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 July 27, 2026 is acknowledged.
Status of the Application
2. Claims 7-8 and 16 are pending under examination. Claims 5-6, 10-15 were withdrawn from further consideration as being drawn to nonelected group. Claims 1-4, 9 are canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive in-part for the following reasons.
Objection to the Informalities-withdrawn
3. The objection to the informalities has been withdrawn in view of the amendment.
Objection to the Specification-maintained
4. The disclosure is objected to because of the following informalities:
(i) The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (page 4, line 28-30, page 5, line 1-2 and page 47, line 1-2). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Response to Arguments:
With reference to the objection to the specification, the applicant’s arguments and the amendment to the specification have been fully considered and found persuasive in-part. With reference to the embedded browser-executable code, the Applicant’s arguments and the amendment have been considered and found unpersuasive because the amendment recites browser executable code ‘www’ and the rejection has been maintained and restated. The objection to the sequence identifier has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 112-withdrawn
5. The rejection of claims under 35 USC 112(b) has been withdrawn in view of the amendment.
Double Patenting-maintained
6. 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.
Claims 7-8 and 16 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 3-10 and 17 of copending Application No. 18/844,944 (hereafter the ‘944). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims 7-8 and 16 are generic to claims 3-10 and 17 in the co-pending application ‘944 or the claims 7-8 and 16 are obvious over the claims 3-10 and 17 in the co-pending application ‘944. Specifically, the claims 7-8 and 16 comprising one oligonucleotide primer set group for amplifying a portion of one or more genes from M. tuberculosis and/or related bacteria in M. tuberculosis complex are within the scope of the claims in the co-pending application ‘944. The only variation is that the claims in the co-pending application recite SEQ ID NO: 1-32 or 35-38, wherein the elected SEQ ID NO: 1-10 are within the scope of the SEQ ID NO: 1-10 in claims 3-10 and 17 of the copending application and the claims 7-8 and 16 are obvious over the claims in the copending application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments:
With reference to the rejection of claims under provisional double patenting the Applicant’s arguments and the amendment have been considered and found persuasive in-part. The rejection of claims 1-4 and 9 is moot in view of the amendment. With reference to the rejection of claim 7-8 and 16, the arguments were fully considered and the rejection has been maintained because the claims remain within the scope of the claims in the co-pending application and the rejection has been restated to address the amendment.
Claim Rejections - 35 USC § 103-maintained
7. 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.
A. Claims 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Miotto et (Respirology, Vol. 23, page 1098-1113, (2018)) in view of Fleischmann et al. (US 6294328) and Lowe et al. (Nucleic acids Research, Vol. 18(7), p. 1757-1760,(1990)).
Miotto et al. teach claim 8, multidrug resistance mycobacterium tuberculosis related genes and associated infection, wherein Miotto et al. teach amplification detection of drug resistance related genes in mycobacterium tuberculosis, wherein the resistance related genes comprise eis, embB, fabG1, rrs and r0678 genes (page 1104-1105, paragraphs under ‘Line probe assays’ and table 1, 3-4).
With reference to claim 7, Miotto et al. teach one or more genes conferring antibiotic resistance to one or more of rifampicin, isoniazid, ethambutol, streptomycin, pyrazinamide, bedaquiline, quinolones, ciprofloxacin (page 1100, table 1).
However, Miotto et al. did not teach primer set of SEQ ID Nos: 1-10.
Fleischman et al. teach DNA sequences for strain analysis in mycobacterium tuberculosis, wherein the DNA sequences of different strains comprise the sequences of SEQ ID Nos 1-10 (SEQ ID NO: 1 or 2 contains the sequences of SEQ ID NO: 1-10, see the sequence alignment).
For SEQ ID NO: 1
AC AAI99683; DE Mycobacterium tuberculosis strain H37Rv genome SEQ ID NO 2. KW Mycobacterium tuberculosis; strain H37Rv; strain CDC 1551; genome; KW variation; epidemiology; patient treatment; epidemic monitoring; ds.CC PN US6294328-B1; CC PD 25-SEP-2001; CC PF 24-JUN-1998; 98US-00103840. CC PA (GENO-) INST GENOMIC RES.
