DETAILED ACTION
Status of the Claims
Claims 2-21 are currently pending and are the subject of this Office Action.
The present application is being examined under the pre-AIA first to invent provisions.
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 obviousness-type 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); and 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 a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
U.S. 9,371,598 B2
Claim 2 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 15 and 18-19 of U.S. Patent No. 9,371,598 B2 (the ‘598 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘598 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claims 15 and 18-19 of the ‘598 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
U.S. 10,612,079 B2
Claims 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 9-10, and 21 of U.S. Patent No. 10,612,079 B2 (the ‘079 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘079 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claims 1, 6, 9-10, and 21 of the ‘079 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
Regarding claim 3, the claims of the ‘079 patent disclose the above method, wherein the ligation comprises the use of a ligase (e.g., as per claim 21 of the ‘079 patent).
Regarding claim 4, the claims of the ‘079 patent disclose the above method, wherein the ligase is T4 DNA ligase (e.g., as per claim 21 of the ‘079 patent).
Regarding claim 5, the claims of the ‘079 patent disclose the above method, wherein the method further comprises the use of one or both of an RNase and a protease (e.g., as per claim 23 of the ‘079 patent).
Regarding claim 6, the claims of the ‘079 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the first probe and the second probe not hybridized to the mitochondrial DNA (e.g., as per claim 22 of the ‘079 patent).
Regarding claim 7, the claims of the ‘079 patent disclose the above method, wherein the amplifying in step (c) comprises the use of a DNA polymerase (e.g., as per claim 6 of the ‘079 patent).
Regarding claim 8, the claims of the ‘079 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the amplification product or a complement thereof (e.g., as per claim 7 of the ‘079 patent).
Regarding claim 9, the claims of the ‘079 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 7 of the ‘079 patent).
Regarding claim 10, the claims of the ‘079 patent disclose the above method, wherein the high-throughput sequencing is digital nucleic acid sequencing or sequencing-by-ligation (e.g., as per claim 7 of the ‘079 patent).
Regarding claim 11, the claims of the ‘079 patent disclose the above method, wherein the biological sample is affixed to a support (e.g., as per claim 20 of the ‘079 patent).
Regarding claim 12, the claims of the ‘079 patent disclose the above method, wherein the support is a slide or a culture dish (e.g., as per claim 20 of the ‘079 patent).
Regarding claim 13, the claims of the ‘079 patent disclose the above method, wherein the biological sample is a tissue sample (e.g., as per claim 20 of the ‘079 patent).
Regarding claim 14, the claims of the ‘079 patent disclose the above method, wherein the tissue sample is a tissue section (e.g., as per claim 20 of the ‘079 patent).
Regarding claim 15, the claims of the ‘079 patent disclose the above method, wherein the tissue section is a fresh, frozen tissue section (e.g., as per claim 20 of the ‘079 patent).
Regarding claim 16, the claims of the ‘079 patent disclose the above method, wherein the tissue section is a fixed tissue section (e.g., as per claim 21 of the ‘079 patent).
Regarding claim 17, the claims of the ‘079 patent disclose the above method, wherein the fixed tissue section is a formalin-fixed, paraffin-embedded (FFPE) tissue section (e.g., as per claim 21 of the ‘079 patent).
Regarding claim 18, the claims of the ‘079 patent disclose the above method, wherein the biological sample further comprises a second mitochondrial DNA at a different location in the biological sample; step (a) further comprises contacting the biological sample with a third probe and a fourth probe, wherein:
the third probe comprises a first sequence that hybridizes to a first portion of the second mitochondrial DNA and the first universal priming site;
the fourth probe comprises a second sequence that hybridizes to a second portion of the second mitochondrial DNA and the second universal priming site;
the third probe and the fourth probe hybridized to the second mitochondrial DNA are capable of being ligated together; and
one or both of: (i) the third probe further comprises a nucleic acid sequence identifying the location to where the third probe was delivered and (ii) the fourth probe further comprises a nucleic acid sequence identifying the location to where the fourth probe was delivered;
step (b) further comprises ligating the third probe and the fourth probe together to generate a second ligation product;
step (c) further comprises amplifying the second ligation product using the first amplification primer and the second amplification primer to produce a second amplification product; and
step (d) further comprises determining all or a portion of the sequence of the second amplification product or a complement thereof, and using the determined sequence to detect the second mitochondrial DNA at a location in the biological sample (e.g., as per claim 1 of the ‘079 patent).
