hnologyDetailed Action
► The applicant's Preliminary Amendment filed 15 AUG 2022 has been entered. Following the entry of the Preliminary Amendment, Claim(s) 38-57 is/are pending.
► The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . 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 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.
Priority
► The applicant claims priority to provisional application USSN 62/413,708 filed 27 OCT 2016.
Sequence Rules
► This application complies with the sequence rules and the sequence(s) have been entered by the Scientific and Technical Information Center.
35 U.S.C. 112(b)/ 112 (pre-AIA ), second paragraph
► 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.
Claim Rejection(s) under 35 U.S.C. 112(b)/ 112 (pre-AIA ), second paragraph
► Claim(s) 56-57 is/are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite in that it fails to point out what is included or excluded by the claim language.
Claim 56-57 is indefinite because it recites an improper Markush group. Alternative
expressions are permitted if they present no uncertainty or ambiguity with respect to the question of scope or clarity of the claims. One acceptable form of alternative expression, which is commonly referred to as a Markush group, recites members as being "selected from the group consisting of A, B and C." See Ex parte Markush , 1925 C.D. 126 (Comm'r Pat. 1925).
Claim language defined by a Markush grouping requires selection from a closed group “consisting of” the alternative members. Id. at 1280, 67 USPQ2d at 1196. See also Amgen Inc. v. Amneal Pharmaceuticals LLC, 945 F.3d 1368, 1376-78, 2020 USPQ2d 3197 (Fed. Cir. 2020)
Amending Claims 56-57 to the ”selected from the group consisting of” language will overcome this rejection.
35 U.S.C. 103
► 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.
Claim Rejection(s) under 35 U.S.C. 103
► Claim(s) 38-57 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lee [US 2006/0088862 – hereinafter Lee”] in view of Yu et al. [Cellular and Molecular Gasteroenterology and Hepatology2(2) : 158-174 (MAR 2016) – hereinafter “Yu”] and Nagaoka et al. [ US 2011/0183332 – hereinafter “Nagaoka” and Tan et al. [J. of Biomedicine and Biotechnology 2009: Art.No. 574398, 10 pgs -hereinafter “Tan”].and/or Shi et al. [Human Pathology 44:1089-1097(2013) – hereinafter “Shi”] and/or Dake US 2019/0185541- hereinafter “Dake”] and/or Zhang et al. [EMBO 34(23) :2953114:1352(2016) – hereinafter “Zhang”] and/or Liu et al. [US 2018/0017549 – “Liu”] and/or Lee et al. [British J. of Cancer 114:1352( JUN 2016) -hereinafter “Lee”] and/or Kim et al. [British J. of Cancer 114:199 (JAN 2016) -hereinafter “Kim”] and/or Wang et al. [WO 2016/036319 – hereinafter “Wang”] and Bosch et al. [US 2015/0141273 – hereinafter “Bosch”] and Koga et al. [ Gasteroenterology Research and Practice Vo. 2008 Art. ID #605273 (2008) – hereinafter “Koga”].
Claim 38 is drawn to a method of identifying one or more biomarkers in a stool sample which method comprises
a) mixing the sample with a buffer, a surfactant and a ribonuclease inhibitor to form a suspension;
b) separating the suspension into a portion enriched for eukaryotic cells and a portion enriched for bacterial cells and retaining the portion enriched for eukaryotic cells;
c) adding a chaotropic agent and optionally a surfactant to the portion enriched for eukaryotic cells to form a lysate;
d) fractioning the lysate into a cell debris layer, a layer comprising eukaryotic nucleic acids and a lipid layer;
e) collecting the layer comprising eukaryotic nucleic acids and optionally the lipid layer, wherein the layer comprising eukaryotic nucleic acids comprises a plurality of extracted nucleic acids, and
f) analyzing the extracted nucleic acids by microarray sequencing, molecular barcoding, probe capture, polymerase chain reaction (PCR), ddPCR, RT-PCR, RT -qPCR, or nucleic acid sequencing to identify the eukaryotic biomarkers.
