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 .
Applicant’s response to the Office Action mailed June 05, 2025, filed November 04, 2025 is acknowledged. Applicant cancels claims 4-6 and 8-13. Applicant newly adds claims 14-18. As discussed below, newly added claims 17 and 18 are withdrawn from consideration as being directed to a non-elected invention. Claims 1-3, 7 and 14-18 are currently pending. Claims 1-3, 7 and 14-16 are under examination.
Any objection or rejection of record in the previous Office Action, which is not addressed in this action has been withdrawn in light of Applicant’s amendments and/or arguments. This action is Final.
Election/Restrictions
Newly submitted claims 17 and 18 are directed to an invention that is independent or distinct from the invention originally claimed for the following reasons:
The originally filed claims 1-13 were directed to a gene expression analysis method for a test sample, an internal standard gene for gene expression analysis and a composition for expression analysis of an internal standard gene, whereas the newly added claims 17 and 18 are directed to a composition comprising a first nucleic acid molecule that consist of a sequence selected from a group of specific SEQ ID NO’s. The newly cited composition recites different components, structures, and functions, than the originally presented composition for expression analysis of an internal standard gene. Had all of the claims originally been present for examination a Requirement for Restriction would have been issued because the two separate unrelated products would have been deemed patentably distinct.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claims 17 and 18 are withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
Priority
This application, filed on January 16, 2022, is a 371 of PCT/JP2020/027649, filed on July 16, 2020 and claims priority to foreign application JP2019-134181, filed on July 19, 2019.
It is noted that no translation of the foreign application has been provided. Therefore, the effective filing date of the instant application is determined to be July 16, 2020, which is the filing date of the PCT application.
Claim Objections
Claims 1 and 14 are objected to because of the following informalities:
In claim 1, line 11, “the
In claim 14, line 10, “the the first primer” should read “
Appropriate correction is required.
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 1-3, 7 and 14-16 are 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.
Claim 1 recites the limitation "the expression level" in line 13. There is insufficient antecedent basis for this limitation in the claim.
Claims 2-3 and 15 depend from claim 1 and are therefore included in this rejection.
Claim 7 is vague and indefinite for the following reasons:
In claim 7, the term “the gene” in lines 11 and 12 are unclear and confusing. Is this the internal standard gene or another gene?
Claim 14 recites the limitation "the expression level" in line 12. There is insufficient antecedent basis for this limitation in the claim.
Claims 15 and 16 depend from claim 14 and are therefore included in this rejection.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 7 and 14-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions (i.e., product of nature, a law of nature, a natural phenomenon, or an abstract idea) without significantly more. This rejection is maintained and modified as necessitated by amendments.
Every claimed invention must be examined to determine whether the claimed invention complies with 35 U.S.C. 101, particularly whether the claimed invention falls within a 35 U.S.C. 101 judicial exception of non-patentable subject matter (e.g., an abstract idea, law of nature, natural phenomenon, natural product etc.). Phenomena of nature, though just discovered, natural products, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work. See MPEP 2106. As per the “2019 Revised Subject Matter Eligibility Guidance” (Federal Register Vol. 84, No. 4, available 01-07-2019), claims drawn to a process, machine, manufacture or composition of matter are further analyzed according to a two-part process to determine if A) the claim(s) is/are “directed to” a judicial exception because the claims(s) recite(s) a judicial exception (i.e. prong one) that is not integrated into a practical application (i.e. prong two) and, if so, if B) the claim(s) provide(s) an inventive concept, i.e. recite(s) additional elements that amount to significantly more than the judicial exception.
Subject Matter Eligibility Test for Products and Processes
Step 1 - Is the Claim to a Process, Machine, Manufacture or Composition of Matter? YES
Claims 1-3, 7 and 14-16 are directed to one of the statutory classes. Claims 1 and 14, a gene expression analysis method for a test sample obtained from a breast cancer tissue or a normal mammary gland tissue (Process). Claim 7, a composition for expression analysis of an internal standard gene (Composition).
