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 .
This Office Action is in reply to Applicants’ correspondence of 11/07/2025. Applicants’ remarks and amendments have been fully and carefully considered but are not found to be sufficient to put this application in condition for allowance. New grounds of rejection are presented in this Office Action. Any rejections or objections not reiterated herein have been withdrawn in light of the amendments to the claims or as discussed in this Office Action. This Action is NON-FINAL.
Please note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Status
Claims 11, 13, and 20-23 are pending and being examined on the merits.
Specification
The objections to the specification are withdrawn in light of Applicant’s amendments.
Claim Objections
The objection to claim 12 is withdrawn in light of Applicant’s cancellation of claim 12. It is acknowledged that the informality noted (“log10(LMNA expression)” vs “-log10(LMNA expression)”) was corrected when the limitations of claim 12 were added to claim 11.
Claim Rejections - 35 USC § 112b – Indefiniteness
Withdrawn 112b: The rejection of claims 11-13 under 35 U.S.C. 112(b) as detailed in the Office Action of 5/7/2025 is withdrawn in light of Applicant’s amendments to the claims and cancellation of claim 12.
New 112b:
Claims 11, 13, and 20-23 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 11 is directed to a method of endometriosis diagnosis. However, diagnosing the patient with endometriosis is not required by said claim. Step (d) recites “when the determined gene signature value is above the defined threshold, diagnosing the patient under study with endometriosis” (emphasis added) after having compared the value of the combination of gene expression levels to a defined threshold. However, the scope of this claim also encompasses wherein the value is not above the defined threshold, which would not result in a diagnosis of endometriosis. Therefore, given that the preamble of the claim is to a method of diagnosing endometriosis and diagnosing a patient with endometriosis is not required, the claim is indefinite.
Claim 13 depends from claim 11, inherits this deficiency, and is rejected on the same basis.
Claim 20 is directed to a method of diagnosing endometriosis in a patient. However, diagnosing the patient with endometriosis is not required by said claim. Step (c) recites “diagnosing the patient with endometriosis when the detected gene signature value is above the threshold value” (emphasis added). Therefore, the scope of the claim also encompasses a gene signature value below the threshold value and not diagnosing the patient with endometriosis. Given that the preamble of the claim is to a method of diagnosing endometriosis and diagnosing a patient with endometriosis is not required, the claim is indefinite.
Claims 21-23 depend from claim 20, inherit this deficiency, and are rejected on the same basis.
Claim 23 is directed to the method of claim 20 “wherein the threshold is ‘-14’”. However, there is no equation presented that would lend clarity as to how -14 is arrived at as a threshold value. It is unclear, in claim 23, how “-14” is calculated just from the limitations of claim 20. Claim 20 states that the threshold value is a combination of the gene expression levels of LMNA, KDM6B, CIC, PER1, and PPDPF with minimized Type I and Type II error rates for a given device, but no device is provided and no equations are presented to make -14 make sense as a threshold value. Clarification is required.
Claim Rejections - 35 USC § 101
Claims 11, 13, and 20-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (e.g.: a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The claim(s) is/are directed to a judicial exception encompassing abstract ideas and natural phenomena. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception as set forth below. The judicial exception is not integrated into a practical application of the judicial exception.
The unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., No. 10-1150 (March 20, 2012). “[L]aws of nature, natural phenomena, and abstract ideas” are not patentable. Diamond v. Diehr, 450 U. S. 175, 185 (1981); see also Bilski v. Kappos, 561 U. S._, (2010) (slip op., at 5). “Phenomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U. S. 63, 67 (1972).
Additionally, the unpatentability of abstract ideas was confirmed by the U.S. Supreme court in Bilski v. Kappos, No. 08-964, 2010 WL 2555192 (June 28, 2010) and in Alice Corp. v. CLS Bank Inti, 134 S. Ct. 2347, 2354 (2014).
The following inquiries are used to determine whether a claim is drawn to patent- eligible subject matter:
Step 1. Is the claim to a process, machine, manufacture, or composition of matter? Yes - the claims are directed to methods.
