Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claims 1-20 are pending and will be examined.
Double Patenting
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claims 1-20 are provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 1-20 of copending Application No. 18648154 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claims 1-20 are provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 1-20 of copending Application No. 18626712 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claims 1-20 are provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 1-20 of copending Application No. 18649979 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claims 1-20 are provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 1-20 of copending Application No. 18651577 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(e) the invention was described in (1) an application for patent, published under section 122(b), by another filed in the United States before the invention by the applicant for patent or (2) a patent granted on an application for patent by another filed in the United States before the invention by the applicant for patent, except that an international application filed under the treaty defined in section 351(a) shall have the effects for purposes of this subsection of an application filed in the United States only if the international application designated the United States and was published under Article 21(2) of such treaty in the English language.
Claim(s) 1-20 is/are rejected under pre-AIA 35 U.S.C. 102(e) as being anticipated by Bielas et al. (US 10011871; July 2018)
With regard to claim 1, Bielas teaches a single molecule identifier adaptor molecule for use in sequencing a double-stranded target nucleic acid molecule comprising a single molecule identifier (SMI) sequence,
the SMI sequence comprising at least one degenerate or semi-degenerate nucleic acid sequence;
and an SMI ligation adaptor that allows the SMI adaptor molecule to be ligated to the double-stranded target nucleic acid sequence (Figure 2, where the specific regions of adapter regions at the 5’ end and 3’ end are depicted in detail; Figure 3b, where adapters are ligated to the 5’ and 3’ end; col. 3, lines 3-22; col. 11, line 55 to col. 12, line 23, where generally speaking there are adapters for sample identifiers and the other provide unique identifiers for each strand).
With regard to claim 2, Bielas teaches a single molecule identifier adaptor molecule of claim 1, wherein the SMI sequence is single-stranded (Figure 2, where the specific regions of adapter regions at the 5’ end and 3’ end are depicted in detail; Figure 3b, where adapters are ligated to the 5’ and 3’ end; col. 3, lines 3-22; col. 11, line 55 to col. 12, line 23, where generally speaking there are adapters for sample identifiers and the other provide unique identifiers for each strand).
With regard to claim 3, Bielas teaches a single molecule identifier adaptor molecule of claim 1, wherein the SMI sequence is double-stranded (Figure 2, where the specific regions of adapter regions at the 5’ end and 3’ end are depicted in detail; Figure 3b, where adapters are ligated to the 5’ and 3’ end; col. 3, lines 3-22; col. 11, line 55 to col. 12, line 23, where generally speaking there are adapters for sample identifiers and the other provide unique identifiers for each strand).
With regard to claim 4, Bielas teaches a single molecule identifier adaptor molecule of claim 1, wherein the double-stranded target nucleic acid molecule is a double-stranded DNA or RNA molecule (Figure 2, where the specific regions of adapter regions at the 5’ end and 3’ end are depicted in detail; Figure 3b, where adapters are ligated to the 5’ and 3’ end; col. 3, lines 3-22; col. 11, line 55 to col. 12, line 23, where generally speaking there are adapters for sample identifiers and the other provide unique identifiers for each strand).
With regard to claim 5, Bielas teaches a single molecule identifier adaptor molecule of claim 1, further comprising at least two PCR primer binding sites, or at least two sequencing primer binding sites, or both (Figure 2, where the specific regions of adapter regions at the 5’ end and 3’ end are depicted in detail; Figure 3b, where adapters are ligated to the 5’ and 3’ end; col. 3, lines 3-22; col. 11, line 55 to col. 12, line 23, where generally speaking there are adapters for sample identifiers and the other provide unique identifiers for each strand).
With regard to claim 6, Bielas teaches a single molecule identifier adaptor molecule of claim 1, further comprising a double-stranded fixed reference sequence (Figure 2, where the specific regions of adapter regions at the 5’ end and 3’ end are depicted in detail; Figure 3b, where adapters are ligated to the 5’ and 3’ end; col. 3, lines 3-22; col. 11, line 55 to col. 12, line 23, where generally speaking there are adapters for sample identifiers and the other provide unique identifiers for each strand).
