DETAILED ACTION
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/6/2026 has been entered. Claim 1 has been amended. Claims 5, 12-14 have been canceled. Claims 25-27 have been added. Claims 1-4, 6-11, 15-27 are pending and under examination.
New Grounds of Rejections
Claim Rejections - 35 USC § 112
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 2 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
(a) Claim 2 is indefinite and does not provide a clear nexus between the step recited in the claim 1 and the wherein clause recited in the instant claim. Specifically, it is unclear how one is to establish the time of and/or after direct differentiation state of a cell to establish is something is elevated or not based on the step of performing an isothermal nucleic acid method as recited in the claim. It is unclear if the determining of the differentiation state is intended to be represented irrespective of the amplification steps or based on detection by the isothermal nucleic acid amplification method. Further it is unclear as to the metes and bounds of the term “elevated” in the context of the claims and what reference standpoint is supposed to be used to make the comparison. Clarification is required.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
7. Claims 1-4, 6-11, 15-27 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Taniguchi et al {Taniguchi, used interchangeably herein} WO 2021095798, publication date May 20, 2021, translated document.
Regarding claims 1 and 15-16, Taniguchi et al teach a method for detecting RNA from undifferentiated cells in a cell population of interest, the method comprising detecting, by an isothermal nucleic acid amplification method, RNA from an undifferentiation marker gene in a sample containing a nucleic acid derived from the cell population of interest, (see abstract and entire document, especially beginning at pages 9-32).
With regards to the limitation “wherein the RNA from the undifferentiation marker gene satisfies:(i) a ratio of an RNA expression level in the undifferentiated cells to an RNA expression level in non-undifferentiated cells is 104 or more times, and/or (ii) the RNA expression level in the non-undifferentiated cells is 1x104 copies or less per pg of a total RNA level (se entire document, especially beginning at pages 7-11).
Regarding claim 2, for the purpose of application of prior art and given the ambiguity noted above, the claim is being given the broadest reasonable interpretation by the examiner. In this case, Taniguchi meets the limitation of the claim by teaching that the mixing rate of undifferentiated cells in the undifferentiated cell population during the differentiation process is in the range of 0.1% (1 x 103) to .0.00005 (5 x 107) (page 8 and 9).
Regarding claims 3, 19 and 20, Taniguchi teaches the method according to claim 1, wherein the undifferentiated cells are pluripotent stem cells or somatic stem cells (see entire document, especially page 5, lines 8-12).
Regarding claim 4, The specification teaches at paragraph at [0055] that the limit of detection can be for example, less than 10 copies in X pg of RNA purified from non-undifferentiated cells. The specification teaches “when undifferentiated cells are to be detected with high sensitivity, X is preferably 1 or more, more preferably 10 or more and even more preferably 100 or more. Taniguchi teaches the method according to claim 1, wherein the method further comprises determining a presence of the RNA to be detected in the sample in an amount equal to or higher than a limit of detection of the isothermal nucleic acid amplification method and in the non-undifferentiated cells in an amount equal to or below the limit of detection of the isothermal nucleic acid amplification method (see entire document, especially pages 10-12).
Regarding claim 6, Taniguchi teaches the method according to claim 1, wherein the detecting comprises synthesizing and amplifying a nucleic acid from the RNA isothermally using at least four different primers specifically designed to recognize six distinct regions on a target sequence (see entire document, especially pages 12-15 and examples).
Regarding claim 7, Taniguchi teaches the method according to claim 1, wherein the nucleic acid is amplified by DNA polymerase having strand displacement activity (see entire document, especially last paragraph on pages 12-13).
Regarding claims 8-10, Taniguchi teaches the method according to claim 7, wherein the nucleic acid is synthesized by reverse transcriptase from the RNA and amplified isothermally with the DNA polymerase having strand displacement activity using at least four different primers specifically designed to recognize six distinct regions on a target sequence (See entire document, especially pages.
Regarding claims 11 and 18, Taniguchi teaches the method according to claim 1, wherein the isothermal nucleic acid amplification method is a LAMP method and/or RT-LAMP assay (see abstract and entire document, especially pages 12-15, and Examples).
Regarding claims 21-27, Taniguchi teaches wherein the undifferentiation marker gene comprises at least one selected from the group consisting of SFRP2, CNMD, USP44, LIN28A, LINC00678, PRDM14 and ESRG (see entire document, especially examples). Thus, Taniguchi meets the limitations of the claims recited above.
8. Claim(s) 1-4, 6-11, 15-19, 21-27 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yasui et al {Yasui, used interchangeably herein} (Stem cell Reviews and Reports, 18: 2995-3007, Epub date June 3, 2022, entire document).