Lee teach, see at least paras 24-26 a method identifying one or more eukaryotic biomarker (i.e. human derived biomarkers of CRC out of stool samples That said, Lee does not teach the nucleic acid prep method recited by Claim 38, however such a method was known as evidenced by Yu in view of Nagakoa and Tan Yu teaches a method of isolating nucleic acid from a stool sample. Yu teaches transferring (mixing) the fecal sample into Hank's balanced salt solution (a buffer) and Tween- 20 (a surfactant) and vortexing to suspend the aggregates (form a suspension) (page 159, col. 2, last full para). Yu does not expressly teach that the sample is mixed with a ribonuclease inhibitor to form a suspension. However Nagaoka does teach the use of an RNase inhibitor. For example Nagaoka teaches a method of preparing a stool sample by adding the sample to a solution for removing the nucleic acid amplification reaction inhibitory substance, wherein the removal solution is obtained by dilution using a buffer and contains a detergent, wherein the buffer contains an RNAse inhibitor (para 0007, 0037, 0051, 0062, 0065, 0074). Nagaoka teaches mixing the stool sample with a removal solution, which consists of a buffer, a surfactant and a ribonuclease inhibitor to form a suspension (para 0074). Nagaoka teaches that it is preferable to use a buffer that contains an RNase inhibitor such as guanidine thiocyanate or guanidine hydrochloride (para 0074). It would have been obvious to a person of ordinary skill in the art before the effective filing date to combine the method of Yu (mixing the sample with a buffer and surfactant to form a surfactant) with Nagaoka to mix the sample with a ribonuclease inhibitor to because both are directed towards nucleic acid extraction from fecal samples using a buffer and surfactant. The ordinary artisan would have been motivated to mix the ribonuclease inhibitor with the sample immediately because Nagaoka teaches that stool samples are normally supplied to nucleic acid recovery and analysis soon after preparation because nucleic acids present in stool are extremely susceptible to decomposition para 62. Nagaoka also teaches that RNA is extremely susceptible to decomposition, so it is preferable to use a buffer that contains an RNase inhibitor para 74). Yu also teaches that centrifugation followed to separate the suspension into the supernatant enriched for bacterial cells and the pellet enriched for human cells (page 159, col. 2, last full para). Yu teaches the fecal nucleic acids were extracted from the human-enriched (eukaryotic cells) pellet suspended in the lysis buffer using Specific A protocol on NucliSENS EasyMag system (page 159-page 160, bridging para). As evidenced by BioMerieux SA ("NucliSENS Lysis Buffer" (2015)), the NucliSENS EasyMag system used in Yu necessarily included adding a chaotropic agent because the NucliSENS Lysis Buffer contains guanidine thiocyanate (chaotropic agent), which will release all nucleic acids present (form a lysate). Nagaoka also teaches that a denaturing agent such as a chaotropic agent may be added directly to the stool-derived solid para 74. Yu also necessarily teaches fractionating the lysate into a layer comprising eukaryotic nucleic acid (step d) because Yu necessarily collects the layer comprising eukaryotic nucleic acids to perform qPCR and microarray analysis (page 159-160, bridging para-page 160, first full.
Yu does not explicitly teach that the lysate is also fractionated into a cell debris
layer and a lipid layer. However, Tan teaches target nucleic acid should be free of contaminates including protein, carbohydrate, and/or lipids, as the quality and integrity of the isolated nucleic acid will directly affect results of all succeeding scientific research (page 1, col 1-2, bridging para). Tan teaches that extraction can be performed by centrifugation, solution-based, and column-based protocols (abstract). It would have been obvious to a person of ordinary skill in the art before the effective filing date to fractionate the lysate into a cell debris layer and a lipid layer because Tan teaches target nucleic acid should be free of contaminates including protein, carbohydrate, or lipids, as the quality and integrity of the isolated nucleic acid will directly affect results of all succeeding scientific research.
Claim 39 is drawn to an embodiment of the method of claim 38, wherein the stool sample is a human stool sample. Claim 40 is drawn to an embodiment of the method of claim 38, wherein the separating step comprises centrifugation or a column-based method. Claim 42 is drawn to an embodiment of the method of claim 38, wherein the separating step comprises differential filtration.
At least Yu teach these limitation(s), see the section entitled “Methods”
Claim 41 is drawn to an embodiment of the method of claim 38, wherein the separating step utilizes targeted probes that bind eukaryotic cells. Claim 45 is drawn to an embodiment of the method of claim 38, wherein the fractionating step utilizes targeted probes that bind eukaryotic cells.
At least, Koga teach this limitation, see the entire document. In particular Koga teach the use of magnetic bead immobilized antibodies capable of binding to human cell exfoliated in order to isolate said cells out of stool for subsequent analysis which in one embodiment comprises the analysis of cellular nucleic acid by PCR.
Yu teach “centrifugation” as recited by Claim 44 , see the section of Yu entitled “Methods” which begins on pg. 159.
As regards Claim(s) 43 and 46, it was well known, absent an unexpected results, repeating sample processing step(s) multiple times in order to insure the completeness of each of said processing steps.
As to Claim(s) 47-48 , see the section of Yu entitled “Methods” which begins on pg. 159.
As regards Claim(s) 49 and 52-55 , Yu teach extracting RNA (i.e. mRNA ), see at least the section of Yu entitled “Methods” which begins on pg. 159.
As regards Claim(s) 50-51, note that Yu teach centrifugation and the use of the NucliSENS Easy Mag extraction system. see at least the section of Yu entitled “Methods” which begins on pg. 159. Note especially the para bridging pgs 159-160.
