DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
Priority
2. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 112 first paragraph, as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 61395850, fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. This application does not include sufficient support for the limitation of instant claim 22 “performing massively parallel sequencing.” Therefore, as the priority document 61398159 provides full support for the method as claimed, the claims are afforded an earliest priority date of 21 June 2011.
Claim Rejections - 35 USC § 103
3. The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
4. This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
5. Claims 22-25 and 27 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Fan et al (United States Patent Application No. US 20100112575, published 06 May 2010) in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009).
Regarding the method of claim 22, Fan teaches a method of preparing a DNA fraction from a biological sample of a subject for analyzing genetic features ([0086]) comprising extracting cell-free DNA from peripheral blood draws ([0085]). Fan teaches adding at least one adaptor to the extracted cell-free DNA (samples were blunt-ended and ligated to universal adaptors; [0087] and [0088]) and performing a universal amplification on at least some of the adapted DNA (18 cycles of PCR were performed to enrich for fragments with adaptors; [0087] and [0088]). Fan teaches sequencing the library on a Roche 454 Genome Sequencer FLX system (i.e., massively parallel sequencing; abstract [0088]) to determine “abnormal distribution of a fetal chromosome” (e.g., insertions, deletions or other genetic features; [0021]).
Fan does not teach selectively enriching for a plurality of amplified adapted DNA comprising one or more loci to produce enriched DNA.
However, Gnirke teaches a hybridization pull-down method to selectively enrich specific DNA loci prior to sequencing (abstract and FIG 1).
It would have been obvious to one having ordinary skill in the art to have modified the method taught by Fan with the selective enrichment taught by Gnirke to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Fan teaches that only a small percentage of the isolated cell-free DNA represents fetal DNA ([0059]) and Gnirke teaches that their pull-down based enrichment method is simple, robust, and capable of targeting >15,000 sequences at once (abstract and pg. 183 column 1 ¶ 1). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
Regarding claim 23, Fan teaches that the biological sample is a peripheral blood sample ([0086]).
Regarding claim 24, Fan teaches that the method identifies genetic features such as insertions and deletions ([0021]).
Regarding claims 25 and 27, Gnirke teaches the selective enrichment of >15,000 loci (abstract) using hybrid capture methods (FIG 1).
6. Claims 22-24 and 26 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Fan et al (United States Patent Application No. US 20100112575, published 06 May 2010) in view of Wisniewski et al (United States Patent Application No. US 20120178918, effectively filed 01 April 2010).
Regarding the method of claim 22, Fan teaches a method of preparing a DNA fraction from a biological sample of a subject for analyzing genetic features ([0086]) comprising extracting cell-free DNA from peripheral blood draws ([0085]). Fan teaches adding at least one adaptor to the extracted cell-free DNA (samples were blunt-ended and ligated to universal adaptors; [0087] and [0088]) and performing a universal amplification on at least some of the adapted DNA (18 cycles of PCR were performed to enrich for fragments with adaptors; [0087] and [0088]). Fan teaches sequencing the library on a Roche 454 Genome Sequencer FLX system (i.e., massively parallel sequencing; abstract [0088]) to determine “abnormal distribution of a fetal chromosome” (e.g., insertions, deletions or other genetic features; [0021]).
Fan does not teach selectively enriching for a plurality of amplified adapted DNA comprising one or more loci to produce enriched DNA.
However, Wisniewski teaches a targeted multiplex amplification of a DNA sample to enrich cell free fetal nucleic acids ([0006] and [0254]).
It would have been obvious to one having ordinary skill in the art to have modified the method taught by Fan with the selective enrichment taught by Wisniewski to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Fan teaches that only a small percentage of the isolated cell-free DNA represents fetal DNA ([0059]) and Wisniewski teaches that their method is able to enrich short nucleic acids (e.g., cell free fetal DNA) from a nucleic acid composition comprising a high background of longer nucleic acids (abstract). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
Regarding claim 23, Fan teaches that the biological sample is a peripheral blood sample ([0086]).
Regarding claim 24, Fan teaches that the method identifies genetic features such as insertions and deletions ([0021]).
Regarding claim 26, Wisniewski teaches that the enrichment comprises targeted multiplex amplification ([0254]).
7. Claim 28 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Fan et al (United States Patent Application No. US 20100112575, published 06 May 2010) in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009) as applied to claim 22 above, and further in view of McCloskey et al (United States Patent Application No. US 20070020640, published 25 January 2007).
Regarding claim 28, the method of claim 22 is discussed fully above and incorporated here. Fan does not teach that the adaptor further comprises a molecular barcode, wherein sequence reads derived from the same original cell-free DNA molecule are identified using the molecular barcode.
However, McCloskey teaches a method of “authenticating” a nucleic acid amplification product (abstract) comprising appending a random barcode to a sample of DNA molecules ([0021]). McCloskey teaches that the length of this random sequence is sufficient to provide a “unique identity” to each target nucleic acid molecule in the sample prior to amplification (i.e., individual sequences are identified using the random barcode; [0021]).