With regard to claim 7, Bielas teaches a single molecule identifier adaptor molecule of claim 2, wherein the degenerate or semi-degenerate nucleic acid sequence comprises a first nucleotide n-mer sequence that is between approximately 3 and 20 nucleotides in length (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 8, Bielas teaches a single molecule identifier adaptor molecule of claim 7, wherein the first nucleotide n-mer sequence is a degenerate sequence (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 9, Bielas teaches a single molecule identifier adaptor molecule of claim 3, wherein the degenerate or semi-degenerate nucleic acid sequence comprises a first nucleotide n-mer sequence, a second n-mer sequence that is complementary to the first nucleotide n-mer sequence (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 10, Bielas teaches a single molecule identifier adaptor molecule of claim 9, wherein the first n-mer sequence comprises a nucleotide sequence that is between approximately 3 and 20 nucleotides in length (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 11, Bielas teaches a single molecule identifier adaptor molecule of claim 9, wherein the first nucleotide n-mer sequence is a degenerate sequence (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 12, Bielas teaches a single molecule identifier adaptor molecule of claim 1, wherein the degenerate or semi-degenerate DNA sequence comprises a randomly fragmented double stranded nucleic acid derived from an alternative source (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 13, Bielas teaches a single molecule identifier adaptor molecule of claim 1, wherein the SMI ligation adaptor is selected from a T-overhang, an A-overhang, a CG overhang, a blunt end, or any other ligatable nucleic acid sequence (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 14, Bielas teaches a single molecule identifier adaptor molecule of claim 1, wherein the SMI adaptor molecule is Y-shaped, U-shaped, or a combination thereof (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
With regard to claim 15, Bielas teaches a method of obtaining the sequence of a double-stranded target nucleic acid comprising
ligating a double-stranded target nucleic acid molecule to at least one SMI adaptor molecule to form a double-stranded SMI-target nucleic acid complex; amplifying the double-stranded SMI-target nucleic acid complex, resulting in a set of amplified SMI-target nucleic acid products; and sequencing the amplified SMI-target nucleic acid products (Figure 3B, where the targets are ligated with dual cypher adapters, and they are amplified and sequenced).
With regard to claim 16, Bielas teaches a single molecule identifier adaptor molecule of claim 15, wherein the double-stranded target nucleic acid molecule is a double-stranded DNA or RNA molecule (Figure 3B, where the targets are ligated with dual cypher adapters, and they are amplified and sequenced).
With regard to claim 17, Bielas teaches a method of claim 15, further comprising generating an error-corrected double-stranded consensus sequence by
(i) grouping the sequenced SMI-target nucleic acid products into families of paired target nucleic acid strands based on a common set of SMI sequences; and
(ii) removing paired target nucleic acid strands having one or more nucleotide positions where the paired target nucleic acid strands disagree, or
alternatively removing nucleotide positions from nucleic acid strands where the paired strands disagree at that specific position (Example 1 and 3, where computation and barcodes were used to deconvolute using the sequencing reads; Figure 3 legend, which briefly explains the process of using the cypher barcode as a basis to align and understand reads).
With regard to claim 18, Bielas teaches a method of claim 15, wherein the double-stranded target nucleic acid molecule is a sheared double-stranded DNA or RNA fragment.
With regard to claim 19, Bielas teaches a method of claim 18, wherein the sheared double-stranded nucleic acid fragment further comprises a double-stranded target nucleic acid sequence ligation adaptor (Example 1 and 3, where computation and barcodes were used to deconvolute using the sequencing reads; Figure 3 legend, which briefly explains the process of using the cypher barcode as a basis to align and understand reads).
With regard to claim 20, Bielas teaches a method of claim 19, wherein the double-stranded target nucleic acid sequence ligation adaptor is selected from a T-overhang, an A-overhang, a CG overhang, a blunt end, or any ligatable nucleic acid sequence (col. 6, lines 1-14, where the barcode or UMI are between 5 and 50 bases in length and can vary within that range).
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Lapidus et al. (US Patent 8,802,368; August 2014).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681
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