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 .
Election/Restrictions
It is acknowledged that in the reply filed July 13, 2026, Applicant elected Group 4, claims 20, 21, 23, 25-28, 34, 35, 49, 54 61, 69, and 72 as well as species (A) AFP, (B) chr17_57915773-57915774, and (C) a methylation profile, without traverse. In the reply, Applicant amended claims 1, 15, 16, 49, and 54.
Claims 1, 15, 16, 20, 21, 23, 25-28, 34, 35, 49, 54, 57-61, 69, 72, 74, 76, 83 are currently pending.
Claims 1, 15, 16, 25, 57-60, 74, 76, and 83 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected subject matter, there being no allowable generic or linking claim. In the case of claim 25, the nonelected subject matter is the unelected species comprising the combination of all recited CpG sites. Election was made without traverse in the reply filed on July 13, 2026.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 have been examined herein to the extent that they read the elected species.
Priority
It is acknowledged that the instant application is a 371 of international PCT Application NO. PCT/US2022/025826, filed April 21, 2022, and that is claims benefit of provisional 63/177,933, filed April 21, 2021. The effective filing date of the claims and species under examination is considered to be April 21, 2021.
Regarding claim 21, the specification indicates that the elected species chr17_57915773-57915774 reads on the gene MIR21 (Table 11). However, MIR21 (as well as several other of the recited genes of claim 21) does not appear to be supported by the provisional application. The provisional disclosure does not explicitly recite MIR21 and appears to instead support the association of gene VMP1 with the elected CpG site chr17_571915773-57915774 (pg. 56). MIR21 and VMP1 occupy overlapping but distinct regions within chromosome 17 (see discussion of MIR21’s location in the rejections under 35 U.S.C. 112(b) below). Therefore, the effective filing date of claim 21 is considered to be April 21, 2022, which is the filing date of the PCT application.
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.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 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.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected because the CpG sites are recited in Table 11 as chromosomal positions, but the claims are not restricted to a particular genome build or reference. Chromosomal positions are relative, and the same coordinates may refer to different sequences depending on the reference used. It is unclear whether the claimed CpG sites are intended to be restricted to hg19 (par. 243), or if the claims could encompass the same coordinates in a number of different reference genomes. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected for referring to specific figures and/or tables in the specification. MPEP 2173.05(s) states that “Where possible claims are to be complete in themselves. Incorporation by reference to a specific table or figure ‘is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicated a drawing or table into a claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.”"
Claim 21 is rejected because it is unclear which of the recited genes are intended to be encompassed by the elected CpG site. According to the specification, the elected species chr17_57915773-57915774 is associated with the gene MIR21 (pg. 23, Table 11). However, in UniProt, MIR21 is indicated as lying in the range chr17:57918627-57918698 (using hg19, consistent with the instant specification – see below). Given these contradictions, is not clear how a person with ordinary skill in the art would assess whether a CpG site is “of” a particular gene. Does the claim encompass CpG sites which are within a gene, within a certain distance of a gene, which are operatively associated with a particular gene, or is something else required? For the purposes of compact prosecution, both possible ranges for CpG sites “of” MIR21 are addressed in the prior art rejections below.
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Claim 26 is rejected as indefinite over the recitation of “β-value.” It is unclear whether “β-value” merely identifies the value (and all requirements of said value are set forth in the claim), or if “β-value” is intended to indicate additional structural requirements beyond those recited in the claims. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
Claim 61 is rejected as indefinite over the recitation of “the polypeptide profile.” This phrase lacks antecedent basis because the claim on which it depends does not recite a polypeptide profile. It is therefore unclear whether any polypeptide profile would meet this limitation or if there is a particular polypeptide profile which is required. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
Claim 61 is rejected as indefinite over the recitation of “the demographic profile.” This phrase lacks antecedent basis because the claim on which it depends does not recite a demographic profile. It is therefore unclear whether any demographic profile would meet this limitation or if there is a particular demographic profile which is required. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter.
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 therefore, subject to the conditions and requirements of this title.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4, Monday, January 7, 2019).
Step 1: The claims are directed to the statutory category of a process.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
The instant claims recite a natural phenomenon. The claims are directed to the naturally occurring methylation status of CpG sites present in samples obtained from individuals.
The instant claims recite abstract ideas. The claims recite steps of “determining” a methylation status and “generating” a methylation or biomarker profile. Neither the specification nor the claims set forth a limiting definition for “determining” or “generating” and the claims do not set forth how this step is accomplished. The “determining” or “generating” steps broadly encompass mental processes. For example, one may “determine” a methylation status by looking at data and thinking about whether a site is methylated or not and one may "generate" a profile by looking at data and thinking about how it relates to a specific site. Mental processes, which are concepts performed in the human mind (including observation, evaluation, judgement, and opinions) are considered to be abstract ideas.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
The claims do NOT recite additional steps or elements that integrate the recited judicial exception(s) into a practical application of the exception(s). For example, the claims do not practically apply the judicial exception by including one or more additional elements that the courts have stated integrate the exception into a practical application:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or a technological field;
An additional element that applies or used a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
An additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
An additional element effects a transformation or reduction of a particular article to a different state or thing;
An additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
In addition to the judicial exceptions, claim 34 recites a step of “performing” next generation sequencing. This step is not considered to integrate the judicial exceptions into a practical application because it merely adds insignificant extra-solution activity (data gathering) to the judicial exceptions.
