DETAILED ACTION
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 08/21/2026 has been entered.
Status of Claims
Claim 23-32, 34, 36, 38, and 40-48 are pending and under examination.
Claims 1-22, 33, 35, 37 and 39 have been canceled.
Response to Amendment
Based on the amended claims and remarks, the prior art rejection over on Shema-Yaacoby has been modified to address the amended claims (see below).
New double patenting rejection(s) have been set forth.
Claim Rejections - 35 USC § 103
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.
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.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 23-32, 34, 36, 38, 40-48 are rejected under 35 U.S.C. 103 as being unpatentable over Shema-Yaacoby et al. (WO 2017/034970 A1 where US 2019/0284603 is used as the corresponding document - hereinafter “Yaacoby”; already of record), in view of Weitz et al. (US 2016/0201129 – hereinafter “Weitz”), Epstein et al. (US 2017/0343539 – hereinafter “Epstein”; already of record) , and Bibillo et al. (US 2019/0040454 – hereinafter “Bibillo”; already of record).
Regarding claim 23, Yaacoby discloses a method determining an epigenetic state of a biological element (Yaacoby discloses technologies to study the contribution of epigenetic mechanisms to cancer initiation and progression; [0017] including a method for screening drug targets and drug candidates based on changes in the combinatorial pattern of histone modifications; [0018]), comprising:
(a) forming a plurality of first droplet that comprise: i) a biological element, wherein the biological element contains or is suspected of containing at least one nucleosome comprising one or more epigenetic features and a genomic region, ii) a lysis buffer, and iii) a nuclease (Yaacoby discloses the method comprises obtaining isolated chromatin fragments by separating single cells into droplets formed by an aqueous solution in oil emulsion, wherein each droplet comprises a single cell, a nuclease, and a lysis buffer; [0025, 0032]);
(d) providing a plurality of second droplets that comprise a nucleic acid molecule comprising a barcode sequence, an adaptor, and a protecting function against unwanted ligation (Yaacoby discloses covalently linking an oligonucleotide sequence to the isolated chromatin fragments by introducing a second droplet comprising the oligonucleotide and a barcode; [0019, 0025, 0032]. The oligonucleotides comprise either a ssDNA, biotin, phosphoryl group, or a restriction enzyme site at the 3’ end or 5’ end; [0020, 0260]);
(e) processing the nucleic acid molecule of one or more second droplets of the plurality of second droplets by fusing a first droplet of the plurality of first droplets with a second droplet of the plurality of second droplets to identify said one or more epigenetic features, wherein processing comprises: (i) ligating the barcode sequence and the adaptor to an end of the genomic region of one or more nucleosomes to obtain one or more barcoded nucleosome sequences, and (ii) obtaining sequence information from one or more barcoded nucleosome sequences comprising the barcode sequence on the nucleosome sequence (Yaacoby; Introducing the oligonucleotide sequence may comprise fusing the second droplet with the first droplet; [0025]. The method is used in the study of epigenetics as discussed in “Example 10”. “Applicants can use the microfluidics to lyse single cells, digest their chromatin and index nucleosomes to originating cell. In this case, the nucleosomes are ligated to adaptors containing both barcode and biotin.”; fig. 5 – “Single nucleosome decoding”, [0017, 0205, 0253, 0255, 0258, 0260]); and
(f) using said one or more epigenetic features and said barcode sequence to determine barcode epigenetic state of the biological element of one or more of the plurality of first droplets ([0017, 0205, 0254-0255]).