Regarding claim 19, the claims of the ‘079 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the third probe and the fourth probe not hybridized to the second mitochondrial DNA (e.g., as per claim 22 of the ‘079 patent).
Regarding claim 20, the claims of the ‘079 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the second amplification product or a complement thereof (e.g., as per claim 7 of the ‘079 patent).
Regarding claim 21, the claims of the ‘079 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 7 of the ‘079 patent).
U.S. 10,669,246 B2
Claims 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 10,669,246 B2 (the ‘246 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘246 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claim 1 of the ‘246 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
Regarding claim 3, the claims of the ‘246 patent disclose the above method, wherein the ligation comprises the use of a ligase (e.g., as per claim 1 of the ‘246 patent).
Regarding claim 4, the claims of the ‘246 patent disclose the above method, wherein the ligase is T4 DNA ligase (e.g., as per claim 1 of the ‘246 patent).
Regarding claim 5, the claims of the ‘246 patent disclose the above method, wherein the method further comprises the use of one or both of an RNase and a protease (e.g., as per claim 23 of the ‘246 patent).
Regarding claim 6, the claims of the ‘246 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the first probe and the second probe not hybridized to the mitochondrial DNA (e.g., as per claim 1 of the ‘246 patent).
Regarding claim 7, the claims of the ‘246 patent disclose the above method, wherein the amplifying in step (c) comprises the use of a DNA polymerase (e.g., as per claim 8 of the ‘246 patent).
Regarding claim 8, the claims of the ‘246 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the amplification product or a complement thereof (e.g., as per claim 1 of the ‘246 patent).
Regarding claim 9, the claims of the ‘246 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 1 of the ‘246 patent).
Regarding claim 10, the claims of the ‘246 patent disclose the above method, wherein the high-throughput sequencing is digital nucleic acid sequencing or sequencing-by-ligation (e.g., as per claim 1 of the ‘246 patent).
Regarding claim 11, the claims of the ‘246 patent disclose the above method, wherein the biological sample is affixed to a support (e.g., as per claim 12 of the ‘246 patent).
Regarding claim 12, the claims of the ‘246 patent disclose the above method, wherein the support is a slide or a culture dish (e.g., as per claim 12 of the ‘246 patent).
Regarding claim 13, the claims of the ‘246 patent disclose the above method, wherein the biological sample is a tissue sample (e.g., as per claim 12 of the ‘246 patent).
Regarding claim 14, the claims of the ‘246 patent disclose the above method, wherein the tissue sample is a tissue section (e.g., as per claim 13 of the ‘246 patent).
Regarding claim 15, the claims of the ‘246 patent disclose the above method, wherein the tissue section is a fresh, frozen tissue section (e.g., as per claim 13 of the ‘246 patent).
Regarding claim 16, the claims of the ‘246 patent disclose the above method, wherein the tissue section is a fixed tissue section (e.g., as per claim 13 of the ‘246 patent).
Regarding claim 17, the claims of the ‘246 patent disclose the above method, wherein the fixed tissue section is a formalin-fixed, paraffin-embedded (FFPE) tissue section (e.g., as per claim 12 of the ‘246 patent).
Regarding claim 18, the claims of the ‘246 patent disclose the above method, wherein the biological sample further comprises a second mitochondrial DNA at a different location in the biological sample; step (a) further comprises contacting the biological sample with a third probe and a fourth probe, wherein:
the third probe comprises a first sequence that hybridizes to a first portion of the second mitochondrial DNA and the first universal priming site;
the fourth probe comprises a second sequence that hybridizes to a second portion of the second mitochondrial DNA and the second universal priming site;
the third probe and the fourth probe hybridized to the second mitochondrial DNA are capable of being ligated together; and
one or both of: (i) the third probe further comprises a nucleic acid sequence identifying the location to where the third probe was delivered and (ii) the fourth probe further comprises a nucleic acid sequence identifying the location to where the fourth probe was delivered;
step (b) further comprises ligating the third probe and the fourth probe together to generate a second ligation product;
step (c) further comprises amplifying the second ligation product using the first amplification primer and the second amplification primer to produce a second amplification product; and
step (d) further comprises determining all or a portion of the sequence of the second amplification product or a complement thereof, and using the determined sequence to detect the second mitochondrial DNA at a location in the biological sample (e.g., as per claim 21 of the ‘246 patent).
