GE HEALTHCARE UK LIMITED

Patent Trials and Appeals Board

Jan 7, 2022

2021001343 (P.T.A.B. Jan. 7, 2022)

UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 14/441,569 05/08/2015 Peter James Tatnell 265261-US-8 (34428-0097) 5053 29052 7590 01/07/2022 EVERSHEDS SUTHERLAND (US) LLP 999 PEACHTREE STREET, N.E. SUITE 2300 ATLANTA, GA 30309 EXAMINER BERTAGNA, ANGELA MARIE ART UNIT PAPER NUMBER 1637 NOTIFICATION DATE DELIVERY MODE 01/07/2022 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): patentdocket@eversheds-sutherland.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte PETER JAMES TATNELL, KATHRYN LOUISE LAMERTON, ALLEN STUART PIERCE, and ELIZABETH ASHMAN Appeal 2021-001343 Application 14/441,569 Technology Center 1600 Before DONALD E. ADAMS, RICHARD M. LEBOVITZ, and JAMIE T. WISZ, Administrative Patent Judges. WISZ, Administrative Patent Judge. DECISION ON APPEAL Pursuant to 35 U.S.C. § 134(a), Appellant appeals from the Examiner’s decision to reject claims 1, 2, 5-7, 9-15, 17, 18, 20-28, and 30- 32.1 We have jurisdiction under 35 U.S.C. § 6(b). We AFFIRM. 1 We use the word “Appellant” to refer to “applicant” as defined in 37 C.F.R. § 1.42. Appellant identifies Danaher Corporation as the real party-in- interest. Appeal Br. 2. Appeal 2021-001343 Application 14/441,569 2 CLAIMED SUBJECT MATTER The Specification describes “methods and kits which can be used to amplify nucleic acids by combining an FTA™ Elute solid support with PCR reagents for one step amplification of nucleic acid samples.” Spec. 1. According to the Specification, “[t]he invention has applications in the long term storage and easy processing of nucleic acids and is particularly useful in genotyping, diagnostics and forensics.” Id. Claim 1 is illustrative of the claimed subject matter and is reproduced below: 1. A method for amplification of nucleic acid comprising the steps: i) contacting a solid support comprising a chaotropic salt with a cellular sample containing nucleic acid, ii) transferring said solid support to a reaction vessel if the solid support is not present in a reaction vessel prior to the addition of said cellular sample, iii) incubating said nucleic acid from step i) on the solid support with a nucleic acid amplification reagent solution, iv) amplifying the nucleic acid to produce amplified nucleic acid in the presence of the solid support using quantitative polymerase chain reaction (qPCR), v) quantifying the amplified nucleic acid in the presence of the solid support, and vi) using Short Tandem Repeat (STR) profiling by exposing the solid support to a STR reaction mix and analyzing the STR reaction mix to produce an STR profile in the presence of the solid support in the reaction vessel. Appeal Br. 15 (Claims App.). Appeal 2021-001343 Application 14/441,569 3 REJECTIONS The Examiner rejected claims 1, 2, 5-7, and 9-13 under 35 U.S.C. § 112 as being indefinite. The Examiner rejected claims 1, 2, 5-7, and 9-13 under 35 U.S.C. § 103 as being unpatentable over Harvey,2 Thompson,3 Hennessy,4 and Santos,5 as evidenced by the GE publication.6 The Examiner rejected claims 14, 15, 17, 18, 20-22, 24-28, and 30 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman.7 The Examiner rejected claim 23 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman, and further in view of Gunstream.8 2 Harvey et al., US 2010/0106057 A1, published Apr. 29, 2010 (“Harvey”). 3 Thompson et al., An Overview of DNA Typing Methods for Human Identification: Past, Present, and Future, Methods on Molecular Biology Vol. 830, 3-16 (2012) (“Thompson”). 4 Hennessy et al., US 2012/0122093 A1; published May 17, 2012 (“Hennessy”). 5 Santos et al., Use of FTA Elute Card Impregnated with Cervicovaginal Sample Directly into the Amplification Reaction Increases the Detection of Human Papilloma Virus DNA, Brazilian Journal of Microbiology, 389-392 (2012) (“Santos”). 6 GE Healthcare Life Sciences, Helping you build a smarter diagnostic assay, 1-29 (2013) (“GE publication”). 7 Seaman et al., Detection and quantitation of HPV in genital and oral tissues and fluids by real time PCR, Virology Journal, Vol. 7, 194, 1-17 (2010) (“Seaman”). 