Ex Parte Fathollahi et alDownload PDFPatent Trial and Appeal BoardMay 21, 201411397307 (P.T.A.B. May. 21, 2014) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE __________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte BAHRAM FATHOLLAHI, JAVIER A. FARINAS, ANDREA W. CHOW, and STEPHANE MOURADIAN __________ Appeal 2012-003437 Application 11/397,307 Technology Center 1600 __________ Before LORA M. GREEN, JEFFREY N. FREDMAN, and CHRISTOPHER G. PAULRAJ, Administrative Patent Judges. PAULRAJ, Administrative Patent Judge. DECISION ON APPEAL This is an appeal1 under 35 U.S.C. § 134 involving claims to a method for processing a protein sample in a microfluidic device. The Examiner rejected the claims on the grounds of obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 Appellants identify the Real Party in Interest as Caliper Life Sciences, Inc. (See App. Br. 3.) Appeal 2012-003437 Application 11/397,307 2 STATEMENT OF THE CASE Background The invention generally relates to methods and apparatuses for the analysis of proteins. “More particularly, embodiments of the present invention are directed toward the enzymatic digestion of proteins within a microfluidic device” (Spec. ¶ 2). The Claims Claims 1-16 are on appeal. Independent claim 1, the only independent claim, is representative and reads as follows: 1. A method of processing a protein sample in a microfluidic device, the method comprising the steps of: providing a microfluidic device comprising a fluid network that includes a sample reservoir, a waste reservoir, a plurality of parallel channels connecting the sample reservoir to the waste reservoir, and a plurality of reagent reservoirs that introduce reagents at various points along each of the plurality of parallel channels, wherein each of the reagent reservoirs is in fluid communication with at least two of the plurality of parallel channels; placing immobilized trypsin in a portion of each of the plurality of channels; placing a sample into the sample reservoir; placing the reagents required to carry out reduction, alkylation, and quenching into the reagent reservoirs; applying a single negative pressure driving force to the waste reservoir that generates a continuous flow of the sample from the sample reservoir, through the plurality of channels, to the waste reservoir, wherein the flow sequentially exposes the sample to the reduction, alkylation, and quenching reagents before the sample flows through the immobilized trypsin; and collecting the sample in the waste reservoir. Appeal 2012-003437 Application 11/397,307 3 The Issues The Examiner has rejected the claims as follows: I. Claims 1, 12, 15, and 16 were rejected under 35 U.S.C. § 103(a) as unpatentable over the combination of Kopf-Sill ’185,2 Anderson,3 and Timperman.4 II. Claims 2-5 were rejected under 35 U.S.C. § 103(a) as unpatentable over the combination of Kopf-Sill ’185, Anderson, and Timperman as further combined with Gao.5 III. Claims 6-11 were rejected under 35 U.S.C. § 103(a) as unpatentable over the combination of Kopf-Sill ’185, Anderson, and Timperman as further combined with Kopf-Sill ’358.6 IV. Claim 13 was rejected under 35 U.S.C. § 103(a) as unpatentable over the combination of Kopf-Sill ’185, Anderson, and Timperman as further combined with Wang.7 2 Kopf-Sill et al., US 6,858,185 B1, published Feb. 22, 2005. 3 Anderson, US 2004/0072251A1, published Apr. 15, 2004. 4 Timperman, US 2003/0089605 A1, published May 15, 2003. 5 Gao et al., Integrated Microfluidic System Enabling Protein Digestion, Peptide Separation, and Protein Identification, 73 ANAL. CHEM. 2648-2655 (2001). 6 Kopf-Sill et al., US 2001/0045358 A1, published Nov. 29, 2001. 7 Wang et al., Integration of immobilized trypsin bead beds for protein digestion within a microfluidic chip incorporating capillary electrophoresis separations and an electrospray mass spectrometry interface, 14 RAPID COMMCNS MASS SPEC. 1377- 1383 (2000). Appeal 2012-003437 Application 11/397,307 4 V. Claim 14 was rejected under 35 U.S.C. § 103(a) as unpatentable over the combination of Kopf-Sill ’185, Anderson, and Timperman as further combined with Wolk.8 The only issue presented on appeal is whether the Examiner presented a prima facie case of obviousness of independent claim 1 based on the combination of Kopf-Sill ’185, Anderson, and Timperman. Appellants have not presented any specific arguments for the dependent claims, but rather only argue that “any claim depending from a nonobvious claim is also nonobvious” (App. Br. 15-17). Accordingly, the dependent claims stand or fall with independent claim 1 because they have not been separately argued. 