Regarding claim 19, the claims of the ‘246 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the third probe and the fourth probe not hybridized to the second mitochondrial DNA (e.g., as per claim 22 of the ‘246 patent).
Regarding claim 20, the claims of the ‘246 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the second amplification product or a complement thereof (e.g., as per claim 22 of the ‘246 patent).
Regarding claim 21, the claims of the ‘246 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 29 of the ‘246 patent).
U.S. 10,962,532 B2
Claims 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of U.S. Patent No. 10,962,532 B2 (the ‘532 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘532 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claim 1 of the ‘532 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
Regarding claim 3, the claims of the ‘532 patent disclose the above method, wherein the ligation comprises the use of a ligase (e.g., as per claim 2 of the ‘532 patent).
Regarding claim 4, the claims of the ‘532 patent disclose the above method, wherein the ligase is T4 DNA ligase (e.g., as per claim 3 of the ‘532 patent).
Regarding claim 5, the claims of the ‘532 patent disclose the above method, wherein the method further comprises the use of one or both of an RNase and a protease (e.g., as per claim 1 of the ‘532 patent).
Regarding claim 6, the claims of the ‘532 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the first probe and the second probe not hybridized to the mitochondrial DNA (e.g., as per claim 5 of the ‘532 patent).
Regarding claim 7, the claims of the ‘532 patent disclose the above method, wherein the amplifying in step (c) comprises the use of a DNA polymerase (e.g., as per claim 6 of the ‘532 patent).
Regarding claim 8, the claims of the ‘532 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the amplification product or a complement thereof (e.g., as per claim 7 of the ‘532 patent).
Regarding claim 9, the claims of the ‘532 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 8 of the ‘532 patent).
Regarding claim 10, the claims of the ‘532 patent disclose the above method, wherein the high-throughput sequencing is digital nucleic acid sequencing or sequencing-by-ligation (e.g., as per claims 9-10 of the ‘532 patent).
Regarding claim 11, the claims of the ‘532 patent disclose the above method, wherein the biological sample is affixed to a support (e.g., as per claim 11 of the ‘532 patent).
Regarding claim 12, the claims of the ‘532 patent disclose the above method, wherein the support is a slide or a culture dish (e.g., as per claim 12 of the ‘532 patent).
Regarding claim 13, the claims of the ‘532 patent disclose the above method, wherein the biological sample is a tissue sample (e.g., as per claim 13 of the ‘532 patent).
Regarding claim 14, the claims of the ‘532 patent disclose the above method, wherein the tissue sample is a tissue section (e.g., as per claim 14 of the ‘532 patent).
Regarding claim 15, the claims of the ‘532 patent disclose the above method, wherein the tissue section is a fresh, frozen tissue section (e.g., as per claim 15 of the ‘532 patent).
Regarding claim 16, the claims of the ‘532 patent disclose the above method, wherein the tissue section is a fixed tissue section (e.g., as per claim 16 of the ‘532 patent).
Regarding claim 17, the claims of the ‘532 patent disclose the above method, wherein the fixed tissue section is a formalin-fixed, paraffin-embedded (FFPE) tissue section (e.g., as per claim 17 of the ‘532 patent).
Regarding claim 18, the claims of the ‘532 patent disclose the above method, wherein the biological sample further comprises a second mitochondrial DNA at a different location in the biological sample; step (a) further comprises contacting the biological sample with a third probe and a fourth probe, wherein:
the third probe comprises a first sequence that hybridizes to a first portion of the second mitochondrial DNA and the first universal priming site;
the fourth probe comprises a second sequence that hybridizes to a second portion of the second mitochondrial DNA and the second universal priming site;
the third probe and the fourth probe hybridized to the second mitochondrial DNA are capable of being ligated together; and
one or both of: (i) the third probe further comprises a nucleic acid sequence identifying the location to where the third probe was delivered and (ii) the fourth probe further comprises a nucleic acid sequence identifying the location to where the fourth probe was delivered;
step (b) further comprises ligating the third probe and the fourth probe together to generate a second ligation product;
step (c) further comprises amplifying the second ligation product using the first amplification primer and the second amplification primer to produce a second amplification product; and
step (d) further comprises determining all or a portion of the sequence of the second amplification product or a complement thereof, and using the determined sequence to detect the second mitochondrial DNA at a location in the biological sample (e.g., as per claim 23 of the ‘532 patent).