Step 2A, prong 1. Is the claim directed to a law of nature, a natural phenomenon, or an abstract idea (judicially recognized exceptions)? Yes — Where the claims are directed to “calculating and minimizing Type I error rate and Type II error rate” and calculating gene expression levels as the sum of the logarithms of normalized gene expression using a generic device and diagnosing endometriosis by comparing a determined value to a threshold, the claim is directed to an abstract idea (mental process and mathematical process). Where the claim is directed to the association of the expression levels of a set of genes and a diagnosis of endometriosis the claim is directed to a natural phenomenon (a gene-expression:phenotype relationship).
Step 2A, prong 2. Does the claim integrate the judicial exception into a practical application? No - The judicial exception(s) to which the claims are directed are not integrated into a practical application because there are no required particular practical steps recited with specificity related to the endometriosis diagnosis, such as applying a particular endometriosis treatment to the subject. Furthermore, as noted in the 112b rejection above, the claims (11 and 20) do not require that endometriosis be diagnosed in a patient.
Step 2B. Does the claim recite additional elements that amount to significantly more than the judicial exception? No - The claims recite only routine steps related to measuring gene expression. It is known in the art to measure gene expression in relation endometriosis, as evidenced by the GEO data set GSE135485, published on October 1, 2019, which is a data set of expression profiling via high throughput sequencing in endometrial samples (GSE135485, 2019).
Additionally, it is noted that the specification indicates that the practical step of using a device to measure gene expression would be known to experts in the field. For example, the specification provides (page 14, lines 3-7), that experts in the field would understand how the methodology of determining gene expression would vary depending on the device used and the configuration that would be needed for said device.
So even where a practical step of the claim may require measuring gene expression or calculating and minimizing Type I and Type II error rates using conventional methods that have been practiced in the art, in University of Utah Res. Foundation v. Ambry Genetics Corp. (Fed Cir, 2014), the Court addressed claims that recite known methodological steps for collecting data (specifically genetic information) to be used in the application of a judicial exception, and held that:
Having determined that the comparison steps of claims 7 and 8 are abstract ideas, we move to the second step of Alice and ask whether the particular mechanism for the comparisons added by claims 7 or 8 renders the claims patent-eligible. For this step, Alice dictates that we ask whether the remaining elements, either in isolation or combination with the other non-patent-ineligible elements, are sufficient to “transform the nature of the claim’ into a patent-eligible application.” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297). There must be a further inventive concept to take the claim into the realm of patent-eligibility. Id. at 2355. The second paragraph of claim 7 describes the way in which the sequences are compared: they are compared by 1) hybridizing a BRCA gene probe and 2) detecting the presence of a hybridization product. Similarly, claim 8 requires 1) amplification of the BRCA1 gene and 2) sequencing of the amplified nucleic acids. The non-patent-ineligible elements of claims 7 and 8 do not add “enough” to make the claims as a whole patent- eligible.
Additionally, In University of Utah Research v. Ambry Genetics the courts stated, "Recently in Alice the Supreme Court reiterated its two-step test to determine patent eligibility for any claims that allegedly encompass abstract ideas. First, "we determine whether the claims at issue are directed to [a] patent-ineligible concept. If so, we then ask, ‘what else is there in the claims before us?" Id. at 2355 (quoting Mayo, 132 S. Ct. at 1296-97) (citations and punctuation omitted). That is, we next ask whether the remaining elements, either in isolation or combination with the other non-patent- ineligible elements, are sufficient to " ‘transform the nature of the claim’ into a patent- eligible application." Id. at 2355 (quoting Mayo, 132 S. Ct. at 1297). Put another way, there must be a further "inventive concept" to take the claim into the realm of patent eligibility."
For these reasons the claims are rejected under 35 USC 101 as directed to subject matter that is not significantly more than a judicial exception.
Response to Remarks
As noted in the Remarks of 11/7/2025, the previous Office Action of 5/7/2025 did not include the subject matter of claim 12 (or claim 13) in the rejection of claim 11 under 35 USC 101. Upon further consideration, the contents of claim 12 (now claim 11 and similarly represented in claim 21), are included in a new rejection of all claims under 35 USC 101, for the reasons presented above. Due to this new rejection, this Office Action is Non-Final.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683