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 .
Claims 1-19 are currently pending and under examination.
Information Disclosure Statement
The Information Disclosure Statements filed June 24, 2022; and April 08, 2024 have been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/patents-application- process/filing-online/legal-framework-efs-web), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1),
1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete.
Required response – Applicant must:
Include a Sequence Listing Incorporation by Reference paragraph at page 1 of the
specification. The Sequence Listing Incorporation by Reference paragraph should list the size of the ASCII text file as 6,921 bytes.
Claim Objections
Claims 16 and 19 are objected to because of the following informalities:
In claim 16, line 1, “the adapter” should read “the adapters”.
In claim 19, line 2, “a agent” should read “an agent”.
Appropriate correction is required.
Claim Interpretation
The term “random nucleotide” is being interpreted to include any nucleotide sequence of 3-30 nucleotides in length. A randomization process can lead to any possible sequence of
nucleotides, and by the sequence alone it is impossible to determine if said sequence is a result of a randomization process or not. Therefore, any nucleotide sequence of 3-30 nucleotides in length is seen as falling within the scope of the definition.
Claim Rejections - 35 USC § 112
Claims 4 and 7 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 4 is considered vague and indefinite for the following reasons:
In claim 4, the limitations “a base sequence of the random sequence” in line 1, are unclear and confusing. It is unclear as to which part of the “random nucleotide” is to be considered the base sequence? Is it a certain number of bases that are to be considered the base sequence of the random nucleotide? For examination purposes, any sequence of 1 or more nucleotides is considered to fall within the scope of the definition.
Claim 7 is considered vague and indefinite for the following reasons:
In claim 7, the limitations “a base sequence of the random sequence” in line 1, are unclear and confusing. It is unclear as to which part of the “random nucleotide” is to be considered the base sequence? Is it a certain number of bases that are to be considered a base sequence of the random nucleotide? For examination purposes, any sequence of 1 or more nucleotides is considered to fall within the scope of the definition.
Additionally, in claim 7, “the base sequence of the random nucleotide is constituted so that a melting temperature (Tm) value of the double-stranded nucleic acid molecule is 20°C or higher”, in lines 2-3 is unclear and confusing. It is unclear as to how the base sequence should be put together so that the melting temperature is 20°C. Is there a specific length and/or order of the base sequence that is required?
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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 the appropriate paragraphs of 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 –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2, 4 and 6 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Ng et al. (“Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation”. Nat Methods 2, Pgs. 105–111, published January 09, 2005), cited on the IDS filed April 08, 2024.
Regarding claim 1, NG teaches double-stranded nucleic acid molecule comprising a sense strand containing a type II restriction enzyme recognition site and a random nucleotide sequence of a length of 3 to 30 nucleotides (nt) and an anti-sense strand containing a complementary sequence to the sense strand and a 3'-end A tail (Figure 1).
Regarding claim 2, NG teaches a random nucleotide sequence of a length of 1 to 10 nt is further contained in the 3'-end of the sense strand or the 5'-end of the anti-sense strand (Figure 1).
Regarding claim 4, NG teaches a base sequence of the random nucleotide further contained in the 5'-end of the anti-sense strand consists of only thymine (T), cytosine (C), guanine (G) or a combination thereof (Figure 1 and Supplementary Figure 1).
Regarding claim 6, NG teaches the type IIs restriction enzyme is MmeI, (Page 110, Right Column, Last Paragraph and Figure 1).
Claims 1-2, and 5-6 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Sen et al. (“Restriction enzyme–generated siRNA (REGS) vectors and libraries”. Nat Genet 36, Pgs. 183–189, published January 04, 2004), cited on the IDS filed April 08, 2024.
Regarding claim 1, Sen teaches double-stranded nucleic acid molecule comprising a sense strand containing a type II restriction enzyme recognition site and a random nucleotide sequence of a length of 3 to 30 nucleotides (nt) and an anti-sense strand containing a complementary sequence to the sense strand and a 3'-end A tail (Overhangs are designated by Ns and may therefore be an A tail, Figure 1).
Regarding claim 2, Sen teaches a random nucleotide sequence of a length of 1 to 10 nt is further contained in the 3'-end of the sense strand or the 5'-end of the anti-sense strand (Figure 1).
Regarding claim 5, Sen teaches the 3'-end of the sense strand and the 5'-end of the anti-sense strand are connected to each other by a loop to have a hairpin structure (Figure 1).
Regarding claim 6, Sen teaches the type IIs restriction enzyme is MmeI, (Page 184, Left Column, First-Third Paragraph and Figure 1).
Claim Rejections - 35 USC § 103
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 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.
Claims 1-19 are rejected under 35 U.S.C. 103 as being unpatentable over Hwang et al. (KR 20170020091 A, published February 22, 2017), cited on the IDS filed June 24, 2022, in view of Head et al. (“Library construction for next-generation sequencing: Overviews and challenges”, Biotechniques;56(2):61, published February 01, 2014).
