Ex Parte Mohammed et al

Patent Trial and Appeal BoardSep 19, 2012

11791137 (P.T.A.B. Sep. 19, 2012)

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. 11/791,137 10/08/2008 Mansoor S. Mohammed 034827-4103 9253 23524 7590 09/20/2012 FOLEY & LARDNER LLP 150 EAST GILMAN STREET P.O. BOX 1497 MADISON, WI 53701-1497 EXAMINER CROW, ROBERT THOMAS ART UNIT PAPER NUMBER 1634 MAIL DATE DELIVERY MODE 09/20/2012 PAPER 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. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte MANSOOR S. MOHAMMED and NATASA DZIDIC __________ Appeal 2011-010397 Application 11/791,137 Technology Center 1600 __________ Before ERIC GRIMES, LORA M. GREEN, and JEFFREY N. FREDMAN, Administrative Patent Judges. GRIMES, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. §134 involving claims to methods of determining the quality of a nucleic acid array. The Examiner has rejected the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. STATEMENT OF THE CASE The Specification discloses the use of “fluorescence detection to evaluate the quality of a printed nucleic acid array without the need to add or Appeal 2011-010397 Application 11/791,137 2 otherwise link a fluorescent compound or dye to the nucleic acid” (Spec. 3, ¶ 0008). The Specification discloses that “it is believed that the ions and/or nucleic acid in a printing solution have autofluorescent properties which can be detected with an appropriate device” (id. at 6, ¶ 0024). Claims 1, 4, 5, 7, 8, 11-14, 21-40, and 43-54 are on appeal. Claim 1 is representative and reads as follows: 1. A method for determining the printing quality of a nucleic acid array prior to hybridization, said method comprising: (a) printing an array of nucleic acid samples onto a solid support, each sample comprising nucleic acid in an ionic solution; and (b) detecting the autofluorescence of printed nucleic acid samples to determine the quality of printing. The claims stand rejected under 35 U.S.C. § 103(a) as follows: • Claims 1, 4, 5, 21, 24-26, 28-30, 32-34, 43, 44, 47-49, and 51-53 in view of Kuo1 and Lockhart;2 • Claims 7, 8, 11-14, and 35-40 in view of Kuo, Lockhart and Bao;3 • Claims 21-23 and 43-46 in view of Kuo, Lockhart and Abramson;4 • Claims 27, 31, 50, and 54 in view of Kuo, Lockhart and Reichel.5 1 Kuo et al., Patent Application Publication US 2003/0013124 A1, Jan. 16, 2003. 2 Lockhart et al., Patent Application Publication US 2003/0215841 A1, Nov. 20, 2003. 3 Bao et al., EP 1 026 260 A1, Aug. 9, 2000. 4 Abramson et al., US 5,405,774, Apr. 11, 1995. 5 Reichel et al., Patent Application Publication US 2004/0112980 A1, June 17, 2004. Appeal 2011-010397 Application 11/791,137 3 Issue The Examiner rejects all of the claims on appeal as obvious in view of Kuo and Lockhart, either by themselves or combined with an additional reference. Because Appellants rely on the same arguments with respect to all of these rejections, we will consider them together. The Examiner finds that Kuo discloses “a method for determining the printing quality of a nucleic acid array … comprising: printing an array of nucleic acid samples onto a solid support …, each sample comprising nucleic acid in an ionic solution” and “detecting fluorescence of printed samples to determine the quality of printing” (Answer 6). The Examiner finds that Kuo does not teach that “the autofluorescence of the nucleic acids is detected” (id.). The Examiner finds that Lockhart discloses printing a nucleic acid array and “detection of the intrinsic fluorescence of the nucleic acids, which … allow[s] calculation of a background signal for each spot in the array …, which allows the establishment of a threshold value for determining whether non-specific binding has occurred” (id.). The Examiner concludes that it would have been obvious to modify Kuo’s method of “determining the printing quality of an array by detecting fluorescence in the printed sample … so that the detected fluorescence is the autofluorescence of the nucleic acids,” as taught by Lockhart (id.), because doing so would provide the “advantage of allowing the establishment of a threshold value for determining whether non-specific binding has occurred as a result of allowing calculation of a background signal for each spot in the array as explicitly taught by Lockhart” (id. at 7). Appeal 2011-010397 Application 11/791,137 4 Appellants contend that Kuo and Lockhart would not have made obvious the claimed method because Kuo assesses printing quality by detecting a fluorescent label and Lockhart would not have motivated one of skill in the art to use nucleic acid autofluorescence to determine printing quality (Appeal Br. 7-8). The issue presented is: Does the evidence of record support the Examiner’s conclusion that it would have been obvious, based on Lockhart, to modify Kuo’s method by detecting the autofluorescence of printed nucleic acid samples? Findings of Fact 1. Kuo discloses that a fluorescent-labeled oligonucleotide “was spotted onto the activated slides … at a variety of concentrations, 1.25, 2.5, 5, 10, 20, and 40 μM” (Kuo 5, ¶ 0044). 2. Kuo’s nucleic acid solutions included a buffer (id.), and therefore were ionic solutions (Spec. 4, ¶ 0015). 3. Kuo discloses that the “fluorescence signal intensity of each spot … was analyzed.… The net fluorescence signal intensity was calculated by subtracting the average background signal from the signal measured at each spot.” (Id. at 5, ¶ 0045.) 4. Lockhart discloses that “arrays of large numbers of different oligonucleotide probes (DNA chips) may effectively be used to … quantify the relative abundance of the target sequences in a complex nucleic acid pool” (Lockhart 1, ¶ 0007). 5. Lockhart discloses that the term “background” refers to “hybridization signals resulting from nonspecific binding, or other Appeal 2011-010397 Application 11/791,137 5 interactions, between the labeled target nucleic acids and components of the oligonucleotide array” (id. at 4, ¶ 0035). 6. Lockhart discloses that “[b]ackground signals may also be produced by intrinsic fluorescence of the array components themselves” (id.). 