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 .
DETAILED ACTION
1. The Applicant’s response to the office action filed on August 27, 2025 is acknowledged.
Status of the Application
2. Claims 1-14 are pending under examination. Claims 16-21 are withdrawn previously from further consideration as being drawn to nonelected group. Claim 15 is canceled. The Applicant’s arguments have been fully considered and found persuasive in-part for the following reasons.
Objection to Nucleotide and/or Amino Acid Sequence Disclosures-maintained
3. This application contains sequence disclosures that are encompassed by the
definitions for nucleotide and amino acid set forth in 37CFR 1.821(a)(1) and (a)(2).
However, this application fails to comply the requirements of 37 CFR 1.821 through
1.825. Nucleotide and/or amino acid sequences appearing in the specification (see para
00095-00097, table 1) are not identified by sequence identifiers in accordance with 37
CFR 1.821(d). Further, this application fails to comply with the requirements of 37 CFR
1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the
disclosure or a CRF of the “Sequence Listing.”.
Response Arguments:
The objection to the specification (sequence noncompliance) has been maintained because the Applicant did not address the objection nor provided the sequence listing and sequence identifiers for the sequences recited in the cited paragraphs of the specification.
Claim Rejections - 35 USC § 102-maintained
4. 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.
Claims 1-14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al. (WO2017/151828).
Chen et al. teach a method of claim 1, for tracking an origin of a nucleic acid fragment
by barcoding comprising:
a) providing a reaction mixture comprising a plurality of double stranded nucleic acid
fragments and a plurality of beads, wherein each bead comprises at least two different
immobilized barcode templates from at least two different populations of barcode
templates, wherein each population of barcode template comprises multiple copies
(clonally amplified or clusters) of the same barcode template, wherein each barcode
template comprises a barcode sequence, wherein said barcode sequence is configured
to be an identifier of the barcode template (para 0003-00014, 00032-00037, 00049-
00068, 00071-00076, claim 1, 21);
b) producing at least two barcode-attached subfragments from said nucleic acid
fragment, wherein the at least two barcode-attached subfragments from the same
nucleic acid fragment is each attached to the barcode sequence with a same
sequence from the same bead (para 0003-00014, 00032-00037, 00049-00068, 00071-
00076, claim 1, 21); and
c) tracking/identifying the origin of said barcode-attached subfragments by their said
barcode sequence, wherein barcode-attached subfragments with the same sequence
tracks to the same nucleic acid fragment (para 0003-00014, 00032-00037, 00049-
00068, 00071-00076, claim 1, 21).
With reference to claim 2, Chen et al. teach that said reaction mixture is not
compartmentalized into aliquots or droplets (para 0003-0004, 00063-00064, 00091,
00093).
With reference to claim 3, Chen et al. teach that said beads in said reaction mixture
comprise at least about 1000 different barcode sequences in total (para 0003-0004,
00068).
With reference to claim 4, Chen et al. teach that at least one of said barcode template
populations on each bead are also present on at least another bead as a common shared
barcode template population among said plurality of beads (para 00093, 00071-00076).
With reference to claim 5-6, Chen et al. teach that the amount of said common shared
barcode template is less than about 50% or less than 10% of total barcode template on
said bead (para 00033, 00036, 0094).
With reference to claim 7, Chen et al. teach that said double stranded nucleic acid
comprises a double stranded DNA, or a DNA/RNA hybrid, or a combination thereof
(para 00016).
With reference to claim 8, Chen et al. teach that said double stranded nucleic acid is
greater than about 1000bp (para 00051).
With reference to claim 9, Chen et al. teach that said double stranded nucleic acid
fragment comprises a nucleic acid molecule comprising DNA or RNA in natural, modified, amplified, or other chemically treated forms or a combination thereof (para
0003).
With reference to claim 10, Chen et al. teach that said double stranded nucleic acid
fragment is nonspecifically bound to said bead first before any reactions (para 0016.
With reference to claim 11, Chen et al. teach that said double stranded nucleic acid
fragment is strand transferred with a transposome and forms a strand transfer
complex before interacting with said bead (para 0007-00014).
With reference to claim 12, Chen et al. teach that said producing barcode-attached
subfragment comprises steps of ligation, hybridization, strand transfer reaction,
tagmentation, amplification, primer extension, or a combination thereof (para 00053-
00064, 00074-00076).
With reference to claim 13, Chen et al. teach that said strand transfer reaction or said
tagmentation reaction comprises utilizing a transposase, wherein said transposase is
selected from a group consisting of Tn, Mu, Ty, and Tc transposases in a wildtype, a
mutant or a tagged version thereof, and a combination thereof (para 00075-00076).
