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 .
Status of Claims
Currently, claims 1-3, 8, 9, 11-13, 16, 17, 19, and newly added claims 20-22 are pending in the instant application. Claims 8, 12, and 16 are withdrawn from consideration as being drawn to non-elected species. Claims 1-3, 9, 11, 13, 17, and 19-22 are currently under examination.
All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant Application. Response to Applicant's arguments follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
It is noted that the claim amendments dated 4/13/2026 do not indicate all of the subject matter that was amended. In the interest of compact prosecution, a final office action is set forth herein. However, applicant should take care to properly annotate all claim amendments. Failure to do so in the future will result in the issuance of a Notice of Non-Responsive Amendment.
Interview
Applicant’s comments regarding the Interview of April 9 is acknowledged. It is noted, however, that the instant claim amendments dated 4/13/2026 were not presented. A copy of the claims discussed is present in the appendix to the interview summary, mailed 4/16/2026. While the examiner did provide guidance as to how to obviate the 101 and 102 rejections, the claims have not been amended sufficiently to overcome the rejections. This is addressed in the appropriate sections below. An allowable claim is also set forth at the end of this office action.
Claim Rejections - 35 USC § 101
Claims 1-3, 9, 11, 13, 17, and 19-22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural correlation/law of nature and an abstract idea without significantly more. This judicial exception is not integrated into a practical application and the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons set forth below.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena 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); see also M.P.E.P. § 2106. The unpatentability of abstract ideas was confirmed by the U.S. Supreme court in Bilski v. Kappos, 561 U.S. 593, 601 (June 28, 2010) and Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014). See also Myriad v Ambry, CAFC 2014-1361, -1366, December 17, 2014. The unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66, 71 (2012). “[L]aws of nature, natural phenomena, and abstract ideas” are not patentable. Dia-mond v. Diehr, 450 U. S. 175, 185 (1981); see also Bilski v. Kappos, 561 U. S. at 601 (2010).
Claims Analysis:
As set forth in MPEP 2106, the claims have been analyzed to determine whether they are directed to one of the four statutory categories (STEP 1).
The instant claims are directed to methods and therefore are directed to one of the four statutory categories of invention.
The claims are then analyzed to determine if they recite a judicial exception (JE) (STEP 2A, prong 1) [Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1293 (2012), Alice Corp. Pry. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347 (2014)].
The claimed invention recites methods for identifying DLBCL or PCNSL by detecting methylation of CpG in different target sequences. However, this recitation is a natural correlation between the presence of methylated CpGs in the targets and DLBCL or PCNSL. With regard to the natural correlation, as in Mayo, the relationship is itself a natural process that exists apart from any human action. Additionally, the recitations of “identifying” in claims 1 and 3, as well as the comparing step in claims 1-3 are directed to abstract ideas because they encompass comparisons and conclusions which can occur entirely within the mind. It is therefore determined that the claims are directed to judicial exceptions.
The claims are then analyzed to determine whether they recite an element or step that integrates the JE into a practical application (STEP 2A, prong 2) [Vanda Pharmaceuticals Inc., v. West-Ward Pharmaceuticals, 887 F.3d 1117 (Fed. Cir. 2018)].
The claims recite steps of detecting the presence of hypermethylated CpG regions however this does not integrate the JE into a practical application because it is a mere data gathering step to use the correlation and does not add a meaningful limitation to the method. Although the claims have been amended to recite “treating a subject identified as having DLBCL or PCNSL with chemotherapy or radiation”, this is not sufficient to integrate the recited JE’s because this is conditional. For example, in claim 1, 2, and its dependents, the recitation of “to identify a subject as having DLBCL or PCNSL” is an intended use limitation and not required by the claims. In claim 2, this conditionality is also evidenced by the phrase “detecting if any CpG regions of the one or more… are hypermethylated”. The newly added “wherein” clause merely recites a property of the hypermethylation, while the treating step appears to be performed to any subject, regardless of the results of the detecting step. In this situation, the treating step has no relationship to the JE’s since it appears all subjects tested are treated, and therefore cannot practically apply the JE. In claim 3, the identifying step and the treating step appear to be dependent on the detecting step in step c, however this step is conditional in that detecting hypermethylation is not required by the claims as evidenced by the use of the term “if”.
In the absence of steps or elements that integrate the JE into a practical application, the additional elements/steps are considered to determine whether they add significantly more to the JE either individually or as an ordered combination, to “’transform the nature of the claim’ into a patent eligible application” [Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1293 (2012), Alice Corp. Pry. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347 (2014)] (STEP 2B).