Yaacoby does not teach (b) synchronizing enzymatic activity of the nuclease in the plurality of first droplets by collecting the plurality of first droplets under conditions that temporarily inactivate said nuclease, wherein the collecting is performed during and throughout the formation of the plurality of first droplets and the plurality of first droplets is collected at a temperature of -20°C to 10°C such that the nuclease is held inactive in each first droplet from its formation until step (c) and (c) incubating the collected plurality of first droplets at a temperature of 20°C to 40°C to thereby synchronously activate the nuclease in the plurality of first droplets. However, Weitz teaches the analogous art of a method (Weitz; Example 1, [0093-0107]) comprising (a) forming a first type of droplet comprising a biological element (Weitz; [0103]), (b) synchronizing enzymatic activity of the nuclease in the plurality of first droplets by collecting the plurality of first droplets under conditions that temporarily inactivate said nuclease, wherein the collecting is performed during and throughout the formation of the plurality of first droplets and the plurality of first droplets is collected at a temperature of -20°C to 10°C such that the nuclease is held inactive in each first droplet from its formation until step (c) (Weitz teach the syringes connected to the droplet maker were kept on ice throughout drop making and the droplets were collected on ice; [0103, 0105]) (c) incubating the collected plurality of first droplets at a temperature of 20°C to 40°C to thereby synchronously activate the nuclease in the plurality of first droplets (Weitz teach after droplet formation and collection on ice, the emulsion samples were wicked into glass capillary tubes and mounted on a confocal microscope stage heated to 37˚C). It would have been obvious to one of ordinary skill in the art before the effective filing date to have modified the method of Yaacoby to comprise (b) synchronized collecting of the first type of droplet at a temperature of -20°C to 10°C and (c) synchronized incubating of the first type of droplet at a temperature of 20°C to 40°C, as taught by Weitz, because Weitz teaches synchronized collecting of the first type of droplet at a temperature of -20°C to 10°C increases the density of the oil in which the droplets are collected thus making separation faster, and synchronized incubating of the first type of droplet at a temperature of 20°C to 40°C allows the target cell to be measured under conditions which simulate the temperature of the human body; [0103-0106]. NOTE: When the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, the prior art products necessarily possess the characteristics of the claimed product. See MPEP 2112.01. As stated in In re Best, 562 F.2d 1252, 1255 (CCPA 1977): Where, as here, the claimed and prior art products are identical or substantially identical, or are produced by identical or substantially identical processes, the PTO can require an applicant to prove that the prior art products do not necessarily or inherently possess the characteristics of his claimed product. Whether the rejection is based on “inherency” under 35 U.S.C. § 102, on “prima facie obviousness” under 35 U.S.C. § 103, jointly or alternatively, the burden of proof is the same, and its fairness is evidenced by the PTO’s inability to manufacture products or to obtain and compare prior art products. See MPEP 2112. In this case, Yaacoby modified by Weitz would result in the claimed conditions that temporarily inactivate said nuclease and temperature of 20°C to 40°C to activate the nuclease. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since Yaacoby and Weitz both teach a method for studying biological elements in droplet formations.
Modified Yaacoby does not teach one or more asymmetrically barcoded nucleosome sequences comprising the barcode sequence on only one end of the nucleosome sequence. However, Epstein teaches the analogous art of labeling fragmented nucleosomal DNA with barcoded adapters, wherein the barcoded adapters may comprise DNA, RNA, nucleotide analogs or combinations thereof, and a protecting function comprising a three-carbon spacer, wherein the nucleosomal DNA is labeled on only a single free end (Epstein; [0055-0056]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, because Epstein teaches the barcoded adapter comprising the protecting function prevents self-ligation and concatemerization of the adapter at the 5’ end; [0056]. Thus, obtaining sequence information from one or more asymmetrically barcoded nucleosome sequences comprising the barcode sequence on only one end of the nucleosome sequence; [0007, 0055-0056]. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Yaacoby and Epstein both teach labeling nucleosomal DNA with adapters.
Modified Yaacoby does not teach wherein the protecting function against unwanted ligation is on a 3’-end of the nucleic acid molecule. However, Bibillo teach the analogous art of a method for detecting, diagnosing, and/or prognosing cancer in a subject using sequence information of a nucleic acid molecule (Bibillo; [0189]) wherein the nucleic acid molecule is modified to include the addition of a C3 spacer to the 3’ end of a polynucleotide (Bibillo; [0113]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the nucleic acid molecule and protecting function of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, because Bibillo teach the C3 spacer on the 3’-end of the nucleic acid molecule protects the nucleic acid molecule from being mistaken as an RNA primer by functioning as an effective blocking agent against polymerase extension (Bibillo; [0113]).