37 C.F.R. § 41.37(c)(1)(vii) (2011). FINDINGS OF FACT FF1. Kopf-Sill ’185 discloses a microfluidic device with a single vacuum source (Kopf-Sill ’185, Title). FF2. Kopf-Sill ’185 teaches that “[r]eservoirs or wells are locations at which samples, components, reagents and the like are added into the device for assays to take place” and that “[t]he reservoirs are typically placed so that the sample or reagent is added into the system upstream from the location at which it is used” (Kopf-Sill ’185, 10:13-19). FF3. Kopf-Sill ’185 discloses embodiments of a microfluidic device that include sample wells (602, 702), a main channel (604, 704, 804) and multiple flow reduction channels in a parallel configuration (e.g., 608, 610, 708, 710, 808, 810), reagent 8 Wolk et al., US 2001/0049148 A1, published Dec. 6, 2001. Appeal 2012-003437 Application 11/397,307 5 reservoirs (e.g., 612, 712, 812) that are each fluidly coupled to two different channels (e.g., 622, 722, 822)), and a waste well (806) (Kopf-Sill ’185, Figs. 6-8). FF4. Kopf-Sill ’185 discloses that “an assay of interest is optionally performed at all of the various concentrations of sample material in the flow reduction channel,” and that “reagent usage is decreased by the decrease in flow rate produced by the flow reduction channels” (Kopf-Sill ’185, 13:1-6). FF5. Kopf-Sill ’185 teaches that “movement of fluidic materials through the microfluidic devices of the invention is driven by a pressure source” and that “[t]he pressure source is typically a vacuum source applied at the downstream terminus of the main channel” (Kopf-Sill ’185, 17:11-15). FF6. Kopf-Sill ’185 teaches that “[w]aste well 806, 806B includes a vacuum source at one end of the channel system to draw the suspension through the channel” (Kopf-Sill ’185, 17:56-58). FF7. Kopf-Sill ’185 teaches that “[b]y directing fluid through the flow reduction channels . . ., the flow rate in a microfluidic device is modulated in response to the addition of material to the main channel,” and that “[a]n added advantage of this flow rate modulation is that, in addition to maintaining a continuous or constant flow rate, subsequent reagent addition need not be in larger amounts to meet an increased flow rate demand” (Kopf-Sill ’185, 19:55-59). Appeal 2012-003437 Application 11/397,307 6 FF8. Kopf-Sill ’185 teaches that “[a]lternatively, reagent materials are added to the flow reduction channels” (Kopf-Sill ’185, 4:7-8). FF9. Anderson teaches the digestion of a protein sample to peptides using the following protocol: The digestion is carried out by first denaturing the protein sample (e.g., with urea or guanidine HCl), reducing the disulfide bonds in the proteins (e.g., with dithiothreitol or mercaptoethanol), alkylating the cysteines (e.g., by addition of iodoacetamide), quenching excess iodoacetamide by addition of more dithiothreitol or mercaptoethanol, and finally (after removal or dilution of the denaturant) addition of the selected proteolytic enzyme (e.g. trypsin), followed by incubation to allow digestion. (Anderson, ¶ 68.) FF10. Anderson teaches an embodiment where: [T]hree subsamples of the plasma peptide digest are prepared: one undiluted (to which is add[ed] the required amount of the thyroglobulin labeled monitor peptide, and those of other proteins in Group 3 abundance class: FIG. 9), a second diluted about 1,000 fold (Group 2, to which we add about the same amount of the labeled complement C2 monitor peptide), and a third diluted about 1,000,000 fold (Group 1, to which is add[ed] the albumin monitor peptide). (Anderson, ¶104.) FF11. Anderson “teaches supports with binding agents which can collect from a sample target peptides and proteins of varying concentrations” (Anderson, ¶29). FF12. Timperman teaches a microfluidic system for proteome analysis in which “the sample processing reagent is a Appeal 2012-003437 Application 11/397,307 7 protease (such as trypsin) immobilized on a first solid phase disposed in a portion of the channel” (Timperman, ¶9). FF13. Timperman teaches that “different channels can comprise different types or amounts of protease . . . to perform a plurality of reactions of substantially identical samples (e.g., obtained from a single sample plug) in parallel,” and that “the extent of digestion may be controlled by precisely controlling the amount of time a sample is exposed to protease to produce larger peptides or peptides comprising overlapping sequences” (Timperman, ¶¶ 114-115). FF14. Timperman teaches that “[t]he