Step 2A, Prong One — Does the Claim Recite an Abstract Idea, Law of Nature, or Natural Phenomenon? YES
Claims 1-3, 7 and 14-16 recite the abstract idea of receiving and processing data using mental steps. Claims directed to nothing more than abstract ideas, natural phenomena, and laws of nature are not eligible for patent protection (see MPEP 2106.04). Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, determining, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include:
• Calculating the expression level of a given gene (mental process, human is capable of receiving/ collecting data, observing/evaluating, organizing information and mathematical relationship; claims 1-3 and 14-16).
• Classifying a subtype of breast cancer (mental process, human is capable of receiving/ collecting data, observing/evaluating/determining, organizing information; claims 1-3, 7 and 14-16).
Therefore, the claims recite elements that constitute one or more judicial exceptions.
Step 2A, Prong Two — Does the Claim Recite an Additional Elements that Integrate the Judicial Exception into a Practical Application? NO.
The Supreme Court has long distinguished between principles themselves, which are not patent eligible, and the integration of those principles into practical applications, which are patent eligible. However, absent are any additional elements recited in the claim beyond the judicial exceptions which integrate the exception into a practical application of the exception. The “integration into a practical application” requires an additional element or a combination of additional elements in the claim to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that it is more than a drafting effort designed to monopolize the exception.
The claim analysis continues with identifying additional elements beyond the judicial exceptions that might evidence integration of the judicial exceptions into a practical application. The steps or elements in addition to the judicial exceptions are: “normalizing the amount of the first primer or probe to copies of the given gene using the amount of second primer or probes” and “the internal standard gene is used in gene expression analysis for a test sample derived from a breast cancer patient” as well as “[using] a primer and a probe (First or second that may be labeled)” and “using PCR”, which is not indicative of integration into practical application. These steps, recited at a high level of generality, comprise routine data gathering, which is considered an insignificant extra-solution activity. This data gathering is required for using the judicial exceptions. (See MPEP 2106.05(g)). There are no further/additional steps which applies either the identified judicial exception into practical application. Thus, a careful evaluation of the claim as a whole fails to reveal the practical application of the judicial exception to, e.g., effect an improvement to the functioning of a computer or other technology/technical field, effect a particular treatment or prophylaxis for a disease or medical treatment, implement a particular machine that is integral to the claim, or effect a transformation or reduction of a particular article to a different state or thing, or to apply the judicial exception in another meaningful way beyond generally linking its use to a particular technological environment. Accordingly, the claims do not integrate the judicial exception(s) into a practical application and is therefore directed to a judicial exception.
Step 2B - Does the Claim Recite Additional Elements that Amount to Significantly More than the Judicial Exception? NO.
The Supreme Court has identified a number of considerations for determining whether a claim with additional elements amounts to “significantly more” than the judicial exception(s) itself. The claims as a whole are analyzed to determine whether any additional element/step, or combination of additional elements/steps, in addition to the identified judicial exception(s) is sufficient to ensure that the claim amounts to “significantly more” than the exception(s).
The eligibility analysis proceeds with identifying any additional elements or limitations, separate from the judicial exceptions, that might potentially render the claims directed to a judicial exception patent eligible. To render the claims patent- eligible, these elements must comprise meaningful limitations that add to or transform the judicial exception to the effect that it amounts to significantly more than the natural correlation or abstract idea itself - i.e. provide an “inventive concept’. The elements that are in addition to the judicial exception comprise: “normalizing the amount of the first primer or probe to copies of the given gene using the amount of second primer or probes” and “the internal standard gene is used in gene expression analysis for a test sample derived from a breast cancer patient” as well as “[using] a primer and a probe (First or second that may be labeled)” and “using PCR”. When