In the instant situation, the steps of “detecting the presence” of more or more hypermethylated regions or hybridizing nucleic acids with generally recited “QM-MSP” primers and probes for the regions set forth in the claims are recited with a high level of generality and do not provide any particular reagents that might be considered elements that transform the nature of the claims into a patent eligible application because no specific elements/steps are recited. This step is not only a mere data gathering step, but the general recitation of detection of known nucleic acids is well understood, routine, and conventional activity (See MPEP 2106.05(d)(II)). Applicant is reminded that in Mayo, the Court found that “[i]f a law of nature is not patentable, then neither is a process reciting a law of nature, unless that process has additional features that provide practical assurance that the process is more than a drafting effort designed to monopolize the law of nature itself." Further "conventional or obvious" "[pre]solution activity" is normally not sufficient to transform an unpatentable law of nature into a patent-eligible application of such a law”. Flook, 437 U. S., at 590; see also Bilski, 561 U. S., at ___ (slip op., at 14) (“[T]he prohibition against patenting abstract ideas ‘cannot be circumvented by’ . . . adding ‘insignificant post-solution activity’” (quoting Diehr, supra, at 191–192)). The Court also summarized their holding by stating “[t]o put the matter more succinctly, the claims inform a relevant audience about certain laws of nature; any additional steps consist of well understood, routine, conventional activity already engaged in by the scientific community; and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately.” Therefore these limitations/steps do not “‘transform the nature of the claim’ into a patent-eligible application.’” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
When viewed as an ordered combination, the claimed limitations are directed to nothing more than the determination that a natural correlation/phenomena exists. Any additional element consists of using well understood, routine and conventional activity, and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately.
Accordingly, it is determined that the instant claims are not directed to patent eligible subject matter.
Response to Arguments
The response traverses the rejection and asserts that the claims have been amended to recite a specific practical application of a diagnostic method. This argument has been thoroughly reviewed but was not found persuasive for the reasons made of record above. The following exemplary claim would overcome this rejection:
A method of identifying and treating DLBCL and/or PCNSL in a subject comprising:
a) detecting the presence of one or more hypermethylated CpG regions in one or more genes of interest in the DNA from a biological sample obtained from the subject as compared to the methylation level of the one or more genes of interest in a normal or benign tissue sample, wherein the one or more genes of interest are selected from the group consisting of NCOR2, KCNH7, DOCK1…; b) diagnosing the subject as having DLBCL or PCNSL using the methylation levels detected in a); and c) treating the diagnosed subject with chemotherapy or radiation.
Claim Rejections - 35 USC § 112
Claims 1-3, 9, 11, 13, 17, and 19-22 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The claims recite “one or more genes”, however the designation of cg05491001 and cg25567674 do not appear to be directed to any gene, nor is it clear as to which nucleic acid sequence is encompassed by their recitation. While the specification appears to refer to them in the context of Array ID numbers, the specification does not teach which “gene” is encompassed by this designation. Furthermore, the reference to a particular chromosome position is indefinite without a clear definition as to what the chromosomal positions are in reference to. For example, as the genome has been updated over time, chromosomal positions for any particular nucleotide allele change as information is added or deleted from the chromosomal sequences. Therefore, the metes and bounds of the terms are unclear. Likewise, with regard to claims 2 and 3, without a clear indication as to the genomic regions encompassed by the recitation, the metes and bounds of primers and probes to these targets is also unclear.
The claims also refer to cg054 and cg255, however it is not clear if this is merely a shorthand designation for cg05491001 and cg25567674, respectively, or whether they refer to a structurally different target.
The amended claims contain numerous grammatical errors. For example, claim 1 has been amended to recite “one or more genes of interest comprise are selected…”. Therefore it is not clear if the claim requires all of the genes or only “one or more”. Claim 2 has been amended to recite “specific for the CpG regions comprising one or more genes of interest are selected from the group consisting of”. It is not clear what this phrase is attempting to be limited to. Appropriate correction is required.
Response to Arguments
The response traverses the rejection and assert that the claims presented are clear and fully satisfy section 112. This argument has been thoroughly reviewed but was not found persuasive for the reasons made of record above.
Conclusion
No claims are allowed.
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 examiner Jehanne Sitton whose telephone number is (571) 272-0752. The examiner is a hoteling examiner and can normally be reached Mondays-Fridays from 8:00 AM to 2:00 PM Eastern Time Zone.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Winston Shen, can be reached on (571) 272-3157. The fax phone number for organization where this application or proceeding is assigned is (571) 273-8300.
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/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
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