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 .
Claim Rejections - 35 USC § 103
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 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.
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 21-40 are rejected under 35 U.S.C. 103 as being unpatentable over Narayanan et al (US 20160348153 A1) in view of Gundling (US 20140275510 A1).
With regard to claim 21, Narayanan et al. teach a method comprising the steps of obtaining a biological sample present in a fluid-based collection medium; contacting the biological sample with a sample preparation and reverse crosslink treatment reagent to form a mixture in which the biological sample is disposed within the reagent, wherein the reagent comprises guanidine thiocyanate, polysorbate, polyethylene glycol (PEG), and sodium acetate buffer having a pH in a range of from about 4 to about 6.5; (see paragraph 0101), where the pH of the sodium acetate buffer is 5) and incubating the mixture at a temperature in a range of from about 650C to about 1100C for a period in a range of from about 30 seconds to about five minutes (see paragraph 0167, where the mixture was heated to 950C for 15 minutes which is about 5 minutes), wherein the incubation step results in reverse crosslinkage, lysis and nucleic acid binding (see example 3 paragraph 0155-0169)
Narayanan et al. does not exemplify the specific time of 5 minutes. However, Narayan do teach 5-10 minute (paragraph 0123) and 15 minutes (see paragraph 0167). At paragraph 0123 Narayan et al. recognizes that the time can be varied i.e. 5 minutes to 10 minutes depending on temperature. Incubation time is a results-based parameter. The skilled artisan can use the times taught by Narayanan et al. as a starting point and adjust based on the desired result. It is therefore obvious to arrive at the claimed time. The claimed time would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention over the teachings of Narayanan et al. One of ordinary skill in the art will be motivated to look for an incubation time that would result in a stably stored biological sample and extract nucleic acid from the collected sample. (Narayanan et al. paragraph 005).
With regard to claim 22, Narayanan et al. teach polysorbate-20 (see paragraph 0037)
With regard to claim 25, Narayanan et al teach the prior to contact with the treatment reagent, the biological sample has been stored in the collection medium at storage conditions selected from 20C to 80C for at least one week; room temperature for at least one week and 450C for at least 2 weeks (see paragraph 0129 where the sample is stored at ambient temperature for 14 days)
With regard to claim 26, Narayanan et al. teach the step of performing at least one nucleic acid analysis step on the mixture (see paragraph 00168 where real-time PCR was done).
With regard to claim 27, Narayanan et al. teach the biological sample comprises a cervical swab and wherein the nucleic acid analysis detects at least on sexually transmitted infection (see paragraph 0067 where Chlamydia trachomatis/Neisseria gonorrhoeae are disclosed).
With regard to claim 28, Narayanan et al. teach the nucleic acid analysis detects HPV (human papillomavirus) or CT/GC (Chlamydia trachomatis/Neisseria gonorrhoeae) (see paragraph 0067)
With regard to claim 29, Narayanan et al. teach guanidine thiocyanate is present at a concentration of about 5M; polysorbate-20 at a concentration in a range of from about 1% to about 20% and PEG is PEG8000 present at a concentration in a range of from about .1% to about 10% (see paragraphs 0029 and 0037, respectively. Where the concentration of guanidine thiocyanate is 4.5M with meets the limitation of about 5M).
With regard to claim 30, Narayanan et al. teach polysorbate-20 at a concentration of about 10% and PEG8000 at a concentration of about 1.5%
With regard to claim 31, Narayanan et al. teach a method comprising the steps of obtaining a biological sample present in a fluid-based collection medium; contacting the biological sample with a sample preparation and reverse crosslink treatment reagent to form a mixture in which the biological sample is disposed within the reagent, wherein the reagent comprises guanidine thiocyanate, polysorbate, polyethylene glycol (PEG), and Tris buffer having a pH in a range of from about 8 to about 10; and incubating the mixture at a temperature in a range of from about 650C to about 1100C for a period in a range of from about 30 seconds to about five minutes (see paragraph 0167, where the mixture was heated to 950C for 15 minutes which is about 5 minutes), wherein the incubation step results in reverse crosslinkage, lysis and nucleic acid binding (see example 3 paragraph 0155-0169).
