DETAILED ACTION
Comments
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 (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.
Claims 1-15 are pending and examined in the instant Office action.
Information Disclosure Statement
The IDS of 8/9/2024 has been considered.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
Claim 13 recites a data processing apparatus comprising MEANS FOR carrying out steps in claim 1. Page 9, lines 22-27 of the specification disclose that the structure for this “means for” comprises a computer.
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.
35 U.S.C. 101 Rejection #1:
Claims 14-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter. Claim 14 is drawn to a computer program, which is not subject matter eligible. Claim 15 is drawn to a computer-readable medium. Absent a limiting description from the specification, the term “computer-readable medium” is broad enough to comprise transitory elements, such as carrier waves, which are not subject matter eligible.
35 U.S.C. 101 Rejection #2:
Claim(s) 1-15 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Claims 1-12 are drawn to methods, and claim 13 is drawn to a data processing apparatus.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1 : YES; except for claims 14-15) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 1 and 13-15 recite the mental step of comparing methylation levels to reference methylation levels in order to classify the predicted behavior of the Spitzoid tumor.
Each of claims 2-4 recites the metal step of constraining the type of sample.
Claim 5 recites the mental step of classifying the metastatic risk of the AST sample.
Claim 6 recites the mental step of constraining the type of biological sample.
Each of claims 7-8 recites the mental step of constraining the methylation site.
Claim 12 recites the mental step of constraining the subject to be human.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-15 recite(s) an abstract idea/law of nature/natural phenomenon ( Step 2A, Prong 1 : YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment.
As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-15 is/are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
The document of Dorsey et al. [WO 2019/144057 A1; on IDS] teaches that the common techniques for methylation analysis of DNA (e.g. bisulfite sequencing, mass spectrometry, and MS-HRM) are routine and conventional in the prior art.
Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-15 is/are not patent eligible.
Claim Rejections - 35 USC § 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(s) 1-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dorsey et al. [WO 2019/144057 A1; on IDS] in view of Infinium BeadChip [2013].
Claim 1 recites a method for classifying a cutaneous Spitzoid tumor in a subject. The method comprises measuring at least one level of methylation of at least one CpG site in a biological sample obtained from the subject. The at least one CpG site is differentially methylated in Spitzoid tumors, and the tissue sample has been diagnosed as a cutaneous Spitzoid tumor. The method comprises comparing the at least one level of methylation to two different average reference methylation levels obtained from at least two reference biological samples obtained from at least two subjects diagnosed with a benign Spitz nevus and at least two reference biological samples obtained from at least two subjects diagnosed with Spitzoid melanoma. The method comprises classifying the predicted behavior of the cutaneous Spitzoid tumor as a benign Spitz nevus or a Spitzoid melanoma.
Claim 13 is drawn to similar subject matter as claim 1, except claim 13 is drawn to a data processing apparatus.
Claim 14 is drawn to similar subject matter as claim 1, except claim 14 is drawn to a computer program.
Claim 15 is drawn to similar subject matter as claim 1, except claim 15 is drawn to a computer-readable medium.
The document of Dorsey et al. is drawn to methylation markers for melanoma [title]. Paragraph 168 of Dorsey et al. teaches finding distinct patterns of differential methylation in atypical Spitz tumors. Paragraph 168 of Dorsey et al. suggests using the differential methylation patterns to classify a biosample between nevi and melanoma. Paragraph 49 of Dorsey et al. teaches analysis of methylation patterns across a plurality of subjects. Claim 1 of Dorsey et al. teaches differential analysis of methylation patterns to classify a tissue sample between melanoma and benign nevi.
While paragraph 177 of Dorsey et al. teaches validation of published methylation datasets using Illumina 450K methylation data, Dorsey et al. does not point out the seven methylation sites used for analysis in the claims. Infinium BeadChip teaches that the seven methylation sites are within the (about) 450,000 methylation site within the Illumina 450K methylation dataset.
With regard to claims 2-4, paragraph 168 of Dorsey et al. references nevi, Spitzoid melanoma, and atypical Spitzoid tumors.
With regard to claim 5, paragraph 53 of Dorsey et al. teaches melanomas with different metastatic risks.
With regard to claim 6, claim 24 of Dorsey et al. teaches biopsies.
With regard to claims 7-8, Infinium BeadChip teaches that seven methylation sites are within the (about) 450,000 methylation site within the Illumina 450K methylation dataset.
With regard to claim 9, paragraph 111 of Dorsey et al. teaches the use of mass spectroscopic detection methods.
With regard to claim 10, paragraph 78 of Dorsey et al. teaches bisulfite sequencing.
With regard to claim 11, paragraph 110 of Dorsey et al. teaches MS-HRM.
With regard to claim 12, paragraph 98 of Dorsey et al. teaches a human subject.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant invention to use the differential methylation analysis of Dorsey et al. with the Infinium BeadChip wherein the motivation would have been that the Infinium BeadChip provides a resource to simultaneously interrogate thousands of methylation sites on DNA [Infinium BeadChip database cited on page 1 of Infinium BeadChip]. There would have been a reasonable expectation of success in combining Dorsey et al. with Infinium BeadChip because paragraph 177 of Dorsey et al. already teaches Illumina 450K methylation dataset for data validation regarding published studies examining melanoma.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/Primary Examiner, Art Unit 1686 28 September 2026