CC PI Fleischmann RD, White OR, Fraser CM, Venter JC; SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other;
Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches 0; Indels 0; Gaps
Qy 1 TGTCGGGTACCTTTCGAGC 19
|||||||||||||||||||
Db 2712863 TGTCGGGTACCTTTCGAGC
For SEQ ID NO: 2
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other;
Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 TCCATGTACAGCGCCATCC 19
|||||||||||||||||||
Db 2711947 TCCATGTACAGCGCCATCC 2711965
SEQ ID NO: 3
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CGCCGTGGTGATATTCGGC 19
|||||||||||||||||||
Db 4239596 CGCCGTGGTGATATTCGGC 4239614
For SEQ ID NO:4
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches
Qy 1 GCACACCGTAGCTGGAGAC 19
|||||||||||||||||||
Db 4240719 GCACACCGTAGCTGGAGAC 4240701
For SEQ ID NO: 5 with the SEQ ID NO: 2 of the patent US6294328.
For SEQ ID NO: 6
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%;
Matches 19; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GAGTGTTGCCTCAGGACCC 19
|||||||||||||||||||
Db 1473036 GAGTGTTGCCTCAGGACCC 1473018
For SEQ ID NO; 7
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19 Conservative 0; Mismatches 0; Indels 0; Indels 0; Gaps 0;
Qy 1 GCTCGTCCTTCACTTCGCC 19
|||||||||||||||||||
Db 780489 GCTCGTCCTTCACTTCGCC 780507
For SEQ ID NO: 8
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches 0; Gaps 0;
Qy 1 ATCAGTCGTCCTCTCCGGT 19
|||||||||||||||||||
Db 781447 ATCAGTCGTCCTCTCCGGT 781429
For SEQ ID NO: 9
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches 0; Gaps 0;
Qy 1 CTTTTGCACGCAATTGCGC 19
|||||||||||||||||||
Db 1673290 CTTTTGCACGCAATTGCGC 1673308
For SEQ ID NO: 10
SQ Sequence 4403765 BP; 757105A; 1447799C; 1441301G; 757371T; 0U; 189 Other; Query Match 100.0%; Score 19; Length 4403765; Best Local Similarity 100.0%; Matches 19; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 TGTCGGGTACCTTTCGAGC 19
|||||||||||||||||||
Db 2712863 TGTCGGGTACCTTTCGAGC 2712845
Lowe et al. teach a method for designing primers and evaluating their performance
wherein Lowe et al. disclose a computer program for rapid selection of oligonucleotide
primers for polymerase chain reaction, wherein the length of the primers designed to
have 18 to 22 nucleotides or (paragraphs under subheading ‘computer program’ on
page 1757-1758, abstract). Lowe et al. teach that all primers designed for over 10 gene
products were experimentally tested and the results showed that all the amplification
products specified by the primers are of the predicted size and also hybridize with the
appropriate cDNA or internal oligonucleotide probe (see page 1759-1760, col. 2,
paragraph 1, table 1).
It would have been prima facie obvious to a person of ordinary skill in the art before
the effective date of the invention to modify the teaching of Miotto et al. with the known
gene sequence comprising the primer sequences of SEQ ID Nos. 1-10 taught by
Fleischmann et al. and a method to design primers/probes from the known sequence
as taught by Lowe et al. to improve the specificity of primers for detecting target nucleic
acid in a sample. The ordinary person skilled in the art would have motivated to
generate primers from the known sequence as taught by Fleischmann et al. and Lowe
et al. and have a reasonable expectation of success that such primers/ probe generated
from known sequence as taught by Fleischmann et al. would detect target nucleic acid.