Regarding claims 1 and 15-16, Yasui et al teach a method for detecting RNA from undifferentiated cells in a cell population of interest, the method comprising detecting, by an isothermal nucleic acid amplification method, RNA from an undifferentiation marker gene in a sample containing a nucleic acid derived from the cell population of interest, (see entire document, especially page 2996, beginning at last paragraph of col. 1 to col. 2 which teaches that a more precise, accurate and sensitive detection of undifferentiated cells encompass performing loop-mediated isothermal amplification (LAMP); which also encompass RT-LAMP or digital LAMP assays, thus allowing evaluation of pluripotency (undifferentiated) marker RNA in a cell population of interest; see also section entitled “undifferentiated hiPSC spike-in and RNA preparation for RT-LAMP assay” and “Invitro RT-LAMP” at page 2997; see also pages 2999-3002 and 3004 which further discuss RNA from undifferentiated marker genes).
With regards to the limitation “wherein the RNA from the undifferentiation marker gene satisfies:(i) a ratio of an RNA expression level in the undifferentiated cells to an RNA expression level in non-undifferentiated cells is 104 or more times, and/or (ii) the RNA expression level in the non-undifferentiated cells is 1x104 copies or less per pg of a total RNA level (see page 3000, Figure 2 and legend, Figure 3 and legend at pages 3002 and 3003; see also supplementary Materials, e.g., Figures 4-6 and 8).
Regarding claim 2, for the purpose of application of prior art and given the ambiguity noted above, the claim is being given the broadest reasonable interpretation by the examiner. In this case, Yasui meets the limitation of the claim by teaching undifferentiated hiPSC spike-in and RNA preparation for RT PCR (page 2997, col. 1) such that the differentiation state of the cell population is elevated (see also Figures 1-4).
Regarding claim 3, Yasui teaches the method according to claim 2, wherein the undifferentiated cells are pluripotent stem cells (see Abstract and entire document).
Regarding claim 4, The specification teaches at paragraph at [0055] that the limit of detection can be for example, less than 10 copies in X pg of RNA purified from non-undifferentiated cells. The specification teaches “when undifferentiated cells are to be detected with high sensitivity, X is preferably 1 or more, more preferably 10 or more and even more preferably 100 or more. Yasui teaches the method according to claim 1, wherein the method further comprises determining a presence of the RNA to be detected in the sample in an amount equal to or higher than a limit of detection of the isothermal nucleic acid amplification method and in the non-undifferentiated cells in an amount equal to or below the limit of detection of the isothermal nucleic acid amplification method (see page 2997-2998, Figure 1 and supplemental figures, e.g., Figure 6-7).
Regarding claim 6, Yasui teaches the method according to claim 1, wherein the detecting comprises synthesizing and amplifying a nucleic acid from the RNA isothermally using at least four different primers specifically designed to recognize six distinct regions on a target sequence (page 2996, beginning at last paragraph of col. 1 to col. 2 and pages 2997-2998, section entitled “LAMP primer design”, “In vitro RT-LAMP” and “In situ RT-LAMP”).
Regarding claim 7, Yasui teaches the method according to claim 1, wherein the nucleic acid is amplified by DNA polymerase having strand displacement activity (Yasui teaches LAMP assay which relies on a DNA with strand displacement activity {page 2996, beginning at last paragraph of col. 1 to col. 2 and pages 2997-2998, section entitled “LAMP primer design”, “In vitro RT-LAMP” and “In situ RT-LAMP”}).
Regarding claims 8-10, Yasui teaches the method according to claim 7, wherein the nucleic acid is synthesized by reverse transcriptase from the RNA and amplified isothermally with the DNA polymerase having strand displacement activity using at least four different primers specifically designed to recognize six distinct regions on a target sequence ((page 2996, beginning at last paragraph of col. 1 to col. 2 and pages 2997-2998, section entitled “LAMP primer design”, “In vitro RT-LAMP” and “In situ RT-LAMP”; see also supplementary Figures 1, Table 2-4 and 6).
Regarding claims 11 and 18, Yasui teaches the method according to claim 1, wherein the isothermal nucleic acid amplification method is a LAMP and/or RT-LAMP method (see abstract and entire document).
Regarding claim 19, Yasui teaches the method according to claim 1, wherein the undifferentiated cells are pluripotent stem cells (see abstract and entire document).
Regarding claims 21-27, Yasui teaches wherein the undifferentiation marker gene comprises at least one selected from the group consisting of SFRP2, USP44, LIN28A, SOX2, OCT4, NANOG, TDGF1, LINC00678, PRDM14 and ESRG (see pages 2999-3004 and supplementary materials, including supplementary Table 2). Thus, Yasui meets the limitations of the claims recited above.
Prior art
9. The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Li et al (Biosensors and Bioelectronics, 64 (2015) 196-211) teach advances in isothermal amplification including assays associated with Loop-mediated isothermal amplification
Conclusion
10. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681