Regarding claim 24, modified Yaacoby teach the method of claim 23 above, wherein the biological element is chosen from a single cell, a nucleus, and a nucleic acid-containing organelle (Yaacoby; [0025]).
Regarding claim 25, modified Yaacoby teach the method of claim 23 above, wherein said one or more epigenetic features comprise one or more DNA or protein modifications (Yaacoby; chromatin fragments refer to a mixture of DNA and proteins. See Example 10. [0025, 0032, 0251-0260]).
Regarding claim 26, modified Yaacoby teach the method of claim 23 above, wherein the one or more epigenetic features comprise a post-translational modification chosen from acetylation, amidation, deamidation, carboxylation, disulfide bond, formylation, glycosylation, hydroxylation, methylation, myristoylation, nitrosylation, phosphorylation, prenylation, ribosylation, sulphation, sumoylation, ubiquitination and derivatives thereof (Yaacoby; [0047]).
Regarding claim 27, modified Yaacoby teach the method of claim 23 above, wherein the one or more epigenetic features comprise the modification of the presence or absence of methylation of DNA in at least one gene (Yaacoby; [0047, 0091]).
Regarding claim 28, modified Yaacoby teach the method of claim 23 above, wherein the protecting function is a spacing element or a dideoxy-modified base (The modification of the nucleic acid molecule and protecting function of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, has previously been discussed in claim 23 above. Bibillo teach the addition of 3’ C3 spacer to the 3’ end of a polynucleotide or dideoxy 3’ end; [0113]).
Regarding claim 29, modified Yaacoby teach the method of claim 23 above, wherein the nucleic acid molecule further comprises at least one cleavage site (Yaacoby discloses the method may comprise cleaving of the marker from the oligonucleotide sequence; [0021, 0052]).
Regarding claim 30, modified Yaacoby teach the method of claim 28 above, wherein the spacing element is a three carbon (C3) spacer (The modification of the nucleic acid molecule and protecting function of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, has previously been discussed in claim 23 above. Bibillo teach the addition of 3’ C3 spacer to the 3’ end of a polynucleotide; [0113]).
Regarding claim 31, modified Yaacoby teach the method of claim 29 above, wherein the at least one cleavage site is a restriction site comprising a palindromic region (Yaacoby; [0132-0133, 0161]).
Regarding claim 32, modified Yaacoby discloses a method (Yaacoby; [0018]), comprising:
(i) determining an epigenetic state of a biological element from a subject in need thereof (Yaacoby discloses technologies and methods to study the contribution of epigenetic mechanisms to cancer initiation and progression; [0017-0018]),
(ii) diagnosing and/or prognosing drug resistance in the subject based on the epigenetic state (Yaacoby discloses the method comprises screening drug targets and drug candidates based on changes in the combinatorial pattern of histone modifications; [0018]), and
(iii) administering a therapeutic agent to the subject based on the diagnosis and/or prognosis of (ii) (Yaacoby; fig. 3D, [0074, 0225, 0258]),
wherein the epigenetic state of the biological element is determined using a method comprising:
(a) forming a plurality of first droplets that comprise: i) a biological element, wherein the biological element contains or is suspected of containing at least one nucleosome comprising one or more epigenetic features and a genomic region, ii) a lysis buffer, and iii) a nuclease (Yaacoby discloses the method comprises obtaining isolated chromatin fragments by separating single cells into droplets formed by an aqueous solution in oil emulsion, wherein each droplet comprises a single cell, a nuclease, and a lysis buffer; [0025, 0032]);
(d) providing a plurality of second droplets that comprise a nucleic acid molecule comprising a barcode sequence, an adaptor, and a protecting element against unwanted ligation (Yaacoby discloses covalently linking an oligonucleotide sequence to the isolated chromatin fragments by introducing a second droplet comprising the oligonucleotide and a barcode; [0019, 0025, 0032]. The oligonucleotides comprise either a ssDNA, biotin, phosphoryl group, or a restriction enzyme site at the 3’ end or 5’ end; [0020, 0260]);