The claimed primers/probe are functional equivalents of the polynucleotide sequence
taught by Fleischmann et al. in view of Lowe et al. because Lowe et al. explicitly taught
that the primers/probe generated from a known sequence using a computer program
would specifically amplify the target sequence and all primers designed for over 10
gene products from known sequences were experimentally tested and the results showed that all the amplification products specified by the primers are of the predicted
size also hybridizes with the appropriate cDNA or internal oligonucleotide probe (see
page 1760, col. 2, paragraph 1) and such a modification of the known sequences are
considered obvious over the prior art. As noted in In re Aller, 105 USPQ 233 at 235,
more particularly, where the general conditions of a claim such as oligomer length and
sequence, are disclosed in the prior art Miotto et al., Fleischmann et al. and Lowe et
al.), it is not inventive to discover the optimum or workable ranges by routine
experimentation. Routine optimization is not considered inventive and no evidence has
been presented that the selection of hybridization conditions performed was other than
routine, that the products resulting from the optimization have any unexpected
properties, or that the results should be considered unexpected in any way as
compared to the closest prior art and such a modification of the method is considered
obvious over the cited prior art.
B. Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Miotto et
al. (Respirology, Vol. 23, page 1098-1113, (2018)) in view of Fleischmann et al. (US
6294328) and Lowe et al. (Nucleic acids Research, Vol. 18(7), p. 1757-1760, (1990)) as
applied to claims 1-4 and 7-9 above, and further in view of Stratagene Catalog
(Stratagene Catalog, page 39, (1988)).
Miotto et al. and Lowe et al. teach oligonucleotide primer set as discussed above. However, Miotto et al. and Lowe et al. did not specifically teach packaging the primer set in a kit format.
Stratagene Catalog teaches gene characterization kit which includes formatting
kit components (see page 39).
It would have been prima facie obvious to an ordinary person skilled in the art
before the effective filing date of the invention to combine the composition as taught by
Miotto et al. and Lowe et al. with a kit format as discussed by Stratagene catalog to
develop a ready to use kit. The ordinary person skilled in the art would have been
motivated to combine the composition of Miotto et al. and Lowe et al. into a kit format as
taught by Stratagene catalog because Stratagene Catalog explicitly taught assembling
the components of a gene characterizing components into a kit format which provides
premixed ready to use reaction mixture, that saves money and resources (see page 39,
col. 1, paragraph) and such a modification of the composition is considered obvious
over the cited prior art.
Response to Arguments:
With reference to the rejection of claims under 35 USC 103 as being obvious over Miotto in view of Fleischmann and Lowe, and the rejection of claim under 35 USC 103 as being obvious over Miotto in view of Fleischmann and Lowe and further in view of Stratagene Catalog, the Applicant’s arguments and the amendment have been fully considered and found unpersuasive. With reference to the Applicant’s arguments drawn to at least one oligonucleotide primer set group consists of SEQ ID NOs.1-10 for amplifying portions of one or more M. tuberculosis complex genes have been found unpersuasive because the amended claim 8 as presented only requires oligonucleotide set for amplifying one or more genes, however, claim 8 does not require primer pairs for amplifying each of the specific portion of the genes in a reaction mixture. As discussed in the rejection, Miotto teaches drug resistant genes in M. tuberculosis and detection of mutations in Mycobacterium by multiplex allele-specific PCR and detection of amplicons using specific probes or real-time PCR (page 1104-1106, table 3-4 and paragraphs under the subheading ‘line probe assays’ and paragraphs under the subheading ‘Xpert MTB/RIF’) as opposed to the Applicant’s assertions drawn to sequencing. Further, the sequences of said genes of M. tuberculosis are known before the effective filing date of the claimed invention as taught by Fleischman and it would be obvious to generate primers from a known sequence using computer programing to select and design primers as taught by Lowe et al. and packaging the composition of primers into a kit format as taught by Stratagene Catalog. In addition, the claims as present do not require primer pair for each of the genes in a single reaction mixture and with reference to the arguments drawn to multiplex PCR, arguments have been found unpersuasive because the preamble is not given any patentable weight as noted in MPEP 2111.02. For all the above the rejection has been restated to address the amendment.