It would have been obvious to one having ordinary skill in the art to have modified the universal adapters taught by Fan with the random barcode taught by McCloskey to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because McCloskey teaches that this molecular sequence barcode allows for the origin of each sequence to be tracked and to identify redundant sequences to accurately quantify particular variants in the sample ([0093]). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the adapter tagging of nucleic acids.
Double Patenting
8. 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.
9. Claims 22-31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 12571034 and claims 1-13 of U.S. Patent No. 12723281. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims is drawn to preparing a DNA fraction from a biological sample.
The limitations of instant claim 22 are taught in claim 1 of issued patent 12571034 and claim 1 of issued patent 12723281.
The limitations of claims 23-31 are taught in claims 1, 2, 5-7 and 9-11 of issued patent 12571034.
The limitations of claims 23-31 are taught in claims 1-3, 5-7, 10 and 11 of issued patent 12723281.
10. Claims 22-30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 12509730 and claims 1-30 of U.S. Patent No. 12545960. Although the claims at issue aren’t identical, they are not patentably distinct from each other because each set of claims is drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in claim 1 of issued patent 12509730 and claim 1 of issued patent 12545960.
The limitations of claims 23-26 and 28-30 are taught in claims 1, 2, 5, 17 and 20 of issued patent 12509730.
The limitations of claims 23-26 and 28-30 are taught in claims 1, 2, 16, 19 and 21 of issued patent 12545960.
Claim 27 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 12509730 and claims 1-30 of U.S. Patent No. 12545960, each in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009).
Neither issued patent 12509730 nor issued patent 12545960 teach the limitations of claim 27.
However, Gnirke teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by either of the issued patents with the selective enrichment taught by Gnirke to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Gnirke teaches that their pull-down based enrichment method is simple, robust, and capable of targeting >15,000 sequences at once (abstract and pg. 183 column 1 ¶ 1). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
11. Claims 22-26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 12494267. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to methods of amplifying and sequencing isolated cell free DNA.
The method of instant claim 22 is taught by claim 1 of the issued patent.
The limitations of instant claims 23-26 are taught by claims 1, 2, 4 and 14 of the issued patent.
Claim 27 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 12494267 in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009).
The issued patent 12494267 does not teach the limitations of claim 27.
However, Gnirke teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Gnirke to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Gnirke teaches that their pull-down based enrichment method is simple, robust, and capable of targeting >15,000 sequences at once (abstract and pg. 183 column 1 ¶ 1). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
Claim 28 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 12494267 in view of McCloskey et al (United States Patent Application No. US 20070020640, published 25 January 2007).
The issued patent 12494267 does not teach the limitations of claim 28.
However, McCloskey teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the adapters taught by the issued patent to have incorporated the random barcode taught by McCloskey to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because McCloskey teaches that this molecular sequence barcode allows for the origin of each sequence to be tracked and to identify redundant sequences to accurately quantify particular variants in the sample ([0093]). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the adapter tagging of nucleic acids.
12. Claims 22-25, 27, 28, 30 and 31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 11525162. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims is drawn to a method comprising the isolation and sequencing of cell free DNA.
The limitations of instant claim 22 is taught in claim 1 of the issued patent.
The limitations of instant claims 23-25, 27, 28, 30 and 31 are taught in claims 1, 3 and 6 of the issued patent.
Claim 26 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 11525162 in view of Wisniewski et al (United States Patent Application No. US 20120178918, effectively filed 01 April 2010).
The issued patent does not teach the limitations of claim 26.
However, Wisniewski teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Wisniewski to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Wisniewski teaches that their method is able to enrich short nucleic acids (e.g., cell free fetal DNA) from a nucleic acid composition comprising a high background of longer nucleic acids (abstract). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
13. Claims 22-25, 27, 28 and 30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12735746. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims is drawn to methods of enriching and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in claim 1 of the issued patent.
The limitations of instant claims 23-25, 27, 28 and 30 are taught in claims 1, 2, 6 and 9 of the issued patent.
Claim 26 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12735746 in view of Wisniewski et al (United States Patent Application No. US 20120178918, effectively filed 01 April 2010).
The issued patent does not teach the limitations of claim 26.
However, Wisniewski teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Wisniewski to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Wisniewski teaches that their method is able to enrich short nucleic acids (e.g., cell free fetal DNA) from a nucleic acid composition comprising a high background of longer nucleic acids (abstract). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
14. Claims 22-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of copending Application No. 19399491, claims 1-10 of copending Application No. 18733471, and claims 1-24 of copending Application No. 19791103. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to the amplification and sequencing of extracted cell free DNA.
The limitations of instant claim 22 are taught in claim 1 of copending application 19399491, claim 1 of copending application 18733471, and claim 1 of copending application 19791103.