7. Lockhart discloses that “a different background signal may be calculated for each target nucleic acid” (id.). Principles of Law “If a person of ordinary skill can implement a predictable variation [of a known work], § 103 likely bars its patentability.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007). The obviousness analysis “can take account of the inferences and creative steps that a person of ordinary skill in the art would employ.” Id. at 418. Analysis Claim 1 is directed to a method comprising printing an array of nucleic acid samples in an ionic solution onto a solid support and detecting the autofluorescence of the nucleic acid samples. The Specification defines “printing” to mean “depositing nucleic acid samples onto discrete locations of a solid surface” (Spec. 4, ¶ 0013) and defines an “array” as a plurality of samples deposited on a substrate (id. at 3, ¶ 0012). Thus, the step of “printing an array of nucleic acid samples onto a solid support” simply requires depositing at least two nucleic acid samples onto the support. Appeal 2011-010397 Application 11/791,137 6 In addition, although the claim recites a “method for determining the printing quality of a nucleic acid array” and detecting autofluorescence of samples “to determine the quality of printing” (claim 1), Appellants have pointed to no description in the Specification that indicates that detecting autofluorescence to determine printing quality differs from detecting autofluorescence for any other intended purpose. We therefore conclude that the intended use of the detected autofluorescence imposes no actual limitation on the method defined by claim 1. Cf. Bristol-Myers Squibb Co. v. Ben Venue Labs., Inc., 246 F.3d 1368, 1375-76 (Fed. Cir. 2001) (“[T]he expression ‘[a] method for treating a cancer patient to effect regression of a taxol-sensitive tumor, said method being associated with reduced hematologic toxicity’ in the preamble[ ] . . . is only a statement of purpose and intended result. The expression does not result in a manipulative difference in the steps of the claim.”). Kuo discloses that a fluorescent-labeled oligonucleotide probe, in an ionic solution, was spotted onto a substrate at a variety of concentrations. Kuo discloses that the fluorescence signal intensity of each spot was calculated by subtracting the average background signal from the signal measured at each spot. Lockhart discloses that the components of a nucleic acid array possess intrinsic fluorescence, which contributes to the background signal, and that a different background signal can be calculated for each target nucleic acid. In view of Lockhart’s disclosure that the components of a nucleic acid array – i.e., nucleic acids – produce intrinsic fluorescence that contributes to background signals, we agree with the Examiner that it would have been Appeal 2011-010397 Application 11/791,137 7 obvious to one of ordinary skill in the art to modify Kuo’s method by including control (unlabeled) nucleic acid samples and detecting the background fluorescence, i.e. the autofluorescence of the nucleic acid samples, to “allow[ ] the establishment of a threshold value for determining whether non-specific binding has occurred” (Answer 7). Appellants argue that Kuo and Lockhart would not have made obvious the method of claim 1 because Kuo assesses printing quality by detecting a fluorescent label and Lockhart would not have motivated one of skill in the art to use nucleic acid autofluorescence to determine printing quality (Appeal Br. 7-8). Appellants “disagree with the Examiner’s allegation that the mere recognition of these autofluorescent properties motivates the artisan to specifically measure that autofluorescence as an index of array quality” (Reply Br. 2). This argument is not persuasive. Kuo discloses that background fluorescence should be determined in calculating fluorescence. Lockhart discloses that array components have intrinsic fluorescence that contributes to background signals, and discloses calculating a background signal for each target nucleic acid. Thus, as discussed above, the combination of Kuo and Lockhart would have made obvious the detection of background fluorescence of unlabeled nucleic acids on the Kuo array to establish a threshold for identifying nonspecific binding. Appellants also argue that “neither Lockhart nor Kuo recognized the source of the problem – how to assess printing quality … in the absence of a label” (Appeal Br. 8). Appeal 2011-010397 Application 11/791,137 8 This argument is not persuasive. As discussed above, the cited references would have made obvious a method having both of the steps that define the claimed method. Appellants have pointed to no persuasive basis for concluding that detecting autofluorescence for the purpose of determining the printing quality of an array results in any manipulative difference compared to the method made obvious by Kuo and Lockhart. Thus, we affirm the rejection of claim 1 as being obvious in view of Kuo and Lockhart. Claims 4, 5, 21, 24-26, 28-30, 32-34, 43, 44, 47-49, and 51-53 have not been argued separately and therefore fall with claim 1. 37 C.F.R. § 41.37(c)(1)(vii). We also affirm the rejection of claims 7, 8, 11-14, and 35-40 in view of Kuo, Lockhart and Bao; the rejection of claims 21-23 and 43-46 in view of Kuo, Lockhart and Abramson; and the rejection of claims 27, 31, 50, and 54 in view of Kuo, Lockhart and Reichel. Appellants’ only argument is that Bao, Abramson, and Reichel fail to “remedy the deficiencies in the Examiner’s prima facie case of obviousness based on Kuo and Lockhart” (Appeal Br. 10-11), and thus Appellants have waived any additional argument based on Bao, Abramson or Reichel. Conclusion of Law The evidence of record supports the Examiner’s conclusion that it would have been obvious, based on Lockhart, to modify Kuo’s method by detecting the autofluorescence of printed nucleic acid samples. Appeal 2011-010397 Application 11/791,137 9 SUMMARY We affirm the rejection of claims 1, 4, 5, 7, 8, 11-14, 21-40, and 43-54 under 35 U.S.C. § 103(a). TIME PERIOD FOR RESPONSE No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED lp