considered separately and in combination, these elements do not add significantly more to the judicial exception. These steps are well-understood, routine and conventional activities in the field. For example, Shin et al. (U.S. Patent Application Publication US 2010/0137149 A1, published June 03, 2010), cited on the IDS filed May 25, 2023 discloses a gene analysis method for a test sample, (specifically a breast cancer sample, see Table 6) by normalizing the amount of the first primer or probe to copies of the given gene using the amount of second primer or probes, PCR, microarrays and identifying breast cancer (Page 2, [0009]-[0011], [0014]-[0015], Pages 4-14, [0044] and Page 80, [0114] and Tables 2 and 6). Shin additionally discloses normalizing the expression level of the desired gene using the expression level of the internal standard gene (Page 2, [0011], [0014]-[0015] and claims 24-27). Additionally, Lyden et al. (U.S. Patent Application Publication US 2021/0285952 A1, published September 16, 2021, effectively filed December 03, 2018), discloses a gene expression analysis method for a test sample obtained from a breast cancer tissue or a normal mammary gland tissue (Abstract, Page 3, [0019], Page 8, [0054], Page 9, [0062] and [0067] and Page 11, [0081]-[0083]). Lyden discloses adding to the test sample a first primer or probe against of a given gene and measuring the amount of the first primer or probe bound to copies of the given gene, wherein said first primer or probe may be labeled (Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0133] and Pages 17-18, [0136]-[0142]). Lyden teaches adding to the test sample a second primer or probe against WDR1 and measuring the amount of the second primer or probe bound to copies of the at least one internal standard gene, and said second primer or probe may be labeled, as well as normalizing the expression level amount of the first primer or probe bound to copies of the given gene using the expression level amount of the second primer or probe bound to copies of the at least one internal standard gene and calculating the expression level of the given gene in the test sample as a relative value of the amount of the first primer or probe bound to copies of the given gene to the amount of the second primer or probe bound to copies of the at least one internal standard gene (Page 10, [0074], Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0132]-[0135], Pages 17-18, [0136]-[0142], Page 68, [0199] and Table 1). Moreover, Kabos et al. (“Patient-derived luminal breast cancer xenografts retain hormone receptor heterogeneity and help define unique estrogen-dependent gene signatures”, Breast Cancer Res Treat 135, pgs. 415–432, published July 24, 2012), as evidenced by NCBI Gene Expression Omnibus Platform GPL11532, made public January 18, 2011, discloses a gene expression analysis method from a test sample obtained from a breast cancer tissue or a normal mammary gland tissue (Abstract). Kabos discloses using the Affymetrix Human Gene 1.1 ST Array (i.e., using a primer or a probe for the genes or markers thereof, Page 417, Right Column, Fourth Paragraph- Page 418, Left Column 1, First Paragraph). Kabos discloses using a first primer and second primer that may be labeled, as well as probes that measure all gene family members of a given gene (Page 418, Left Column, Last Paragraph—Right Column, First Paragraph and Page 425, Right Column, Last Paragraph). Kabos discloses normalizing expression data (Figs. 6 and 7). Kabos teaches adding to the test sample a primer or probe against internal standard gene comprising the group: ABCF3, FBXW5, MLLT1, FAM234A (ITFG3), PITPNM1, WDR1, NDUFS7, and AP2A1 (Affymetrix Human Gene 1.1 ST Array data as evidenced by NCBI Gene Expression Omnibus Platform GPL11532, Page 418, Left Column, Last Paragraph—Right Column, First Paragraph, Page 425, Right Column, Last Paragraph and Figs. 6-7). NCBI Gene Expression Omnibus Platform GPL11532 describes the genes measured by the “Affymetrix Human Gene 1.1 ST Array”, which comprise ABCF3, FAM234A (ITFG3), FBXW5, MLLT1, PITPNM1, WDR1, NDUFS7, and AP2A1. The claims recite an abstract idea with additional elements. Because these elements are not inventive concepts, the claims do not integrate the abstract idea into a practical application. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Accordingly, the claims do not qualify as patent-eligible subject matter.
For further information, please see the latest revision of MPEP 2104-2106 {Patent Subject Matter Eligibility Under 35 U.S.C. 101}, including MPEP 2106.04 {Eligibility Step 2A: Whether a Claim is Directed to a Judicial Exception} and 2106.05 {Eligibility Step 2B: Whether a Claim Amounts to Significantly More}, as well as the guidance on Subject Matter Eligibility, including the 2019 Guidance issued Jan. 7, 2019, and the October 2019 Update, provided on the USPTO website at https:/Awww.uspto.gov/patent/laws-and-regulations/examination-policy/subject-matter- eligibility.