Regarding claim 1, Hwang teaches double-stranded nucleic acid molecule comprising a sense strand containing a type II restriction enzyme recognition site and a random nucleotide sequence of a length of 3 to 30 nucleotides (nt) and an anti-sense strand containing a complementary sequence (Abstract, Page 2, First Paragraph and Figure 2).
Regarding claim 2, Hwang teaches a random nucleotide sequence of a length of 1 to 10 nt is further contained in the 3'-end of the sense strand or the 5'-end of the anti-sense strand (Abstract, Page 2, First Paragraph and Figure 2).
Regarding claim 3, Hwang teaches the random nucleotide sequence further contained in the 3'-end of the sense strand consists of only cytosine (C), guanine (G), or a combination thereof (Hwang SEQ ID NO: 3).
Regarding claim 4, Hwang teaches a base sequence of the random nucleotide further contained in the 5'-end of the anti-sense strand consists of only thymine (T), cytosine (C), guanine (G) or a combination thereof (Hwang SEQ ID NO: 6).
Regarding claim 5, Hwang teaches the 3'-end of the sense strand and the 5'-end of the anti-sense strand are connected to each other by a loop to have a hairpin structure (Abstract, Page 3, First Paragraph and Figure 2).
Regarding claim 6, Hwang teaches the type IIs restriction enzyme is Earl (Page 3, First Paragraph, Page 4, Second Paragraph and Figure 2).
Regarding claim 7, Hwang teaches a double-stranded nucleic acid molecule and the sense strand comprises a type IIs restriction enzyme recognition site and a random nucleotide of a length of 6 to 10 nt (Abstract, Page 2, First Paragraph and Figure 2).
Regarding claims 8-9, Hwang teaches a sense and antisense strand (Abstract, Page 2, First Paragraph and Figure 2). Hwang teaches using a CustomArray B3 Synthesizer to design the DNA sense and anti-sense strands (Page 3, First Two Paragraphs).
Regarding claim 10, Hwang teaches composition comprising the double-stranded nucleic acid molecule , DNA ligase, and a type IIs restriction enzyme (Abstract, Page 2, First Paragraph, Page 4, Fifth Paragraph and Figure 2).
Regarding claim 11, Hwang teaches the DNA ligase is T4 ligase (Page 4, Fifth Paragraph).
Regarding claim 12, Hwang teaches the composition is used for improving sample detection ability in an indexed DNA library in next generation sequencing (NGS) (Abstract and Page 4, Ninth Paragraph—Page 5, First Paragraph).
Regarding claim 13, Hwang teaches a library of next generation sequencing (Page 4, Ninth Paragraph—Page 5, First Paragraph.
Regarding claim 14, Hwang teaches a library of next generation sequencing, DNA ligase and a type IIs restriction enzyme (Page 4, Ninth Paragraph—Page 5, First Paragraph, and Page 4, First-Fifth Paragraph).
Regarding claim 15, Hwang teaches treating and reacting the double-stranded nucleic acid molecule and DNA ligase in a DNA library for next generation sequencing constructed by linking adapters for next generation sequencing to both ends of a DNA fragment to be analyzed and treating the resulting reaction products with a type IIs restriction enzyme (Abstract, Page 2, First Paragraph, Page 4, Whole Page and Page 6, Second to Last Paragraph and Figure 2).
Regarding claim 16, Hwang teaches adapters on both ends of DNA (Page 4, First-Fifth Paragraph and Page 6, Second to Last Paragraph).
Regarding claim 17, Hwang teaches the type IIs restriction enzyme is Earl (Page 3, First Paragraph, Page 4, Second Paragraph and Figure 2).
Regarding claim 18, Hwang teaches step (b) as discussed above.
Regarding claim 19, Hwang teaches a T4 DNA ligase and a type IIs restriction enzyme (Page 4, First-Fifth Paragraph). Hwang teaches adapters on both ends of DNA (Page 4, First-Fifth Paragraph and Page 6 ). Hwang teaches a library for next generation sequencing (Abstract and Page 4, Ninth Paragraph—Page 5, First Paragraph).
Hwang does not teach or suggest a 3’-end A tail. Hwang does not teach or suggest the base sequence of the random nucleotide is constituted so that a melting temperature (Tm) value of the double-stranded nucleic acid molecule is 20°C or higher. Hwang does not teach or suggest a sense strand consists of a base sequence explicitly defined by SEQ ID NO: I and the anti-sense strand consists of a base sequence defined by SEQ ID NO: 2. Hwang doe not teach or suggest the double-stranded nucleic acid molecule consists of a base sequence explicitly defined by SEQ ID NO: 3. Hwang does not teach or suggest the composition is used for removing free adapters which are not ligated to an insert in the process of constructing the indexed DNA library of next generation sequencing. Hwang does not teach or suggest A kit for removing free adapters in an indexed DNA library of next generation sequencing. Hwang does not teach or suggest linking adapters for next generation sequencing to both ends of a double-stranded DNA fragment of a genomic DNA. Hwang does not teach or suggest the adapter comprises an index sequence, a random barcode sequence or both thereof. Hwang does not teach or suggest washing with a buffer or performing bead clean-up after step (b). Hwang does not teach or suggest preparing an agent for removing free adapters in an indexed DNA library for next generation sequencing.