8 Gunstream, US 2008/0178653 A1, published July 31, 2008. (“Gunstream”). Appeal 2021-001343 Application 14/441,569 4 The Examiner rejected claims 31 and 32 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman, and further in view of Widschwendter9 and Harvey.10 ISSUES AND ANALYSIS Rejection of claims 1, 2, 5-7, and 9-13 under 35 U.S.C. § 112 as being indefinite. The Examiner finds that the limitation in claim 1 which recites, “using Short Tandem Repeat (STR) profiling by exposing the solid support to a STR reaction mix and analyzing the STR reaction mix to produce an STR profile in the presence of the solid support in the reaction vessel,” renders the claim indefinite. Final Act. 6. Specifically, the Examiner finds that “it is not entirely clear as to what is required, at minimum, for the STR profiling step to produce a STR profile in the presence of the solid support in the reaction vessel.” Id. The Examiner finds that STR profiles are most commonly obtained using capillary electrophoresis (CE) and the only example of obtaining an STR profile in the Specification also uses this method. Id. (citing Thompson, 8; Spec. 15). According to the Examiner, “[s]ince one would not expect to be able to subject the solid support to this process (i.e., to pass the solid support through the CE device),” it is not clear if “loading the CE device in the presence of the solid support constitute[s] ‘obtaining a STR 9 Widschwendter et al., Human papillomavirus DNA in sera of cervical cancer patients as tumor marker, Cancer Letters 202, 231-239 (2003), www.sciencedirect.com last visited Dec. 2021 (“Widschwendter”). 10 Harvey et al., US 2008/0196517 A1, published Aug. 21, 2008 (hereinafter “Harvey”). Appeal 2021-001343 Application 14/441,569 5 profile in the presence of the solid support in the reaction vessel,’” or if CE methods for STR profiling are excluded from the claim. Id. Appellant argues that it is clear from the plain meaning of the claim that the solid support is exposed to an STR reaction mix, and the STR reaction mix is analyzed. Appeal Br. 5. Appellant also argues that “the claims nowhere require passing the solid support through any device for performing STR profiling” and there is nothing in the claims or the Specification “that requires the STR reaction mixture (after contacting the solid support) to also be confined to the reaction vessel or in a vicinity of the solid support, and there is not logical or technical conflict between retaining a solid support in the reaction vessel while performing STR profiling on an STR reaction mix that has been exposed to the solid support.” Id. We find that the Examiner has the better position. We agree with the Examiner that it is not clear what it means to “produce an STR profile in the presence of the solid support in the reaction vessel.” Ans. 3 (emphasis added). We understand from Appellant’s arguments and the language of the claims that the STR reaction mix itself (rather than the solid support) is analyzed and that the solid support remains in the reaction vessel. However, it is not clear what situations are encompassed by the language requiring that the STR profile be produced “in the presence of the solid support in the reaction vessel.” Id. We agree with the Examiner that the Specification only describes the use of a capillary electrophoresis device to obtain a STR profile, which does not appear to be a process that occurs “in the presence of the solid support in the reaction vessel.” Spec. 15. Appellant also contends that “the STR profiling may be performed using an apparatus fluidically coupled to the reaction vessel,” but it is also unclear how this describes a Appeal 2021-001343 Application 14/441,569 6 STR profiling process being done “in the presence of the solid support in the reaction vessel.” Reply 5. “[A] patent is invalid for indefiniteness if its claims, read in light of the specification delineating the patent, and the prosecution history, fail to inform, with reasonable certainty, those skilled in the art about the scope of the invention.” Nautilus, Inc. v. Biosig Instruments, Inc., 134 S.Ct. 2120, 2124 (2014). Thus, for the reasons explained above, we affirm the Examiner’s indefiniteness rejection of claims 1, 2, 5-7, and 9-13. Rejections of claims 1, 2, 5-7, and 9-13 under 35 U.S.C. § 103 as being unpatentable over Harvey, Thompson, Hennessy, and Santos, as evidenced by the GE publication. The Examiner finds that Example 3 of Harvey teaches a method that comprises PCR and short tandem repeat (STR) profiling, which includes the recited steps of claim 1. Final Act. 8 (citing Harvey ¶¶ 65-68). The Examiner also finds that Harvey teaches FTA Elute cards, which are pre- punched cellulose based solid supports containing the chaotropic agent, guanidine thiocyante; however, the Examiner acknowledges that this solid support was not used to conduct the method of Example 3 of Harvey. Id. (citing Harvey ¶ 16; Spec. 5). The Examiner also acknowledges that Harvey does not teach that the STR profile is obtained in the presence of the solid support, nor does it teach the use of qPCR, but the Examiner finds that these limitations are taught by other references. Id. at 8-9. Specifically, the Examiner finds that Thompson discusses methods for human STR profiling and teaches that it is important to determine the amount of human DNA in a sample from which the STR profile is to be determined, stating that “the best procedure for performing quantification, utilizes real-time PCR.” Id. at 9 (citing Thompson, 7). The Examiner also