Claim Rejections - 35 USC § 103
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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claims 1-3, 7 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Lyden et al. (U.S. Patent Application Publication US 2021/0285952 A1, published September 16, 2021, effectively filed December 03, 2018), in view of Kabos et al. (“Patient-derived luminal breast cancer xenografts retain hormone receptor heterogeneity and help define unique estrogen-dependent gene signatures”, Breast Cancer Res Treat 135, pgs. 415–432, published July 24, 2012), as evidenced by NCBI Gene Expression Omnibus Platform GPL11532, made public January 18, 2011. This is a new rejection as necessitated by amendments.
Regarding claim 1, Lyden teaches a gene expression analysis method for a test sample obtained from a breast cancer tissue or a normal mammary gland tissue (Abstract, Page 3, [0019], Page 8, [0054], Page 9, [0062] and [0067] and Page 11, [0081]-[0083]). Lyden teaches adding to the test sample a first primer or probe against of a given gene and measuring the amount of the first primer or probe bound to copies of the given gene, wherein said first primer or probe may be labeled (Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0133] and Pages 17-18, [0136]-[0142]). Lyden teaches adding to the test sample a second primer or probe against WDR1 and measuring the amount of the second primer or probe bound to copies of the at least one internal standard gene, wherein said second primer or probe may be labeled (Page 10, [0074], Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0132]-[0135], Pages 17-18, [0136]-[0142], Page 68, [0199] and Table 1). Lyden teaches normalizing the expression level amount of the first primer or probe bound to copies of the given gene using the expression level amount of the second primer or probe bound to copies of the at least one internal standard gene and calculating the expression level of the given gene in the test sample as a relative value of the amount of the first primer or probe bound to copies of the given gene to the amount of the second primer or probe bound to copies of the at least one internal standard gene (Pages 16-17, [0132]-[0135] and Page 18, [0142]). Lyden teaches detecting the presence or absence of HER2 (Page 14, [0114]).
Regarding claim 2, Lyden teaches the test sample is a sample derived from a breast cancer patient (Page 8, [0054]).
Regarding claim 3, Lyden teaches the given gene is a gene for identifying or classifying a subtype of breast cancer (Page 9, [0067] and Page 14, [0114]).
Regarding claim 7, Lyden teaches a composition for expression analysis of an internal standard gene, comprising nucleic acid molecules obtained from a breast cancer tissue or a normal mammary gland tissue (Abstract, Page 3, [0019], Page 8, [0054], Page 9, [0062] and [0067], Page 14, [0115] and Page 11, [0081]-[0083]). Lyden teaches a unit for measuring an expression level of the internal standard gene for gene expression analysis consisting of at least WDR1 (Page 10, [0074], Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0133], Pages 17-18, [0136]-[0142], Page 68, [0199] and Table 1). Lyden teaches the unit for measuring an expression level of the gene is at least one unit selected from the group consisting of a primer and a probe against the gene, and labeled forms thereof and a nucleic acid polymerase (Page 10, [0074], Page 14, [0115]-[0116], Page 15, [0127], Page 16, [0130], Pages 16-17, [0133], Pages 17-18, [0136]-[0142], Page 68, [0199] and Table 1).
Regarding claim 14, Lyden teaches a gene expression analysis method for a test sample obtained from a breast cancer tissue or a normal mammary gland tissue (Abstract, Page 3, [0019], Page 8, [0054], Page 9, [0062] and [0067] and Page 11, [0081]-[0083]). adding to the test sample a first primer or probe against a given gene and measuring the amount of the first primer or probe bound to copies of the given gene, wherein said first primer or probe may be labeled (Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0133] and Pages 17-18, [0136]-[0142]). Lyden teaches adding to the test sample a second primer or probe against an internal standard gene and measuring the amount of the second primer or probe bound to copies of the at least one internal standard gene, wherein said second primer or probe may be labeled (Page 10, [0074], Page 14, [0115]-[0116], Page 15, [0127], Pages 16-17, [0133], Pages 17-18, [0136]-[0142], Page 68, [0199] and Table 1). Lyden teaches normalizing the amount of the first primer or probe bound to copies of the given gene using the amount of the second primer or probe bound to copies of the at least one internal standard gene and calculating the expression level of the given gene in the test sample as a relative value of the amount of the first primer or probe bound to copies of the given gene to the amount of the second primer or probe bound to copies of the at least one internal standard gene (Pages 16-17, [0132]-[0135] and Page 18, [0142]). Lyden teaches detecting the presence or absence of HER2 (Page 14, [0114]).