Head teaches a double stranded DNA, restriction II enzyme recognition site, an anti-sense strand containing a complementary sequence to the sense strand and a 3'-end A tail as well as creating and NGS library (Page 2, Second Paragraph, Page 3, Second Paragraph, Page 4, Fourth-Fifth Paragraph, Page 7, Third Paragraph, Page 13, Second Paragraph, Page 15, Fourth Paragraph and Figures 2 and 4). Head teaches A tailing the 3’ ends facilitate ligation to sequencing adapters (Page 4, Fourth Paragraph). Head teaches fragmenting and or sizing the DNA to a desired length (3-30 nucleotides) and attaching adapters to the ends of the double stranded DNA and quantitating the final NGS library product for sequencing (Page 2, Second Paragraph). Head teaches removing free adapters which are not ligated to an insert in the process of constructing the indexed DNA library of next generation sequencing (Page 3, Third Paragraph, Page 4, Fifth Paragraph and Page 9, Last Two Paragraphs). Head teaches a kit for removing free adapters in an indexed DNA library of next generation sequencing (Page 4, Third and Sixth-Seventh Paragraphs). Head teaches a kit for removing free adapters in an indexed DNA library of next generation sequencing (Page 3, Third Paragraph, Page 4, Fifth Paragraph and Page 9, Last Two Paragraphs). Head teaches using genomic DNA (Page 8, Third Paragraph and Page 11, Third Paragraph). Head teaches the adapters comprise and index/barcode sequence (Page 4, Sixth and Last Paragraph and Page 8, Fourth Paragraph). Head teaches washing with a buffer and performing bead clean up after step (b) (Page 4, First and Fifth Paragraphs, and Page 3, Third Paragraph). Head teaches preparing an agent for removing free adapters in an indexed DNA library for next generation sequencing (Page 4, Third-Seventh Paragraph and Page 9, Second Paragraph). Head teaches extending melt cycles to significantly reduce amplification bias (Page 9, Second Paragraph). Head teaches because the fragment size is also dependent on the reaction efficiency, all reaction parameters, such as temperatures (melting temperature) and reaction time, are critical and must be tightly controlled (e.g., The melting temperature may be designed by user’s choice, Page 5, First Paragraph). Head teaches using bead based clean up methods are more effective at removing excess adapters (Page 4, Fifth Paragraph). Head teaches using these methods reduced sample handing and preparation time as well as improves on traditional protocols by combining DNA fragmentation, end-repair, and adaptor ligation into a single step (Page 2, Third Paragraph and Page 4, Last Paragraph—Page 5, First Paragraph).
As common field of endeavor both Hwang and Head disclose using restriction II enzymes (and recognition sites) as well as methods for NGS library construction and sequencing.
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Hwang with the teaching of Head, using an anti-sense strand containing a 3’-end A tail and a method/kit to remove free adapters in an indexed DNA library for next generation sequencing as well as using bead clean-up. Using a 3’-end A tail would facilitate ligation to sequencing adapters as taught by Head (Page 4, Fourth Paragraph). Additionally, using bead based clean up methods are more effective at removing excess adapters as taught by Head (Page 4, Fifth Paragraph). Moreover, using these methods would allow for reduced sample handing and preparation time as well as improves on traditional protocols by combining DNA fragmentation, end-repair, and adaptor ligation into a single step as taught by Head (Page 2, Third Paragraph and Page 4, Last Paragraph—Page 5, First Paragraph).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the invention to modify the teachings of Hwang with the teachings of Head to choose the base sequence of the random nucleotide is constituted so that a melting temperature (Tm) value of the double-stranded nucleic acid molecule is 20°C or higher because Head teaches that all reaction parameters, such as temperatures (melting temperature) and reaction time, are critical and must be tightly controlled (e.g., chosen to be a specific temperature, above 20°C). Additionally, these claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome of increasing the melting temperature to above 20°C and increase the melt cycles to reduce amplification biased as taught by Head (Page 9, Second Paragraph).
Additionally, it would have been prima facie obvious to a person of ordinary skill in the art at the time the invention was made to have designed the sense strand to consist of a base sequence defined by SEQ ID NO: 1 and the anti-sense strand to consist of a base sequence defined by SEQ ID NO: 2 because Hwang teaches using a CustomArray B3 Synthesizer to design the DNA sense and anti-sense strands and creating an NGS library. Therefore a person of ordinary skill in the art would be able to use the CustomArray B3 synthesizer as taught by Hwang, to design and choose specific sequences required for the user’s need, such as creating a double stranded DNA template to create an NGS library without unexpected or unpredictable results.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/ Examiner, Art Unit 1684
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684