(e) processing the nucleic acid molecule of one or more second droplets of the plurality of second droplets by fusing a first droplet of the plurality of first droplets with a second droplet of the plurality of second droplets to identify the one or more epigenetic features, wherein processing comprises: (i) ligating the barcode sequence and adaptor to an end of the genomic region of one or more nucleosomes to obtain one or more barcoded nucleosome sequences; and (ii) obtaining sequence information from one or more barcoded nucleosome sequences comprising the barcode sequence on the nucleosome sequence (Yaacoby; Introducing the oligonucleotide sequence may comprise fusing the second droplet with the first droplet; [0025]. The method is used in the study of epigenetics as discussed in “Example 10”. “Applicants can use the microfluidics to lyse single cells, digest their chromatin and index nucleosomes to originating cell. In this case, the nucleosomes are ligated to adaptors containing both barcode and biotin.”; fig. 5 – “Single nucleosome decoding”, [0017, 0205, 0253, 0255, 0258, 0260]); and
(f) using said one or more epigenetic features and said barcode sequence to determine the epigenetic state of the biological element of one or more of the plurality of first droplets ([0017, 0205, 0254-0255]).
Yaacoby does not disclose (b) synchronizing enzymatic activity of the nuclease in the plurality of first droplets by collecting the plurality of first droplet under conditions that temporarily inactivate said nuclease, wherein the collecting is performed during and throughout formation of the plurality of first droplets and the plurality of first droplets is collected at a temperature of -20°C to 10°C such that the nuclease is held inactive in each first droplet from its formation until step (c) and (c) incubating the collected plurality of first droplets at a temperature of 20°C to 40°C to thereby synchronously activate the nuclease in the plurality of first droplets.
However, Weitz teaches the analogous art of a method (Weitz; Example 1, [0093-0107]) comprising (a) providing a first type of droplet comprising a biological element (Weitz; [0103]), (b) synchronizing enzymatic activity of the nuclease in the of first droplets by collecting the plurality of first droplet under conditions that temporarily inactivate said nuclease, wherein the collecting is performed during and throughout formation of the plurality of first droplets and the plurality of first droplets is collected at a temperature of -20°C to 10°C such that the nuclease is held inactive in each first droplet from its formation until step (c) (Weitz teach the syringes connected to the droplet maker were kept on ice throughout drop making and the droplets were collected on ice; [0103, 0105]) and (c) incubating the collected plurality of first droplets at a temperature of 20°C to 40°C to thereby synchronously activate the nuclease in the plurality of first droplets (Weitz teach after droplet formation and collection on ice, the emulsion samples were wicked into glass capillary tubes and mounted on a confocal microscope stage heated to 37˚C). It would have been obvious to one of ordinary skill in the art before the effective filing date to have modified the method of Yaacoby to comprise (b) synchronized collecting of the first type of droplet at a temperature of -20°C to 10°C and (c) synchronized incubating of the first type of droplet at a temperature of 20°C to 40°C, as taught by Weitz, because Weitz teaches synchronized collecting of the first type of droplet at a temperature of -20°C to 10°C increases the density of the oil in which the droplets are collected thus making separation faster, and synchronized incubating of the first type of droplet at a temperature of 20°C to 40°C allows the target cell to be measured under conditions which simulate the temperature of the human body; [0103-0106]. NOTE: When the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, the prior art products necessarily possess the characteristics of the claimed product. See MPEP 2112.01. As stated in In re Best, 562 F.2d 1252, 1255 (CCPA 1977): Where, as here, the claimed and prior art products are identical or substantially identical, or are produced by identical or substantially identical processes, the PTO can require an applicant to prove that the prior art products do not necessarily or inherently possess the characteristics of his claimed product. Whether the rejection is based on “inherency” under 35 U.S.C. § 102, on “prima facie obviousness” under 35 U.S.C. § 103, jointly or alternatively, the burden of proof is the same, and its fairness is evidenced by the PTO’s inability to manufacture products or to obtain and compare prior art products. See MPEP 2112. In this case, Yaacoby modified by Weitz would result in the claimed conditions that temporarily inactivate said nuclease and temperature of 20°C to 40°C to activate the nuclease. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since Yaacoby and Weitz both teach a method for studying biological elements in droplet formations.