Regarding claim 19, the claims of the ‘532 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the third probe and the fourth probe not hybridized to the second mitochondrial DNA (e.g., as per claim 24 of the ‘532 patent).
Regarding claim 20, the claims of the ‘532 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the second amplification product or a complement thereof (e.g., as per claim 25 of the ‘532 patent).
Regarding claim 21, the claims of the ‘532 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 26 of the ‘532 patent).
U.S. 11,634,756 B2
Claims 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of U.S. Patent No. 11,634,756 B2 (the ‘756 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘756 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claim 1 of the ‘756 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
Regarding claim 3, the claims of the ‘756 patent disclose the above method, wherein the ligation comprises the use of a ligase (e.g., as per claim 4 of the ‘756 patent).
Regarding claim 4, the claims of the ‘756 patent disclose the above method, wherein the ligase is T4 DNA ligase (e.g., as per claim 5 of the ‘756 patent).
Regarding claim 5, the claims of the ‘756 patent disclose the above method, wherein the method further comprises the use of one or both of an RNase and a protease (e.g., as per claim 6 of the ‘756 patent).
Regarding claim 6, the claims of the ‘756 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the first probe and the second probe not hybridized to the mitochondrial DNA (e.g., as per claim 8 of the ‘756 patent).
Regarding claim 7, the claims of the ‘756 patent disclose the above method, wherein the amplifying in step (c) comprises the use of a DNA polymerase (e.g., as per claim 9 of the ‘756 patent).
Regarding claim 8, the claims of the ‘756 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the amplification product or a complement thereof (e.g., as per claim 10 of the ‘756 patent).
Regarding claim 9, the claims of the ‘756 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 11 of the ‘756 patent).
Regarding claim 10, the claims of the ‘756 patent disclose the above method, wherein the high-throughput sequencing is digital nucleic acid sequencing or sequencing-by-ligation (e.g., as per claims 12-13 of the ‘756 patent).
Regarding claim 11, the claims of the ‘756 patent disclose the above method, wherein the biological sample is affixed to a support (e.g., as per claim 14 of the ‘756 patent).
Regarding claim 12, the claims of the ‘756 patent disclose the above method, wherein the support is a slide or a culture dish (e.g., as per claim 15 of the ‘756 patent).
Regarding claim 13, the claims of the ‘756 patent disclose the above method, wherein the biological sample is a tissue sample (e.g., as per claim 16 of the ‘756 patent).
Regarding claim 14, the claims of the ‘756 patent disclose the above method, wherein the tissue sample is a tissue section (e.g., as per claim 17 of the ‘756 patent).
Regarding claim 15, the claims of the ‘756 patent disclose the above method, wherein the tissue section is a fresh, frozen tissue section (e.g., as per claim 18 of the ‘756 patent).
Regarding claim 16, the claims of the ‘756 patent disclose the above method, wherein the tissue section is a fixed tissue section (e.g., as per claim 19 of the ‘756 patent).
Regarding claim 17, the claims of the ‘756 patent disclose the above method, wherein the fixed tissue section is a formalin-fixed, paraffin-embedded (FFPE) tissue section (e.g., as per claim 20 of the ‘756 patent).
Regarding claim 18, the claims of the ‘756 patent disclose the above method, wherein the biological sample further comprises a second mitochondrial DNA at a different location in the biological sample; step (a) further comprises contacting the biological sample with a third probe and a fourth probe, wherein:
the third probe comprises a first sequence that hybridizes to a first portion of the second mitochondrial DNA and the first universal priming site;
the fourth probe comprises a second sequence that hybridizes to a second portion of the second mitochondrial DNA and the second universal priming site;
the third probe and the fourth probe hybridized to the second mitochondrial DNA are capable of being ligated together; and
one or both of: (i) the third probe further comprises a nucleic acid sequence identifying the location to where the third probe was delivered and (ii) the fourth probe further comprises a nucleic acid sequence identifying the location to where the fourth probe was delivered;
step (b) further comprises ligating the third probe and the fourth probe together to generate a second ligation product;
step (c) further comprises amplifying the second ligation product using the first amplification primer and the second amplification primer to produce a second amplification product; and
step (d) further comprises determining all or a portion of the sequence of the second amplification product or a complement thereof, and using the determined sequence to detect the second mitochondrial DNA at a location in the biological sample (e.g., as per claim 23 of the ‘756 patent).