As regards Claim(s) 56-57, note the teaching of Shi, who teach the ACY1 biomarker and its association with CRC see at least the abstract and Dake who teach the TNFRSF10B biomarker, see at least para 20. Zhang teach EGLN2 and it association with cancer (i.e. breast cancer),see at least the abstract. Liu teach KRAS and its association with CRC, see at least para 25. Lee teach AREG and its association with CRC .Kim teach CDH1 (aka E-cadherin) and its association with CRC. Wang teach GAPDH and it’s use as a control in gene expression analysis. Finally Bosch, teach an extensive laundry list of biomarkers associated with CRC, including ACY1, PHD1 (aka EGLN2) see at least the abstract, para 78 and Figures 1 and 6.
Non-Statutory Obviousness-type 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. See 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);and, 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) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent is shown to be commonly owned with this application. See 37 CFR 1.130(b). It is noted that the doctrine of double patenting is also designed to protect third parties from harassment by multiple patent owners in connection with the same invention.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b). 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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
NSODP Rejection(s)
► Instant Claim(s) 38-57 rejected under the judicially created doctrine of obviousness-type double patenting as being unpatentable over Claims 1-20 of U.S. Patent No. 11,479,820 hereinafter “US-820’” in view of Lee [US 2006/0088862 – hereinafter Lee”] and/or Shi and/or Dake US 2019/0185541- hereinafter “Dake”] and/or Zhang and/or Liu et al. [US 2018/0017549 – “Liu”] and/or Lee and/or Kim et al. [British J. of Cancer 114:199 (JAN 2016) -hereinafter “Kim”] and/or Wang et al. [WO 2016/036319 – hereinafter “Wang”] and Bosch et al. [US 2015/0141273 – hereinafter “Bosch”] and Koga.
Claim(s) 56 is drawn , in part, to an embodiment of the method of Claim 38 wherein the eukaryotic biomarker is selected from a defined group which includes ACY1, Although the conflicting claims are not identical, they are not patentably distinct from each other. The scope encompassed by the invention recited in Claims 38-57 falls with the scope encompassed by the invention recited in Claims 1-20 of US-820’. For example as regards Claim 1 consider at least Claim 1 in US-820’ there, the method of isolating eukaryotic cell (i.e. intact human cells) from a stool sample as well as the extraction of nucleic acids from said eukaryotic recited by Claim(s) 38 is taught. That said, the Claims of US-820’ do not teach biomarkers or their detection as recited by Claim(s) 56-57. However, the detection of CRC biomarkers recited were known. For example, consider Lee at least at paras 24-26. In addition, a long list of potential biomarkers were known, Consider Shi who teach the ACY1 biomarker and its association with CRC see at least the abstract. Dake teach the TNFRSF10B biomarker, see at least para 20. Zhang teach EGLN2 and it association with cancer (i.e. breast cancer),see at least the abstract. Liu teach KRAS and its association with CRC, see at least para 25. Lee teach AREG and its association with CRC .Kim teach CDH1 (aka E-cadherin) and its association with CRC. Wang teach GAPDH and it’s use as a control in gene expression analysis. Finally Bosch, teach an extensive laundry list of biomarkers associated with CRC, including ACY1, PHD1 (aka EGLN2) see at least the abstract, para 78 and Figures 1 and 6. Therefore, absent an unexpected result it would have been prima facie obvious to the PHOSITA at the time of the invention to modify the method of US-820’ wherein all known cancer / CRC biomarkers of the prior art are analyzed by the disclosed method.
Conclusion
C. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Ethan Whisenant whose telephone number is (571) 272-0754. The examiner can normally be reached Monday-Friday from 8:30 am -5:30 pm EST or any time via voice mail. If repeated attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anne Gussow, can be reached at (571) 272-6047.
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/ETHAN C WHISENANT/Primary Examiner, Art Unit 1683 ethan.whisenant@uspto.gov
EXAMINER SEARCH NOTES
28 FEB 2026 - ECW
Databases searched: All available via PE2E SEARCH
CAplus, Medline and BIOSIS via STNext; and Google Scholar (note the search terms used below)
Performed Similarity searches as appropriate
Reviewed the parent(s), if any, and any search(es) performed therein : see the BIB data sheet
Reviewed, the search(es), if any, performed by prior examiners including any international examiners.
Planned Search
Search terms:
All Inventor(s) e.g. Barnell E?/au
Eukaryotic or human
Cell$
Capture
Stool or feces
Magnetic (particle$ or bead$)
PCR or ddPCR or RT-PCR or RT- qPCR or sequencing
RNA or mRNA or miRNA
ACY1 or TNFRSF10B or EGLN2 or KRAS or AREG or CDH1 or GAPDH.
► See the Examiner’s PE2E SEARCH notes/strategy in IFW