Regarding claim 15, Lyden teaches making copies of the given gene and the internal standard gene using polymerase chain reaction (PCR) (Page 11, [0083], Pages 13-14, [0113] [0115]-[0117], Page, 15, [0127], Page 17, [0134] and Page 18, [0142]).
Regarding claim 16, Lyden teaches making copies of the given gene and the internal standard gene using polymerase chain reaction (PCR) (Page 11, [0083], Pages 13-14, [0113] [0115]-[0117], Page, 15, [0127], Page 17, [0134] and Page 18, [0142]).
Lyden does not teach or suggest the breast cancer tissue is classified into any one subtype of breast cancer selected from the group consisting of luminal A, luminal B (HER2-positive), luminal B (HER2- negative), HER2-positive, HER2-positive-like, triple negative, phyllodes tumor, squamous cell cancer, indeterminable, and normal-like. Lyden does not teach or suggest adding to the test sample a second primer or probe against at least one internal standard gene specifically selected from the group consisting of ABCF3, MLLT1, FAM234A, PITPNM1, and AP2A1.
Kabos teaches a gene expression analysis method from a test sample obtained from a breast cancer tissue or a normal mammary gland tissue (Abstract). Kabos teaches using the Affymetrix Human Gene 1.1 ST Array (i.e., using a primer or a probe for the genes or markers thereof, Page 417, Right Column, Fourth Paragraph- Page 418, Left Column 1, First Paragraph). Kabos teaches using a first primer and second primer that may be labeled, as well as probes that measure all gene family members of a given gene (Page 418, Left Column, Last Paragraph—Right Column, First Paragraph and Page 425, Right Column, Last Paragraph). Kabos teaches normalizing expression data (Figs. 6 and 7). Kabos teaches adding to the test sample a primer or probe against internal standard gene comprising the group: ABCF3, FBXW5, MLLT1, PITPNM1, FAM234A (ITFG3), WDR1, NDUFS7, and AP2A1 (Affymetrix Human Gene 1.1 ST Array data as evidenced by NCBI Gene Expression Omnibus Platform GPL11532, Page 418, Left Column, Last Paragraph—Right Column, First Paragraph, Page 425, Right Column, Last Paragraph and Figs. 6-7). NCBI Gene Expression Omnibus Platform GPL11532 describes the genes measured by the “Affymetrix Human Gene 1.1 ST Array”, which comprise ABCF3, FBXW5, MLLT1, FAM234A (ITFG3), PITPNM1, WDR1, NDUFS7, and AP2A1. Kabos teaches the breast cancer tissue is classified into any one subtype of breast cancer selected from the group consisting of luminal A, luminal B (HER2-positive), luminal B (HER2- negative), HER2-positive, HER2-positive-like, triple negative, phyllodes tumor, squamous cell cancer, indeterminable, and normal-like (Page 420, Left Column, First Paragraph, Page 428, Right Column, Last Paragraph—Page 429, Left Column, First Paragraph).
As a common field of endeavor both Lyden and Kabos disclose methods for gene expression analysis using a first and second probe or primer that may be labeled.