With reference to claim 14, Chen et al. teach that said tracking/identifying the origin
of said barcode-attached subfragments comprises sequencing to determine the identity
of duplicated nucleic acid fragments, copy number variation information, haplotype
phasing information and/or structural variation of the nucleic acid fragment (para 00073,
0004). For all the above the claims are anticipated.
Response to the Arguments:
A. With reference to the rejection of claims under 35 USC 102(a)(1) as being anticipated by Chen et al., the Applicant’s arguments were found unpersuasive. With reference to no teaching of different barcoded templates from different populations by Chen et al, the arguments were found unpersuasive because the Examiner cited portions of Chen et al. teach immobilized different barcode templates from different samples from patients (para 0003, 0033-0036, 0053, 0063-0068) which indicates barcodes tagged with different templates from different patient samples which is within the scope of different barcode templates (two or more) from different populations (two or more). The para 0036 teach template and barcode distribution is a Poisson distribution which results into a proportion of beads comprising two barcode templates. Further, para 0054, 0063 and Fig. 14 teach each bead comprising plurality (two or more) of barcode templates, which is within the scope of the limitations as required by the claim 1 and the rejection of claims is maintained.
B. The rejection of claims under 35 USC 102(a)(1) as being anticipated by Drmanac et al. has been withdrawn in view of the amendment.
New Grounds of Rejections necessitated by IDS with fee
Claim Rejections - 35 USC § 102
5. 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.
Claims 1, 3-10, 12 and 14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Frenz et al. (US 2017/0198345).
Frenz et al. teach a method of claim 1, for tracking/identifying an origin of a nucleic acid fragment by barcoding comprising: a) providing a reaction mixture comprising a plurality of double stranded nucleic acid fragments and a plurality of beads, wherein each bead comprises at least two different immobilized barcode templates from at least two different populations of barcode templates, wherein each population of barcode template comprises multiple copies (clonally amplified or clusters) of the same barcode template, wherein each barcode template comprises a barcode sequence, wherein said barcode sequence is configured to be an identifier of the barcode template (para 0017-0019, 0012-0016, 0032-0035, 0058-0060, 0110-0113);
b) producing at least two barcode-attached subfragments from said nucleic acid fragment, wherein the at least two barcode-attached subfragments from the same nucleic acid fragment are each attached to the barcode sequence with a same sequence from the same bead (para 0019-0021, 0034-0035, 0058-0061); and
c) tracking/identifying the origin of said barcode-attached subfragments by their said barcode sequence, wherein barcode-attached subfragments with the same sequence tracks to the same nucleic acid fragment (para 0058-0061, 0082, 0110-0113).
With reference to claim 3, Frenz et al. teach that said beads in said reaction mixture comprise at least about 1000 different barcode sequences in total (para 0026, 0032, 0076).
With reference to claim 4-6, Frenz et al. teach that at least one of said barcode template populations on each bead is also present on at least another bead as a common shared barcode template population among said plurality of beads and the amount of said common shared barcode template is less than about 50% or less than 10% of total barcode template on said bead (para 0058-0061).
With reference to claim 7-9, Frenz et al. teach that said double stranded nucleic acid comprises a double stranded DNA, or a DNA/RNA hybrid, or a combination thereof; and said double stranded nucleic acid fragment comprises a nucleic acid molecule comprising genomic DNA, long fragment DNA or RNA in natural, modified, amplified, or other chemically treated forms or a combination thereof (para 0066-0067, 0070, 0020).
With reference to claim 10, Frenz et al. teach that said double stranded nucleic acid fragment is nonspecifically bound to said bead first before any reactions (para 0058-0059).
With reference to claim 12, Frenz et al. teach that said producing barcode-attached subfragment comprises steps of ligation, hybridization, amplification, primer extension, or a combination thereof (para 0004, 0083).
With reference to claim 14, Frenz et al. teach that said tracking/identifying the origin of said barcode-attached subfragments comprises sequencing to determine the identity of duplicated nucleic acid fragments, copy number variation information, haplotype phasing information, structural variation of the nucleic acid fragment (para 0128-0135, 0061). For all the above the claims are anticipated.
Conclusion
No claims are allowable.
Applicant's submission of an information disclosure statement under 37 CFR 1.97(c) with the timing fee set forth in 37 CFR 1.17(p) on August 29, 2025 prompted the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 609.04(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SURYAPRABHA CHUNDURU whose telephone number is (571)272-0783. The examiner can normally be reached 8.00am-4.30pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681