Claim Rejections - 35 USC § 101
8. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 7-8 and 16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. The claims 7-8 and 16 recite primers which represent product, a statutory category. Claims 7-8 and 16 recite a judicial exception (law of nature) without significantly more because said primers are considered as a law of nature products, said products exist in nature. This judicial exception is not integrated into a practical application because the judicial exception is not markedly different from law of nature (Fleischmann et al. (US 6294328)). The claim(s) do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements recited in the claims (kit) do not add significantly more to the claimed product. The additional elements are not themselves natural laws, but neither are they sufficient to transform the nature of the claims because they consist of well-understood, routine, conventional activity already engaged in by the scientific community. The additional elements consist
of well-understood, routine, conventional activity already engaged in by the scientific community (Fleischmann et al. (US 6294328)). The additional elements, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately. The Court has made clear that to transform an unpatentable law of nature into a patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words "apply it." Essentially, appending conventional steps specified at a high level of generality, to laws of nature, natural phenomena, and abstract ideas
cannot make those laws, phenomena, and ideas patent-eligible. The Court’s decision rested upon an examination of the particular claims in light of the Court's precedents, specifically Bilski, Flook and Diehr. The Court repeated the long- standing exceptions (laws of nature, natural phenomena, and abstract ideas) to categories of patent eligibility defined in 35 U.S.C. § 101. In conducting the analysis, the Court addressed the "machine-or-transformation" test explained in Bilski with a reminder that the test is
an "important and useful clue" to patentability but that it does not trump the "law of nature" exclusion. A claim that recites a law of nature or natural correlation, with additional elements/steps that involve well-understood, routine, conventional activity previously engaged in by researchers in the field is not patent-eligible, regardless of whether the steps result in a transformation. On the other hand, reaching back to Neilson, the Court pointed to an eligible process that included not only a law of nature (hot air promotes ignition) but also several unconventional steps involving a blast furnace) that confined the claims to a particular useful application of the principle. For these reasons, the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to Arguments:
With reference to the rejection of claims under 35 USC 101, the Applicant’s arguments and the amendment have been fully considered and found unpersuasive. With reference to the Applicant’s arguments drawn to oligonucleotide primer set consisting of SEQ ID Nos. 1-10 directed to a multiplex PCR reaction mixture, the arguments have been found unpersuasive because the sequence comprising said 1-10 seq ID Nos. is known and exists in nature and the claimed primer sequences are part of the DNA sequence existing in nature. The primer sequences are not modified or transformed from the existing known sequence. Further, the arguments drawn to multiplex PCR have been found unpersuasive because preamble is not given any patentable weight because said limitation does not add anything more to the known existing sequences. For all the above the rejection has been maintained and restated to address the amendment.
New Rejections Necessitated by the Amendment
Nucleotide and/or Amino Acid Sequence Disclosures
9. This application fails to comply with the requirements of 37 CFR 1.821 - 1.825. This application contains a “Sequence Listing” as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3)). A copy of the "Sequence Listing" in computer readable form (CRF) has been submitted on 7/27/2026; however, the content of the CRF does not comply with one or more of the requirements of 37 CFR 1.822 through 1.824, as indicated in the "Error Report" (7/28/2026) that indicates the "Sequence Listing" could not be accepted.
Claim Rejections - 35 USC § 112
10. The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 7-8 and 16 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. Clam 8 recites ‘at least one group of oligonucleotide primer sets’. The claims do not recite more than one group and it is not clear what the limitation ‘at least one’ refers to. Further, claim 8 recites each set comprises a pair of forward and reverse primers specific for said portion. It is unclear if the set consisting of 1-10 SEQ IDs represent a forward primer set or a reverse primer set and also it is not clear which combination of SEQ ID Nos. in the primer set group represents a pair of forward and reverse primers that amplifies which one or more genes as claimed.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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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/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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