Regarding claim 19, the claims of the ‘756 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the third probe and the fourth probe not hybridized to the second mitochondrial DNA (e.g., as per claim 24 of the ‘756 patent).
Regarding claim 20, the claims of the ‘756 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the second amplification product or a complement thereof (e.g., as per claim 25 of the ‘756 patent).
Regarding claim 21, the claims of the ‘756 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 26 of the ‘756 patent).
U.S. 12,234,505 B2
Claims 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-27 of U.S. Patent No. 12,234,505 B2 (the ‘505 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘505 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claims 1-2 of the ‘505 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
Regarding claim 3, the claims of the ‘505 patent disclose the above method, wherein the ligation comprises the use of a ligase (e.g., as per claim 3 of the ‘505 patent).
Regarding claim 4, the claims of the ‘505 patent disclose the above method, wherein the ligase is T4 DNA ligase (e.g., as per claim 3 of the ‘505 patent).
Regarding claim 5, the claims of the ‘505 patent disclose the above method, wherein the method further comprises the use of one or both of an RNase and a protease (e.g., as per claim 13 of the ‘505 patent).
Regarding claim 6, the claims of the ‘505 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the first probe and the second probe not hybridized to the mitochondrial DNA (e.g., as per claim 1 of the ‘505 patent).
Regarding claim 7, the claims of the ‘505 patent disclose the above method, wherein the amplifying in step (c) comprises the use of a DNA polymerase (e.g., as per claim 13 of the ‘505 patent).
Regarding claim 8, the claims of the ‘505 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the amplification product or a complement thereof (e.g., as per claim 1 of the ‘505 patent).
Regarding claim 9, the claims of the ‘505 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 14 of the ‘505 patent).
Regarding claim 10, the claims of the ‘505 patent disclose the above method, wherein the high-throughput sequencing is digital nucleic acid sequencing or sequencing-by-ligation (e.g., as per claim 14 of the ‘505 patent).
Regarding claim 11, the claims of the ‘505 patent disclose the above method, wherein the biological sample is affixed to a support (e.g., as per claims 5-6 of the ‘505 patent).
Regarding claim 12, the claims of the ‘505 patent disclose the above method, wherein the support is a slide or a culture dish (e.g., as per claims 5-6 of the ‘505 patent).
Regarding claim 13, the claims of the ‘505 patent disclose the above method, wherein the biological sample is a tissue sample (e.g., as per claim s 5-6 of the ‘505 patent).
Regarding claim 14, the claims of the ‘505 patent disclose the above method, wherein the tissue sample is a tissue section (e.g., as per claims 5-6 of the ‘505 patent).
Regarding claim 15, the claims of the ‘505 patent disclose the above method, wherein the tissue section is a fresh, frozen tissue section (e.g., as per claims 5-6 of the ‘505 patent).
Regarding claim 16, the claims of the ‘505 patent disclose the above method, wherein the tissue section is a fixed tissue section (e.g., as per claim 5 of the ‘505 patent).
Regarding claim 17, the claims of the ‘505 patent disclose the above method, wherein the fixed tissue section is a formalin-fixed, paraffin-embedded (FFPE) tissue section (e.g., as per claim 5 of the ‘505 patent).
Regarding claim 18, the claims of the ‘505 patent disclose the above method, wherein the biological sample further comprises a second mitochondrial DNA at a different location in the biological sample; step (a) further comprises contacting the biological sample with a third probe and a fourth probe, wherein:
the third probe comprises a first sequence that hybridizes to a first portion of the second mitochondrial DNA and the first universal priming site;
the fourth probe comprises a second sequence that hybridizes to a second portion of the second mitochondrial DNA and the second universal priming site;
the third probe and the fourth probe hybridized to the second mitochondrial DNA are capable of being ligated together; and
one or both of: (i) the third probe further comprises a nucleic acid sequence identifying the location to where the third probe was delivered and (ii) the fourth probe further comprises a nucleic acid sequence identifying the location to where the fourth probe was delivered;
step (b) further comprises ligating the third probe and the fourth probe together to generate a second ligation product;
step (c) further comprises amplifying the second ligation product using the first amplification primer and the second amplification primer to produce a second amplification product; and
step (d) further comprises determining all or a portion of the sequence of the second amplification product or a complement thereof, and using the determined sequence to detect the second mitochondrial DNA at a location in the biological sample (e.g., as per claim 1 of the ‘505 patent).