immobilized protease allows the use of high concentrations of enzyme with negligible production of autolysis products” (Timperman, ¶113). FF15. Timperman teaches “[i]n still another aspect, however, flow through one or more selected channels of the device is hydrodynamic and mediated mechanically through valves placed at appropriate channel junctions as is known in the art,” and “[t]herefore, in one aspect, flow of reagents in each of the channels 8 of the device 5 is independently controlled” (Timperman, ¶130). PRINCIPLES OF LAW “[I]f a technique has been used to improve one device, and a person of ordinary skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond his or her skill.” KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007). The question to ask is “whether the improvement is Appeal 2012-003437 Application 11/397,307 8 more than the predictable use of prior art elements according to their established functions.” Id. However, “[o]bviousness does not require absolute predictability of success ... all that is required is a reasonable expectation of success.” In re Kubin, 561 F.3d 1351, 1360 (Fed. Cir. 2009) (citing In re O'Farrell, 853 F.2d 894, 903–04 (Fed. Cir. 1988)). “A reference may be said to teach away when a person of ordinary skill, upon reading the reference, would be discouraged from following the path set out in the reference, or would be led in a direction divergent from the path that was taken by the applicant.” In re Gurley, 27 F.3d 551, 553 (Fed. Cir. 1994). However, the “mere disclosure of alternative designs does not teach away.” In re Mouttet, 686 F.3d 1322, 1334 (Fed. Cir. 2012) (citing In re Fulton, 391 F.3d 1195, 1201 (Fed. Cir. 2004)). ANALYSIS As recognized by the Examiner, Kopf-Sill ’185 discloses a method of processing a sample within a microfluidic device comprising a fluid network with a plurality of parallel channels connecting a sample reservoir to a waste reservoir, and a plurality of reagent reservoirs that sequentially introduce reagents at various points along each of the plurality of parallel channels, wherein each of the reagent reservoirs is in fluid communication with at least two of the plurality of parallel channels, and wherein (Ans. 5; FF1-7). The Examiner acknowledges that Kopf-Sill ’185 fails to specifically teach that the microfluidic device can be used in a method “for processing proteins involving exposing the sample to reduction, alkylation, and quenching reagents sequentially, and that immobilized trypsin is placed in a portion of each of the channels” (id.). Appeal 2012-003437 Application 11/397,307 9 The Examiner, however, finds that Anderson teaches the digestion of proteins by exposing the sample proteins to reduction, alkylation, and quenching reagents sequentially, “wherein the proteins may be subdivided into undiluted, diluted 1000 fold, and diluted 10000000 fold subsamples” (Ans. 6; FF9-10). The Examiner further finds that Anderson teaches that “tryptic peptides created by trypsin digestion of the protein can be collected” (Ans. 6; FF11). Additionally, the Examiner finds that Timperman further teaches that the microfluidic device configured for protein digestion may comprise a plurality of channels, each containing different types or amounts of a protease such as trypsin immobilized on a solid phase disclosed in a portion of the channels, to maintain the trypsin within the channel . . ., so that a desired amount of digested polypeptide products may be obtained (Ans. 6; FF12-13). We believe the Examiner has made a prima facie showing that a person of ordinary skill in the art would have found it obvious to use the microfluidic device of Kopf-Sill ’185 to perform trypsin digestion of a protein sample at different concentrations as disclosed by Anderson, and to further use immobilized trypsin within the channels as disclosed by Timperman, which would result in the claimed method. We have considered Appellants’ arguments, but are not persuaded otherwise. Appellants have not presented any evidence of secondary (objective) considerations rebutting the prima facie case of obviousness. Appellants first argue that their “claimed method does not involve performing method steps on different concentrations of the same sample Appeal 2012-003437 Application 11/397,307 10 concurrently,” and that their “purpose in processing a protein sample in a microfluidic device having a plurality of parallel channels is to increase the rate at which a sample is processed” (App. Br. 13-14 (emphasis in original). Appellants assert that reducing the flow of sample, as taught