Narayanan et al. does not exemplify the specific time of 5 minutes. However, Narayan do teach 5-10 minute (paragraph 0123) and 15 minutes (see paragraph 0167). At paragraph 0123 Narayan et al. recognizes that the time can be varied i.e. 5 minutes to 10 minutes depending on temperature. Incubation time is a results-based parameter. The skilled artisan can use the times taught by Narayanan et al. as a starting point and adjust based on the desired result. It is therefore obvious to arrive at the claimed time. The claimed time would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention over the teachings of Narayanan et al. One of ordinary skill in the art will be motivated to look for an incubation time that would result in a stably stored biological sample and extract nucleic acid from the collected sample. (Narayanan et al. paragraph 005).
With regard to claim 32, Narayanan et al. teach polysorbate-20 (see paragraph 0037).
With regard to claim 35, Narayanan et al teach the prior to contact with the treatment reagent, the biological sample has been stored in the collection medium at storage conditions selected from 20C to 80C for at least one week; room temperature for at least one week and 450C for at least 2 weeks (see paragraph 0129 where the sample is stored at ambient temperature for 14 days)
With regard to claim 36, Narayanan et al. teach the step of performing at least one nucleic acid analysis step on the mixture (see paragraph 00168 where real-time PCR was done).
With regard to claim 37, Narayanan et al. teach the biological sample comprises a cervical swab and wherein the nucleic acid analysis detects at least on sexually transmitted infection (see paragraph 0067, where Chlamydia trachomatis/Neisseria gonorrhoeae are disclosed).
With regard to claim 38, Narayanan et al. teach the nucleic acid analysis detects HPV (human papillomavirus) or CT/GC (Chlamydia trachomatis/Neisseria gonorrhoeae) (see paragraph 0067).
With regard to claim 39, Narayanan et al. teach guanidine thiocyanate is present at a concentration of about 5M; polysorbate-20 at a concentration in a range of from about 1% to about 20% and PEG is PEG8000 present at a concentration in a range of from about .1% to about 10% (see paragraphs 0029 and 0037, respectively. Where the concentration of guanidine thiocyanate is 4.5M with meets the limitation of about 5M).
With regard to claim 40, Narayanan et al. teach polysorbate-20 at a concentration of about 10% and PEG8000 at a concentration of about 1.5%
With regard to claim 40, Narayanan et al. does not exemplify a reagent comprising the specific range of from about 0.1% to about 20% or the specific concentration of 10% polysorbate. Narayanan et al. do not exemplify a reagent with a PEG concentration of 1.5%. However, Narayan do teach a range of 0.5% to 4% of PEG800 (see paragraph 008). Narayanan et al. teach a range of 0.1% to 2% of polysorbate (paragraph 0015). At paragraph 0039 Narayan et al. recognizes that reagent concentrations can vary up to 5%. Reagent concentration is a results-based parameter. The skilled artisan can use the concentrations taught by Narayanan et al. as a starting point and adjust based on the desired result. It is therefore obvious to arrive at the claimed composition. The claimed reagent would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention over the teachings of Narayanan et al. One of ordinary skill in the art will be motivated to look for a reagent that could stably store a biological sample and extract nucleic acid from the collected sample. (Narayanan et al. paragraph 005).
With regard to claims 23, 24, 33 and 34, Narayanan et al. do not teach the collection medium comprises formaldehyde and is a cytology medium.
Like Narayanan, Gundling teaches compositions for the extraction of DNA from biological samples. With regard to claims 23, 24, 33 and 34, Gundling teaches this extraction subsequent to the sample having been previously treated with formaldehyde (see paragraphs 0076 and 0077).
It would have been prima facie obvious before the effective filing date that the claimed reagent would be used with samples in a collection media comprising formaldehyde prior to using the reagent. Gundling teaches that examples of fixatives and fixation procedures include, for example, crosslinking fixatives (e.g., aldehydes, such as glutaraldehyde, formaldehyde (formalin), etc.). Crosslinking fixatives act by creating covalent chemical bonds between proteins in tissue. These crosslinking fixatives, especially formaldehyde, tend to preserve the secondary structure of proteins and may protect significant tertiary structure as well (paragraph 0058). Formaldehyde was used as a fixative for biological samples and therefore a skilled artisan would expect that biological samples would have been collected in media containing formaldehyde.