Appeal 2021-001343 Application 14/441,569 7 finds that Santos discloses a method that comprises conducting PCR in the presence of an FTA Elute card. Id. (citing Santos, Abstract, 390). The Examiner concludes that “[i]t would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to further include a qPCR step prior to the STR profiling step when conducting the method of Harvey.” Id. at 10. According to the Examiner, “Thompson provides motivation to do so by teaching that such a step, which is best conducted using real-time PCR (i.e., qPCR), helps one to avoid the poor PCR results that can occur when too much or too little DNA is used for the multiplex PCR preceding capillary electrophoresis in STR profiling methods.” Id. (citing Thompson, 7-8). The Examiner also finds that it would have been obvious for the ordinary artisan to practice the method suggested by Harvey in view of Thompson using the FTA Elute card disclosed in paragraph 16 of Harvey and the ordinary artisan would have had a reasonable expectation of success in doing so because Santos discloses the PCR conditions that are suitable for amplifying DNA on an FTA Elute card. Id. (citing Santos, 390). Lastly, the Examiner finds that “it also would have been prima facie obvious to obtain the STR profile in the method of Harvey [in] the presence of the solid support.” Id. According to the Examiner, it would have been obvious to load the CE device in the presence of the solid support when practicing the method of Harvey. Id. at 11. The Examiner finds that the ordinary artisan would have been motivated to do so because he/she would recognize that doing so would reduce the number of consumables required for the method. Id. The Examiner also finds that the ordinary artisan would have had a reasonable expectation of success because Hennessy teaches that Appeal 2021-001343 Application 14/441,569 8 96-well plates may be used to conduct PCR and to load amplification products into a capillary electrophoresis device. Id. (citing Hennessy ¶¶ 88- 89). Appellant argues that the Examiner does not give sufficient weight to the effect of the chaotropic agent limitation and asserts that “one having ordinary skill in the art would have expected the conventional PCR of Santos to have been inhibited by the presence of a chaotropic agent (such as guanidine thiocyanate), as well-known in the art.” Appeal Br. 7. Thus, according to Appellant, one of ordinary skill in the art would not have had a reasonable expectation of success for performing the claimed technique in the presence of a chaotropic agent. Id. Appellant also asserts that “one having ordinary skill in the art would not have been motivated to substitute the conventional PCR of Santos with the qPCR method of Seaman, because the presence of the solid support would have been expected to undermine qPCR disclosed by Seaman.” Id. at 9. Specifically, Appellant contends that “the solid support would have been expected to interfere with the optical signal detection system required in conducting qPCR.” Id. at 9-10. We find that the Examiner’s position is supported by a preponderance of the evidence. With regard to the chaotropic agent, Appellant cites to Thompson 211 for the assertion that guanidine thiocyanate is a PCR inhibitor and that one of ordinary skill in the art would have expected the 11 Thompson et al., An Investigation of PCR Inhibition using Plexor®-Based Quantitative PCR and Short Tandem Repeat Amplification, American Academy of Forensic Science, Journal of Forensic Science, Vol. 59, No. 6, 1514-1529 (2014), (“Thompson 2”). Appeal 2021-001343 Application 14/441,569 9 conventional PCR of Santos to have been inhibited by the presence of chaotropic agent. Appeal Br. 7 (citing Thompson 2). First, it does not appear that Thompson 2 is prior art because it has a publication date of November 2014 and Appellant asserts a priority date of 2012 or 2013. See Thompson 2; Appeal Br. 10. However, even if we take the teachings of Thompson 2 into account, we agree with the Examiner that Thompson 2 “only discusses results obtained when guanidine thiocyanate was known to be present in solution during the PCR,” as opposed to on the FTA elute card. Ans. 18 (citing Thompson 2, 1518-1519). We also agree with the Examiner that “neither Thompson 2 nor any other evidence of record clearly indicates that solution-phase guanidine thiocyanate would even be present in the qPCR suggested by the references, let alone in an amount sufficient to inhibit qPCR.” Id. The Specification itself cites to a March 2010 Qiagen Sample & Assay Technologies Newsletter for the teaching that “guanidine thiocyanate concentrations up to 100mM in an RNA sample did not affect the reliability of real-time PCR.” Spec. 5. Thus, Appellant has not persuasively shown that one of ordinary skill in the art would have expected that the guanidine