,883 and the rejection of claims under obviousness type of double patenting over the claims in US pat 11,047,003 have been withdrawn in view of the amendment.
New Rejections Necessitated by the Amendment
Claim Rejections - 35 USC § 112
6. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 112-117 and 119-122 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112(pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
As MPEP 2163.06 notes “If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph - written description requirement. In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981)”.
Here, the new limitation of “pooling the plurality of droplets together to form a single pool” in claim 112 appears to represent new matter. The specification discloses pooling the plurality of droplets prior to polymerase and/or reverse transcription (para 0057-0063, 0108-0114, 0101-0102). However, the specification lacks descriptive support for pooling the droplets after exposing the sequences to polymerase and/or reverse transcription as claimed. Since no basis has been found to support for the new limitations in the specification, the claims are rejected as incorporating new matter.
Double Patenting
7. 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.
A. Claims 112-117 and 119-130 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 11,001,883 (hereafter the ‘883) in view of Shoemaker US 2008/0220422).
Although the conflicting claims are not identical, they are not patentably distinct from each other because the claims 112-117 and 119-130 are generic to claims 1-12 of the patent ‘883 or the claims 112-117 and 119-130 are obvious over the claims 1-12 of the patent ‘883. Specifically, the method comprising providing a plurality of droplets containing cells, lysing cells within droplets to produce cell lysate comprising plurality of sequences within the droplets, attaching at least some of the sequences to an adapter bound to a solid support, exposing the cell lysate to a polymerase and/or reverse transcription enzyme to produce plurality of sequences, sequencing some of the sequences comprising performing chromatin immunoprecipitation (ChIP) sequencing on the sequences are within the scope of the claims 1 in combination of claim 8 in the patent ‘883. The only obvious variation is that the claims in the patent does not teach pooling the plurality of droplets together to form a single pool.
Shoemaker et al. teach for identifying nucleic acids comprising amplifying plurality of nucleic acids from plurality of cells in droplets or nanofluidic bins and pooling genome/amplicons for sequencing or downstream analysis (para 0054, 0121-0134, 0160-0164, 0230-0232, 0245-0262).
Therefore, it would have been prima facie obvious to a person of ordinary skill in the art at the time the invention was made to modify the method of the claims as disclosed in the patent ‘883 with the inclusion of pooling sequences as taught by Shoemaker et al. to develop an improved method. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would result in improving the sensitivity of the method because Shoemaker et al. explicitly taught pooling sequences in the bins or droplets would improve cost effective analysis of sequences during sequencing (para 0247-0252)
and such a modification of the method is considered obvious over the cited prior art.
B. Claims 112-117 and 119-130 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No.11,047,003 (hereafter the ‘003) in view of Shoemaker US 2008/0220422) and Shah (Nature Methods, page i-iii, 2009).
Although the conflicting claims are not identical, they are not patentably distinct from each other because the claims 112-117 and 119-130 are generic to claims 1-14 of the patent ‘003 or the claims 112-117 and 119-130 are obvious over the claims 1-14 of the patent ‘003. Specifically, the method comprising providing a plurality of droplets containing cells, lysing cells within droplets to produce cell lysate comprising plurality of sequences within the droplets, attaching at least some of the sequences to an adapter bound to a solid support, exposing the cell lysate to a polymerase and/or reverse transcription enzyme to produce plurality of sequences, sequencing some of the sequences are within the scope of the claims in the patent ‘003. The only obvious variation is that the claims in the patent do not teach pooling the plurality of droplets together to form a single pool and performing chromatin immunoprecipitation sequencing (ChIP-seq).
Shoemaker et al. teach for identifying nucleic acids comprising amplifying plurality of nucleic acids from plurality of cells in droplets or nanofluidic bins and pooling genome/amplicons for sequencing or downstream analysis (para 0054, 0121-0134, 0160-0164, 0230-0232, 0245-0262).
Shah teaches solid phase chromatin immunoprecipitation sequencing (ChIP-seq), wherein Shah teaches that the method generates over 400 million sequence tag reads in a single run that enables whole genome ChIP analysis of complex organisms, with high accuracy (page i, summary, and paragraph under the subheading ‘sensitive ChIP-seq analysis using solid system’).
Therefore, it would have been prima facie obvious to a person of ordinary skill in the art at the time the invention was made to modify the method of the claims as disclosed in the patent ‘003 with the inclusion of pooling sequences as taught by Shoemaker et al. and ChIP-seq as taught by Shah to develop an improved method. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would result in improving the sensitivity of the method because Shoemaker et al. explicitly taught pooling sequences in the bins or droplets would improve cost effective analysis of sequences during sequencing (para 0247-0252) and Shah explicitly taught use of Chip-seq to generate millions of sequence tag reads in a single run with high accuracy to enable whole-genome ChIP analysis (page i, summary, and paragraph under the subheading ‘sensitive ChIP-seq analysis using solid system’) and such a modification of the method is considered obvious over the cited prior art.
C. Claims 123-130 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 17-20 of U.S. Patent No. 11,052,368 (hereafter the ‘368) in view of Shoemaker US 2008/0220422) and Shah (Nature Methods, page i-iii, 2009).
Although the conflicting claims are not identical, they are not patentably distinct from each other because the claims 123-130 are generic to claims 17-20 of the patent ‘368 or the claims 123-130 are obvious over the claims 17-20 of the patent ‘368. Specifically, the method comprising providing a plurality of droplets containing cells, lysing cells within droplets to produce cell lysate comprising plurality of sequences within the droplets, attaching at least some of the sequences to an adapter bound to a solid support, sequencing some of the sequences are within the scope of the claims in the patent ‘368. The only obvious variation is that the claims in the patent do not teach pooling the plurality of droplets together to form a single pool and performing chromatin immunoprecipitation sequencing (ChIP-seq).
Shoemaker et al. teach for identifying nucleic acids comprising amplifying plurality of nucleic acids from plurality of cells in droplets or nanofluidic bins and pooling genome/amplicons for sequencing or downstream analysis (para 0054, 0121-0134, 0160-0164, 0230-0232, 0245-0262).
Shah teaches solid phase chromatin immunoprecipitation sequencing (ChIP-seq), wherein Shah teaches that the method generates over 400 million sequence tag reads in a single run that enables whole genome ChIP analysis of complex organisms, with high accuracy (page i, summary, and paragraph under the subheading ‘sensitive ChIP-seq analysis using solid system’).
Therefore, it would have been prima facie obvious to a person of ordinary skill in the art at the time the invention was made to modify the method of the claims as disclosed in the patent ‘368 with the inclusion of pooling sequences as taught by Shoemaker et al. and ChIP-seq as taught by Shah to develop an improved method. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would result in improving the sensitivity of the method because Shoemaker et al. explicitly taught pooling sequences in the bins or droplets would improve cost effective analysis of sequences during sequencing (para 0247-0252) and Shah explicitly taught use of Chip-seq to generate millions of sequence tag reads in a single run with high accuracy to enable whole-genome ChIP analysis (page i, summary, and paragraph under the subheading ‘sensitive ChIP-seq analysis using solid system’) and such a modification of the method is considered obvious over the cited prior art.
Conclusion
No claims are allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SURYAPRABHA CHUNDURU whose telephone number is (571)272-0783. The examiner can normally be reached 8.00am-4.30pm.
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/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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