Modified Yaacoby does not teach one or more asymmetrically barcoded nucleosome sequences comprising the barcode sequence on only one end of the nucleosome sequence.
However, Epstein teaches the analogous art of labeling fragmented nucleosomal DNA with barcoded adapters, wherein the barcoded adapters may comprise DNA, RNA, nucleotide analogs or combinations thereof, and a protecting function comprising a three-carbon spacer, wherein the nucleosomal DNA is labeled on only a single free end (Epstein; [0055-0056]).
It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, because Epstein teaches the barcoded adapter comprising the protecting function prevents self-ligation and concatemerization of the adapter at the 5’ end; [0056]. Thus, obtaining sequence information from one or more asymmetrically barcoded nucleosome sequences comprising the barcode sequence on only one end of the nucleosome sequence; [0007, 0055-0056]. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Yaacoby and Epstein both teach labeling nucleosomal DNA with adapters.
Modified Yaacoby does not teach wherein the protecting element against unwanted ligation is on a 3’-end of the nucleic acid molecule. However, Bibillo teach the analogous art of a method for detecting, diagnosing, and/or prognosing cancer in a subject using sequence information of a nucleic acid molecule (Bibillo; [0189]) wherein the nucleic acid molecule is modified to include the addition of a C3 spacer to the 3’ end of a polynucleotide (Bibillo; [0113]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the nucleic acid molecule and protecting element of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, because Bibillo teach the C3 spacer on the 3’-end of the nucleic acid molecule protects the nucleic acid molecule from being mistaken as an RNA primer by functioning as an effective blocking agent against polymerase extension (Bibillo; [0113]).
Regarding claim 34, modified Yaacoby teach the method of claim 32 above, wherein the subject is or is suspected to be in a disease state chosen from cancer, an infectious disease, an autoimmune disease, a metabolic disease, an inflammation disease, genetic diseases, and non-genetic diseases (Yaacoby; [0055])
Regarding claim 36, modified Yaacoby teach the method of claim 32 above, wherein the subject is treated with a therapeutic agent chosen from a chemotherapeutic agent, a chemical drug, and biological drug (Yaacoby; [0018, 0074, 0084, 0225, 0258]).
Regarding claim 38, modified Yaacoby teach the method of claim 32 above, wherein the diagnosing and/or prognosing of drug resistance is performed before, concurrent, or after the subject is treated with a first therapy (Yaacoby; [0055, 0199]).
Regarding claim 40, modified Yaacoby teach the method of claim 32 above, wherein the epigenetic state of the biological element comprises loss of one or more chromatin marks for genes that promote drug resistance (Yaacoby; fig. 2(G) demonstrates preferential loss of H3K27me3 from bivalent nucleosomes; [0073]).
Regarding claim 41, modified Yaacoby teach the method of claim 40 above, wherein the epigenetic state comprises the loss of one or more chromatin marks of H3K4me3 or H3K27me3 (Yaacoby; [0056, 0073]).
Regarding claim 42, modified Yaacoby teach the method of claim 23 above, further comprising performing a linear amplification of one or more asymmetrically barcoded nucleosome sequences comprising the barcode sequence on only one end of the nucleosome sequence (The modification of the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, has previously been discussed in claim 13 above. Yaacoby further teaches linear amplification; [0253]).