Regarding claim 19, the claims of the ‘505 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the third probe and the fourth probe not hybridized to the second mitochondrial DNA (e.g., as per claim 1 of the ‘505 patent).
Regarding claim 20, the claims of the ‘505 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the second amplification product or a complement thereof (e.g., as per claim 14 of the ‘505 patent).
Regarding claim 21, the claims of the ‘505 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 14 of the ‘505 patent).
U.S. 12,391,980 B2
Claims 2-17 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12,391,980 B2 (the ‘980 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 2, the claims of the ‘980 patent disclose a method of detecting the location of a DNA in a biological sample comprising (a) contacting the biological sample comprising mitochondrial DNA with a first probe and a second probe, which each hybridizes to portions of the mitochondrial DNA and each has a universal priming site, wherein one or both of the probes further comprises a sequence identifying the location to which the probe was delivered, (b) ligating the probes together, (c) amplifying the ligation products, (d) sequencing all or some of the sequences of the ligation product (e.g. as per claim 1 of the ‘980 patent).
Note that the DEFINITIONS section of the ‘598 patent states that “references to DNA herein may include genomic DNA, mitochondrial DNA, episomal DNA, and/or derivatives of DNA such as amplicons, RNA transcripts, cDNA, DNA analogs, etc.”, therefore reading on the mitochondrial DNA limitation.
Regarding claim 3, the claims of the ‘980 patent disclose the above method, wherein the ligation comprises the use of a ligase (e.g., as per claim 9 of the ‘980 patent).
Regarding claim 4, the claims of the ‘980 patent disclose the above method, wherein the ligase is T4 DNA ligase (e.g., as per claim 9 of the ‘980 patent).
Regarding claim 5, the claims of the ‘980 patent disclose the above method, wherein the method further comprises the use of one or both of an RNase and a protease (e.g., as per claim 8 of the ‘980 patent).
Regarding claim 6, the claims of the ‘980 patent disclose the above method, wherein the method further comprises, between steps (a) and (c), washing away the first probe and the second probe not hybridized to the mitochondrial DNA (e.g., as per claim 1 of the ‘980 patent).
Regarding claim 7, the claims of the ‘980 patent disclose the above method, wherein the amplifying in step (c) comprises the use of a DNA polymerase (e.g., as per claim 11 of the ‘980 patent).
Regarding claim 8, the claims of the ‘980 patent disclose the above method, wherein step (d) comprises sequencing all or a portion of the sequence of the amplification product or a complement thereof (e.g., as per claim 18 of the ‘980 patent).
Regarding claim 9, the claims of the ‘980 patent disclose the above method, wherein the sequencing is high-throughput sequencing (e.g., as per claim 18 of the ‘980 patent).
Regarding claim 10, the claims of the ‘980 patent disclose the above method, wherein the high-throughput sequencing is digital nucleic acid sequencing or sequencing-by-ligation (e.g., as per claim 18 of the ‘980 patent).
Regarding claim 11, the claims of the ‘980 patent disclose the above method, wherein the biological sample is affixed to a support (e.g., as per claim 18 of the ‘980 patent).
Regarding claim 12, the claims of the ‘980 patent disclose the above method, wherein the support is a slide or a culture dish (e.g., as per claim 12 of the ‘980 patent).
Regarding claim 13, the claims of the ‘980 patent disclose the above method, wherein the biological sample is a tissue sample (e.g., as per claim 12 of the ‘980 patent).
Regarding claim 14, the claims of the ‘980 patent disclose the above method, wherein the tissue sample is a tissue section (e.g., as per claim 2 of the ‘980 patent).
Regarding claim 15, the claims of the ‘980 patent disclose the above method, wherein the tissue section is a fresh, frozen tissue section (e.g., as per claim 2 of the ‘980 patent).
Regarding claim 16, the claims of the ‘980 patent disclose the above method, wherein the tissue section is a fixed tissue section (e.g., as per claim 2 of the ‘980 patent).
Regarding claim 17, the claims of the ‘980 patent disclose the above method, wherein the fixed tissue section is a formalin-fixed, paraffin-embedded (FFPE) tissue section (e.g., as per claim 2 of the ‘980 patent).
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684