by Kopf-Sill ’185, would “confer no benefit in Appellants’ method” and be “counterproductive” (id. at 14). We do not find this argument persuasive because the claimed method does not preclude processing the protein sample at different concentrations in the manner taught by Kopf-Sill ’185, even assuming arguendo that doing so would require a reduced flow. Moreover, the claims do not require a minimum flow rate for performing the trypsin digestion, nor is there any suggestion that the device of Kopf-Sill ’185 could not achieve a flow rate required for trypsin digestion in the manner claimed. Therefore, one of ordinary skill in the art would have found reason to perform the trypsin digestion protocol of Anderson in the microfluidic device of Kopf-Sill ’185 in order maintain a continuous flow rate while avoiding the need to add reagents in larger amounts to meet an increased flow demand (FF7). See KSR, 550 U.S. at 419-20 (“In determining whether the subject matter of a patent claim is obvious, neither the particular motivation nor the avowed purpose of the patentee controls. . . . Under the correct [obviousness] analysis, any need or problem known in the field of endeavor at the time of invention and addressed by the patent can provide a reason for combining the elements in the manner claimed.”). Appellants argue against the Anderson reference on the grounds that the reference discloses that “the samples are detected rather than being Appeal 2012-003437 Application 11/397,307 11 collected in a reservoir” (App. Br. 14 (emphasis in original)). However, Anderson teaches collecting peptides and proteins of varying concentrations from the sample target (FF11). One of ordinary skill in the art would therefore have found it obvious to use the waste reservoirs disclosed by Kopf-Sill ’185 to collect the digested peptides. Appellants further argue that Anderson provides no teaching regarding the use of a microfluidic device to carry out reduction, alkylation, and quenching in the manner claimed (App. Br. 14). However, Kopf-Sill ’185 discloses a device that is capable of doing so. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. In re Merck & Co., Inc., 800 F.2d 1091, 1097 (Fed. Cir. 1986). With respect to Timperman, Appellants argue that the reference is similarly silent with regard to continuous flow and collecting a digested sample in a reservoir (App. Br. 14-15). Again, those capabilities are taught by Kopf-Sill ’185 as discussed above. Appellants further argue that Timperman only “teaches a device that is electrophoretically driven,” and teaches away from the claimed method by stating that “flow of reagents in each of the channels 8 of the device 5 is independently controlled” when discussing hydrodynamic flow (App. Br. 15; FF15). But Timperman does not teach that hydrodynamic flow in each of the channels must necessarily be independently controlled when using immobilized trypsin in a microfluidic device, and we therefore do not view that disclosure in Timperman as teaching away from the claimed method of using a single negative pressure driving force to generate continuous flow. Moreover, the fact that Timperman discloses the use of electrophoretic flow does not teach Appeal 2012-003437 Application 11/397,307 12 away from the use of a vacuum source. To the contrary, Timperman’s alternative disclosure of hydrodynamic driven flow would provide reason to try the single vacuum source device disclosed by Kopf-Sill ’185. See Mouttet, 686 F.3d at 1334 (The “mere disclosure of alternative designs does not teach away.”). Kopf-Sill ’185 discloses that reagent materials can be added to the flow reduction channels instead of being placed in reservoirs (FF8). Because Timperman discloses that “immobilized protease allows the use of high concentrations of enzyme with negligible production of autolysis products,” one of ordinary skill in the art would have found motivation to use immobilized trypsin in the flow reduction channels of the Kopf-Sill ’185 device so that so that a desired amount of digested polypeptide products may be obtained (FF14). Accordingly, we find that the combined teachings of Kopf-Sill ’185, Anderson, and Timperman establish a prima face case of obviousness that Appellants have not rebutted. SUMMARY We affirm the rejection of claim 1 under 35 U.S.C. § 103(a) as being rendered obvious by Kopf-Sill ’185, Anderson, and Timperman. Claims 2- 16 fall with claim 1. Appeal 2012-003437 Application 11/397,307 13 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 cdc Copy with citationCopy as parenthetical citation