Regarding claim 43, modified Yaacoby teach the method of claim 23 above, further comprising obtaining sequence information from one or more symmetrically barcoded nucleosome sequences comprising a barcode sequence on both ends of the nucleosome sequence (The modification of the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, has previously been discussed in claim 23 above. Epstein teaches obtaining sequence information from one or more symmetrically or asymmetrically barcoded nucleosome sequences comprising a barcode sequence on one or both ends of the nucleosome sequence; [0007, 0055-0057]).
Regarding claim 44, modified Yaacoby teach the method of claim 23 above, wherein the nucleic acid molecule comprises the protecting function against unwanted ligation only on the 3’-end of the nucleic acid molecule (The modification of the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, and the modification of the nucleic acid molecule and protecting function of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, have previously been discussed in claim 23 above. Bibillo teach the addition of 3’ C3 spacer only on the 3’ end of a polynucleotide; [0113]).
Regarding claim 45, modified Yaacoby teach the method of claim 23 above, wherein the nucleic acid molecule comprises (i) the protecting function against unwanted ligation on the 3’-end, and (ii) a 5’-end capable of ligation (The modification of the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, and the modification of the nucleic acid molecule and protecting function of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, have previously been discussed in claim 23 above. Epstein teaches modifications to the adapter may be made to the first, second, third, and/or fourth terminal bases of the adaptor on the 3’ or 5’ end of the sense or antisense strand; [0056-0057]).
Regarding claim 46, modified Yaacoby teach the method of claim 23 above, wherein the nucleic acid molecule is a double-stranded nucleic acid molecule comprising a first strand and a second strand, wherein the first strand comprises the protecting function against unwanted ligation on its 3’-end and a 5’end capable of ligation, and wherein the second strand comprises a 3’-end capable of ligation (The modification of the nucleic acid molecule of modified Yaacoby with the barcoded adapter comprising DNA, RNA, and/or nucleotide analogs and a protecting function, as taught by Epstein, and the modification of the nucleic acid molecule and protecting function of modified Yaacoby with the C3 spacer on the 3’-end of the nucleic acid molecule, as in Bibillo, have previously been discussed in claim 23 above. Epstein teaches modifications to the adapter may be made to the first, second, third, and/or fourth terminal bases of the adaptor on the 3’ or 5’ end of the sense or antisense strand; [0056-0057]).
Regarding claim 47, modified Yaacoby teach the method of claim 46 above, wherein the second strand further comprises a linker providing releasable conjugation to a solid support on its 5’-end (Yaacoby; figs. 5 & 16).
Regarding claim 48, modified Yaacoby teach the method of claim 47 above, wherein the nucleic acid molecule is releasably conjugated to a solid support via the linker prior to the processing step and is released from the solid support prior to the ligating step (Yaacoby; figs. 5 & 16, [0231]).
Double Patenting
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.
Claims 23 and 32 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 13, 22 and 30 of copending Application No. 17/259,992 (reference application – hereinafter “’992”). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 23, ‘992 disclose a method for determining an epigenetic state of a biological element (‘992 – Claims 13, 22, and 30; preamble), comprising:
(a) forming a plurality of first droplets that comprise: i) a biological element, wherein the biological element contains or is suspected of containing at least one nucleosome comprising one or more epigenetic features and a genomic region, ii) a lysis buffer, and iii) a nuclease (‘992 – Claims 13, 22, 30; step “(a)”);
(b) synchronizing enzymatic activity of the nuclease in the plurality of first droplets by collecting the plurality of first droplets under conditions that temporarily inactivate said nuclease, wherein the collecting is performed during and throughout the formation of the plurality of first droplets and the plurality of first droplets is collected at a temperature of -20°C to 10°C such that the nuclease is held inactive in each first droplet from its formation until step (c) (‘992 – Claims 13, 22, 30; step “(b)”);
(c) incubating the collected plurality of first droplets at a temperature of 20°C to 40°C to thereby synchronously activate the nuclease in the plurality of first droplets (‘992 – Claims 13, 22, 30; step “(c)”);
(d) providing a plurality of second droplets that comprise a nucleic acid molecule comprising a barcode sequence, an adaptor, and a protecting function against unwanted ligation, wherein the protecting function against unwanted ligation is on a 3'-end of the nucleic acid molecule (‘992 – Claims 13, 22, 30; step “(d)”);
(e) processing the nucleic acid molecule of one or more second droplets of the plurality of second droplets by fusing a first droplet of the plurality of first droplets with a second droplet of the plurality of second droplets to identify said one or more epigenetic features, wherein processing comprises:(i) ligating the barcode sequence and the adaptor to an end of the genomic region of one or more nucleosomes to obtain one or more barcoded nucleosome sequences, and (ii) obtaining sequence information from one or more asymmetrically barcoded nucleosome sequences comprising the barcode sequence on only one end of the nucleosome sequence (‘992 – Claims 13, 22, 30; step “(e)”); and
(f) using said one or more epigenetic features and said barcode sequence to determine the epigenetic state of the biological element of one or more of the plurality of first droplets (‘992 – Claims 13, 22, 30; step “(f)”).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant’s arguments, filed 08/21/2026, have been fully considered.