thiocyanate present on the FTA elute card would inhibit qPCR. We also agree with the Examiner that Santos describes the use of a FTA elute card for successfully performing PCR and Appellant has not persuasively argued or provided evidence that the use of a FTA elute card in a method using qPCR would yield any different results. Appellant argues that, because Santos is directed to conventional PCR, and not qPCR, “any success ascribable to the teaching of Santos is for conventional PCR, not qPCR.” Appeal Br. 7. However, Appellant does not provide objective Appeal 2021-001343 Application 14/441,569 10 evidence or persuasive argument as to why one of ordinary skill in the art would expect a different result using qPCR as compared to the conventional PCR in Santos, with respect to the chaotropic agents or otherwise. “Attorneys’ argument is no substitute for evidence.” Johnston v. IVAC Corp., 885 F.2d 1574, 1581 (Fed. Cir. 1989). With respect to Appellant’s contention the presence of the solid support would have been expected to undermine qPCR disclosed by Seaman, we again note that Appellant cites no persuasive evidence to support this assertion. See Appeal Br. 9-10. Furthermore, the Examiner cites to Taylor,12 which teaches how to perform real-time PCR in the presence of a solid support. See Ans. 25-26 (citing Taylor 2). As such, we agree with the Examiner that “Taylor provides evidence to support the conclusion that the ordinary artisan would have been aware of the potential complications a solid support could present when included in a qPCR mixture and would have been able to use his/her ordinarily available skills to address them.” Id. at 26. We also agree that, “in the absence of evidence to the contrary, the ordinary artisan would not have expected the presence of the solid support to compromise the optical detection system required for real-time qPCR.” Id. Appellant further argues that the Examiner erred in relying on the GE publication because the GE publication has a publication date of February 2013, which is after the application priority date of November 9, 2012 or 12 Taylor et al., Real-time PCR Detection of Plasmodium directly from whole blood and filter paper samples, Malaria Journal, Vol. 10, No. 244, 2- 8 (2011), http://www.malariajournal.com/content/10/1/244 last visited Dec. 2021 (“Taylor”). Appeal 2021-001343 Application 14/441,569 11 January 25, 2013. Appeal Br. 10 (citing GE publication 32). However, as explained by the Examiner, the GE publication is being relied upon to show a universal fact one of ordinary skill in the art would have known at the time the application was filed, specifically the chemical composition of the FTA Elute solid support. Ans. 27. As such, use of the GE publication is proper. Thus, for the reasons discussed above, we affirm the Examiner’s rejection of claim 1 over Harvey, Thompson, Hennessy, and Santos, as evidenced by the GE publication. Claims 2, 5-7, and 9-13 are not argued separately and fall with claim 1. See 37 C.F.R. § 41.37(c)(1)(iv). Rejection of claims 14, 15, 17, 18, 20-22, 24-28, and 30 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman. Appellant makes similar arguments for the rejection of claims 14, 15, 17, 18, 20-22, 24-28, and 30 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman. See Appeal Br. 11-12. We affirm this rejection for the reasons discussed above. Rejection of claim 23 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman, and further in view of Gunstream. Appellant makes similar arguments for the rejection of claim 23 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman, and further in view of Gunstream. See Appeal Br. 12. We affirm this rejection for the reasons discussed above. Rejection of claims 31 and 32 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced by the GE publication, in view of Seaman, and further in view of Widschwendter and Harvey. Appellant makes similar arguments for the rejection of claims 31 and 32 under 35 U.S.C. § 103 as being unpatentable over Santos, as evidenced Appeal 2021-001343 Application 14/441,569 12 by the GE publication, in view of Seaman, and further in view of Widschwendter and Harvey. See Appeal Br. 12-13. We affirm this rejection for the reasons discussed above. DECISION SUMMARY In summary: Claim(s) Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 1, 2, 5-7, 9- 13 112 Indefiniteness 1, 2, 5-7, 9- 13 1, 2, 5-7, 9- 13 103 Harvey, Thompson, Hennessy, Santos, GE publication 1, 2, 5-7, 9- 13 14, 15, 17, 18, 20-22, 24-28, 30 103 Santos, GE publication, Seaman 14, 15, 17, 18, 20-22, 24-28, 30 23 103 Santos, GE publication, Seaman, Gunstream 23 31, 32 Santos, GE publication, Seaman, Widschwendter, Harvey 31, 32 Overall Outcome 1, 2, 5-7, 9- 15, 17, 18, 20-28, 30-32 No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R. § 1.136(a)(1)(iv). AFFIRMED