The limitations of claims 23-31 are taught in claims 1-3 and 5-9 of copending application 19399491.
The limitations of claims 23-31 are taught in claims 2-4 and 6-10 of copending application 18733471.
The limitations of claims 23-31 are taught in claims 1-3, 5-7, 10 and 11 of copending application 19791103.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
15. Claims 22-25 and 27-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending Application No. 18678417 and claims 1-14 and 16-21 of copending Application No. 17196659. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in claim 1 of copending application 18678417 and claim 1 of copending application 17196659.
The limitations of instant claims 23-25 and 27-31 are taught in claims 1 and 6 of copending application 18678417.
The limitations of instant claims 23-25 and 27-31 are taught in claims 1-3 and 10 of copending application 17196659.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 26 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-20 of copending Application No. 18678417 and claims 1-14 and 16-21 of copending Application No. 17196659, each in view of Wisniewski et al (United States Patent Application No. US 20120178918, effectively filed 01 April 2010).
The copending applications do not teach the limitations of claim 26.
However, Wisniewski teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Wisniewski to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Wisniewski teaches that their method is able to enrich short nucleic acids (e.g., cell free fetal DNA) from a nucleic acid composition comprising a high background of longer nucleic acids (abstract). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
This is a provisional nonstatutory double patenting rejection.
16. Claims 22-28 and 30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of copending Application No. 19458473. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in claim 1 of the copending application.
The limitations of instant claims 23-28 and 30 are taught in claims 1-3, 13, 18, 20 and 21 of the copending application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
17. Claims 22-27 and 29-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of copending Application No. 18733681. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in claim 1 of the copending application.
The limitations of instant claims 23-27 and 29-31 are taught in claims 1, 2 and 6-10 of the copending application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 28 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of copending Application No. 18733681 in view of McCloskey et al (United States Patent Application No. US 20070020640, published 25 January 2007).
The copending application does not teach the limitations of claim 28.
However, McCloskey teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the adapters taught by the issued patent to have incorporated the random barcode taught by McCloskey to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because McCloskey teaches that this molecular sequence barcode allows for the origin of each sequence to be tracked and to identify redundant sequences to accurately quantify particular variants in the sample ([0093]). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the adapter tagging of nucleic acids.
This is a provisional nonstatutory double patenting rejection.
18. Claims 22-26 and 28-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending Application No. 19382752. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in copending claim 1.
The limitations of instant claims 23-26 and 38-31 are taught in claims 1, 3, 15 and 18-20 of the copending application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 27 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending Application No. 19382752in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009).
The copending application does not teach the limitations of claim 27.
However, Gnirke teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Gnirke to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Gnirke teaches that their pull-down based enrichment method is simple, robust, and capable of targeting >15,000 sequences at once (abstract and pg. 183 column 1 ¶ 1). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
This is a provisional nonstatutory double patenting rejection.
19. Claims 22-26, 28 and 30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of copending Application No. 19399492. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in claim 12 of the copending application.
The limitations of instant claims 23-26, 28 and 30 are taught in claims 3, 4, 12 and 23 of the copending application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 27 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of copending Application No. 19399492 in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009).
The copending application does not teach the limitations of claim 27.
However, Gnirke teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Gnirke to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Gnirke teaches that their pull-down based enrichment method is simple, robust, and capable of targeting >15,000 sequences at once (abstract and pg. 183 column 1 ¶ 1). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
This is a provisional nonstatutory double patenting rejection.
20. Claims 22-26 and 30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 19327646. Although the claims at issue are not identical, they are not patentably distinct from each other because each set of claims are drawn to a method of amplifying and sequencing isolated cell free DNA.
The limitations of instant claim 22 are taught in copending claim 14.
The limitations of instant claims 23-26 and 30 are taught in copending claims 4-6 and 14.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 27 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 19327646 in view of Gnirke et al (Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing, Nature Biotechnology, 27, 182-189, published 01 February 2009).
The copending application does not teach the limitations of claim 27.
However, Gnirke teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent with the selective enrichment taught by Gnirke to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Gnirke teaches that their pull-down based enrichment method is simple, robust, and capable of targeting >15,000 sequences at once (abstract and pg. 183 column 1 ¶ 1). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the manipulation of DNA for sequencing library preparation.
This is a provisional nonstatutory double patenting rejection.
Claim 28 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 19327646 in view of McCloskey et al (United States Patent Application No. US 20070020640, published 25 January 2007).
The copending application does not teach the limitations of claim 28.
However, McCloskey teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the adapters taught by the issued patent to have incorporated the random barcode taught by McCloskey to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because McCloskey teaches that this molecular sequence barcode allows for the origin of each sequence to be tracked and to identify redundant sequences to accurately quantify particular variants in the sample ([0093]). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the adapter tagging of nucleic acids.
This is a provisional nonstatutory double patenting rejection.
Conclusion
21. No claims are allowed.
22. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-T 0800 - 1630.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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