Applicant argues, see pages 7-10 of their remarks, towards the 103 rejection(s) that Yaacoby in view of Rotem that Rotem does not disclose a step of collecting the first type of droplets and holding them at low temperature throughout the whole droplet formation process for complete synchronization, as recited by amended claim 1. The examiner does not agree with applicant’s arguments since Rotem teach “The cells were incubated for 10 min at 4˚C. 15 min at 37˚C, and put back at 4˚C until the next step” and “The cells may be encapsulated in droplets at rates of thousands per second, or missions per hour”, see paragraphs [0095, 0097], thus the rate of production rendering applicants argument towards varying digestion times during encapsulation negligible. However, in an effort to advance prosecution the examiner has withdrawn the rejection over Yaacoby in view of Rotem and set forth a new prior art rejection over Yaacoby in view of Weitz. Weitz explicitly disclose the syringes connected to the droplet maker are kept on ice throughout drop making and the droplets are collected on ice; [0103, 0105]. Accordingly, Yaacoby modified by Weitz would result in the claimed conditions that temporarily inactivate said nuclease since the liquid used to create the droplets, as well as the environment for holding the droplets, are at 0˚C. Further, when the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, the prior art products necessarily possess the characteristics of the claimed product. See MPEP 2112.01. As stated in In re Best, 562 F.2d 1252, 1255 (CCPA 1977): Where, as here, the claimed and prior art products are identical or substantially identical, or are produced by identical or substantially identical processes, the PTO can require an applicant to prove that the prior art products do not necessarily or inherently possess the characteristics of his claimed product. Whether the rejection is based on “inherency” under 35 U.S.C. § 102, on “prima facie obviousness” under 35 U.S.C. § 103, jointly or alternatively, the burden of proof is the same, and its fairness is evidenced by the PTO’s inability to manufacture products or to obtain and compare prior art products. See MPEP 2112.
Citations to art
In the above citations to documents in the art, an effort has been made to specifically cite representative passages, however rejections are in reference to the entirety of each document relied upon. Other passages, not specifically cited, may apply as well.
Other References Cited
The prior art of made of record and not relied upon is considered pertinent to Applicant’s disclosure include:
Weitz et al. (US 2015/0298091) disclose droplet formation and cooling cells using an ice pack.
Agresti et al. (US Patent No. 9,029,085) disclose a fluidic droplet and temperature curve to reach a solid state.
Pantoja et al. (US 2016/0299101) disclose storing droplets on ice until all sample droplets are collected for an assay.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CURTIS A THOMPSON whose telephone number is (571) 272-0648. The examiner can normally be reached on M-F: 7:00 a.m. - 5:00 p.m..
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E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
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/C.A.T./Examiner, Art Unit 1798
/BENJAMIN R WHATLEY/Primary Examiner, Art Unit 1798
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