Therefore it would have been prima facie obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Lyden to include the teachings of Kabos, to select at least one gene from the group ABCF3, MLLT1, PITPNM1, and AP2A1 as well as classifying the breast cancer tissue into any one subtype of breast cancer selected from the group consisting of luminal A, luminal B (HER2-positive), luminal B (HER2- negative), HER2-positive, HER2-positive-like, triple negative, phyllodes tumor, squamous cell cancer, indeterminable, and normal-like, as a person of ordinary skill in the art would recognize that these claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome of a method or composition for gene expression analysis. Additionally, in accordance with MPEP 2141 section Ill (A) citing KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 398, 82 USPQ2d 1385, 1395 (2007) combining prior art elements according to known methods to yield predictable results is obvious. There is a reasonable expectation of success of combining Lyden in Kabos, because both disclose methods for gene expression analysis using a first and second probe or primer that may be labeled. Additionally, Lyden discloses the capability to detect/identify the presence or absence of HER2 (Page 14, [0114]), which would allow for further classification of breast cancer into subtypes elected from the group consisting of luminal A, luminal B (HER2-positive), luminal B (HER2- negative), HER2-positive, HER2-positive-like, triple negative, phyllodes tumor, squamous cell cancer, indeterminable, and normal-like, as disclosed by Kabos, therefore the methods of Kabos are well-suited for the methods taught by Lyden.
Response to Arguments
Applicant’s arguments and amendments filed August 25, 2023, with respect to the
rejections under 35 U.S.C. § 112 have been fully considered and are persuasive.
Therefore, these rejections have been withdrawn.
Applicant’s arguments and amendments filed August 25, 2023, with respect to the
rejections under 35 U.S.C. § 101, have been fully considered and are not deemed to be persuasive.
Therefore, these rejections are maintained as discussed above and below.
Applicant asserts that claim 7 is directed to a composition that is not naturally occurring therefore is directed to eligible subject matter. However, as discussed above, claim 7 includes the limitation of classifying a subtype of breast cancer which can be mental process, wherein the human mind is capable of receiving/collecting data, observing/evaluating/determining and organizing information (classifying). Applicant asserts “unlike prior art methods, the normalization and calculation steps of the instant claims (normalizing using a first and second primers/probes), which employ at least one of the claimed genes, as an internal standard gene results in a highly reliable and accurate measurement of relative gene expression levels in breast tissue samples”. These limitations are not integrations of the exception into a practical application. Instead, these elements reciting generic data gathering steps amount to insignificant presolution activity required to perform the method as discussed above. Therefore, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Applicant’s arguments and amendments filed August 25, 2023, with respect to the
rejections under 35 U.S.C. § 102 have been fully considered and are persuasive in part, specifically Shin does not disclose classifying the breast cancer tissue into any one subtype of breast cancer selected from the group consisting of luminal A, luminal B (HER2-positive), luminal B (HER2- negative), HER2-positive, HER2-positive-like, triple negative, phyllodes tumor, squamous cell cancer, indeterminable, and normal-like.
However, upon further consideration, new rejections under 35 U.S.C. § 103 are made in view of Applicant’s amendments.
As discussed above newly cited Lyden and Kabos disclose a gene expression analysis method and composition for a test sample obtained from a breast cancer tissue or a normal mammary gland tissue, comprising the steps of adding to the test sample a first primer or probe against of a given gene and measuring the amount of the first primer or probe bound to copies of the given gene, wherein said first primer or probe may be labeled, adding to the test sample a second primer or probe against at least one internal standard gene selected from the group consisting of ABCF3, FBXW5, MLLT1, FAM234A, PITPNM1, WDR1, NDUFS7, and AP2A1 and measuring the amount of the second primer or probe bound to copies of the at least one internal standard gene. Lyden and Kabos disclose said second primer or probe may be labeled and normalizing the amount of the first primer or probe bound to copies of the given gene using the amount of the second primer or probe bound to copies of the at least one internal standard gene, as well as calculating the expression level of the given gene in the test sample as a relative value of the amount of the first primer or probe bound to copies of the given gene to the amount of the second primer or probe bound to copies of the at least one internal standard gene. Lyden and Kabos disclose the breast cancer tissue is classified into any one subtype of breast cancer selected from the group consisting of luminal A, luminal B (HER2-positive), luminal B (HER2- negative), HER2-positive, HER2-positive-like, triple negative, phyllodes tumor, squamous cell cancer, indeterminable, and normal-like.
Therefore, for these reasons and those listed above Lyden and Kabos are deemed to render the instant invention obvious.
Terminal Disclaimer
The terminal disclaimer filed on November 04, 2025 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of application 17/628,006 has been reviewed and is accepted. The terminal disclaimer has been recorded, and the nonstatutory double patenting rejections have been withdrawn.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684