Double Patenting
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 21-40 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 19-21 of copending Application No. 17907202 in view of Fischer et al. (US 20090312285 A1) and further in view of Haydock et al (US 20130122496 A1). Instant claim 21 is drawn to a method of disposing the biological sample and performing at least one nucleic acid analysis step on the mixture using a composition comprising guanidine thiocyanate, a polysorbate, PEG and buffer and . Dependent claims 22-40 are drawn to that method using a composition with concentrations of guanidine thiocyanate, polysorbate and its concentration, PEG8000 and its concentration, Tris buffer and its concentration, sodium acetate as buffer and its concentration. Co-pending claim 1 of 17/907, 202 is drawn to a composition comprising guanidine thiocyanate, a buffer selected from sodium acetate and Tris, a polysorbate, a zwitterionic surfactant, EDTA, an alcohol and at least one reducing agent selected form TCEP and DTT and combination thereof. Dependent claims recite limitations drawn to concentrations of guanidine thiocyanate, buffer, polysorbate-20, CHAPS as the zwitterionic surfactant, its concentration, ethanol and its concentration, further comprising and additional agent form SDS, PEG, an antifoaming agent a mixture of biological sample and the composition, specific biological samples, disposing the biological sample in the composition, and performing at least one step selected form shipping mixture to a clinical facility, storing the mixture for at least one week, and performing at least one nucleic acid amplification step on the mixture. The instant claims differ from the co-pending claims of 17/907,202 in that the co-pending claims are drawn to a composition that has a zwitterionic surfactant, alcohol and a reducing agent also as components, whereas the composition used in the instant method claims does not have these components. Both Fischer and Haydock teach compositions that contain the additional components that are missing in the composition of the instant claims (Fischer paragraphs 0035-0036, 0021-0024 and Haydock paragraph 0035). Although the instant claims teach a method using a composition having only guanidine thiocyanate, a polysorbate, PEG and a base buffer, one of ordinary skill in the art would readily recognize that the method using the composition of the instant claims can be modified to arrive at the co-pending 17/907,202 invention before its effective filing date with a reasonable expectation of success in view of Fischer and Haydock. The artisan would be motivated to make the composition used in the claimed method in order to look for a transport medium which will enhance the stability and integrity of the biological sample collected and dispersed in the medium (Fischer, para 0011). Haydock teaches that its compositions can be used to store nucleic acids while protecting against degradation and contamination (para 0005).
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant's arguments filed September 22, 2025, have been fully considered but they are not persuasive.
Applicants argue Narayanan teach a method that is different from the claimed method because Narayanan uses multiple steps and reagents and the instant claims require a single step with a single reagent. Additionally, applicant argue the reagent disclosed by Narayanan is not equivalent to the claimed reagent because it is utilized in a completely different manner and purpose that the claimed reagent. These arguments are not persuasive because the reagent recited in instant claim 1 is the same reagent disclosed by Narayanan (see example 3). Additionally, at paragraphs 0141-0153 whole viruses, bacteria and parasite oocyst and naked RNA in water are added to the lysis buffer and stored at varying temperatures and for varying times and then viability is tested. The reverse crosslinkage, lysis and nucleic acid binding occurs in the single step of adding the buffer to the sample and incubating it at a selected temperature for a variety of days. The sample is tested for viability (via PCR, RT-PCR) and is viable indicating the lysis buffer (same as the reagent in the instantly claims methods) is an effective storage medium for liquid samples. Additionally, as The lysis buffer is the same as the reagent in the instant claims the buffer therefore inherently reverse crosslinks, lyses and binds the nucleic acid in the sample. Applicant argues that Narayanan do not disclose a reagent that is brought into direct contact with a biological sample present in a fluid-based collection medium. This is not persuasive as Narayanan discloses at paragraph 0085 that “The lysis buffer can be used to store nucleic acid molecules in solution (for example by adding a sample containing pathogen(s) to the buffer or on a solid support… Additionally, Narayanan also discloses a liquid sample at paragraphs 0141-0153.
Applicant’s arguments with respect to the provisional non-statutory double patenting rejection have been considered but are not persuasive. Applicant argues that claim 18 was not included in the provisional NSDP and that limitation has been incorporated into all of the newly added claims. This is not persuasive because the while claim 18 was inadvertently omitted from the statement of rejection the provisional NSDP as written applied to claim 18. The provisional NSDP therefore applies to the newly added claims as well.
Conclusion
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 HEATHER CALAMITA whose telephone number is (571)272-2876. The examiner can normally be reached Monday through Friday 8 AM to 4:30 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
HEATHER . CALAMITA
Supervisory Patent Examiner
Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684