In addition to the judicial exceptions, claim 35 recites a step of “obtaining” treated genomic DNA derived from a sample. This step is not considered to integrate the judicial exceptions into a practical application because it merely adds insignificant extra-solution activity (data gathering) to the judicial exceptions.
In addition to the judicial exceptions, the claim 61 recites “providing” methylation, polypeptide, and demographic profiles to a machine learning classifier. This step is not considered to integrate the judicial exception into a practical application because it fails to meaningfully limit the claims and is the equivalent of adding the words “apply it” to the judicial exceptions.
In addition to the judicial exceptions, the claims recite limitations of the sample, the individual, the CpG sites, and the biomarker profile. The claims also recite limitations of how the methylation status is determined (claims 26-28) and how the biomarker profile is generated (claim 61). These elements fail to meaningfully limit the claims and are the equivalent of adding the words “apply it” to the judicial exceptions.
Step 2B: Evaluate Whether the Claim Provides and Inventive Concept
In addition to the judicial exceptions, the claims recite steps of “performing” next generation sequencing, “obtaining” treated genomic DNA, and “providing” profiles to a machine learning classifier. In addition to the judicial exceptions, the claims recite limitations of the sample, the individual, the CpG sites, the biomarker profile, how methylation status is determined, and how the biomarker profile is generated. These limitations do not amount to significantly more because they simply append well-understood, routine, and conventional activities previously known in the art, specified at a high level of generality, to the judicial exceptions.
These steps are recited a high level of generality. “Performing” next generation sequencing, “obtaining” treated genomic DNA, and “providing” profiles to a machine learning classifier merely instruct a scientist to use any known technique for those steps. The additionally recited limitations of the sample, the individual, the CpG sites, the biomarker profile, how methylation status is determined, and how the biomarker profile is generated are generic. The claims do not require the use of any particular non-conventional reagents or equipment or methodology. When recited at this high level of generality, there is no meaningful limitation that distinguishes the steps from well-understood, routine, and conventional activities engaged in by scientists prior to applicant’s invention and at the time the application was filed.
Additionally, the teachings in the specification demonstrate the well-understood, routine, and conventional nature of additional elements because it teaches that the additional elements are well-known or commercially available. For example, the specification teaches the following:
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Further, it is noted that the courts have recognized the following laboratory techniques as well-understood, routine, and conventional activity in the life science arts when they are claimed in a merely generic manner (e.g. at a high level of generality) or as insignificant extra-solution activity.
Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
For the reasons set forth above the claims are not directed to patent eligible subject matter.
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 pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected under 35 U.S.C. 102(a)(1) as anticipated by Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039).
Regarding claim 20, Zhang recites a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (par. 130, 135). Zhang teaches determining a methylation status for each of the one or more CpG sites of the methylation profile from a treated genomic DNA derived from the sample (par. 139) and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (par. 72-73).
Regarding claims 20, 21, and 23, Zhang recites CpG sites explicitly comprising cg15759721, cg07181702, and cg18942579 (par. 73; pg. 31-33, Table 7). The positions of these sites in hg19 are as indicated below:
Identifier
Position
cg15759721
chr17:57918630
cg07181702
chr17:57918683
cg18942579
chr17:57915774
cg15759721 and cg07181702 fall within the area encompassed by MIR2 (chr17:57918627-57918698, according to UniProt), and cg18942579 falls within the boundaries of the elected range (chr17:57915773-57915774). Therefore, Zhang teaches a method of generating a biomarker profile comprising data of the elected CpG site and associated gene MIR21.
Regarding claim 26, Zhang recites that the methylation status of each CpG site is based on a β-value, and wherein the β-value of a CpG site is determined based on the proportion of instances of methylation at the CpG site divided by the sum of the instances of methylation at the CpG site plus the instances where the CpG site is not methylated (par. 199, 228, 325)
Regarding claim 27, Zhang recites that the methylation status is determined using sequencing information derived from the treated genomic DNA (par. 199, 202).
Regarding claims 28 and 34, Zhang recites that the sequencing information is obtained using a next generation sequencing technique and performing said technique (par. 87, 159).
Regarding claim 35, Zhang recites obtaining the treated genomic DNA derived from the sample (par. 132; reference claims 18 + 22)
Regarding claim 49, Zhang recites that the biomarker profile further comprises a polypeptide profile of the individual, wherein the polypeptide profile comprises data of an alpha fetoprotein (AFP) level (par. 247).
Regarding claim 54, Zhang recites that the biomarker profile further comprises a demographic profile of the individual, wherein the demographic profile comprises the age of the individual and/or the sex of the individual (par. 247).
Regarding claim 61, Zhang recites that generating the biomarker profile comprises providing the methylation profile, a polypeptide profile, and/or a demographic profile to one or more machine learning classifiers to generate a biomarker profile (par. 167; par. 247).
Regarding claim 69, Zhang recites that the sample may be a blood sample (par. 91).
Regarding claim 72, Zhang recites that the individual is suspected of having a liver cancer (par. 4).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of Patent No. 10,513,739, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 1, 7)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 7, 8)
treated genomic DNA derived from the sample (claim 1)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate or exchange CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF).
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of Patent No. 12,359,257, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 1)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 1, 3)
treated genomic DNA derived from the sample (claim 1, 8-10)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF).
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of Patent No. 12,351,876, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 1)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 1, 4)
treated genomic DNA derived from the sample (claim 1, 9-11)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF).
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of Patent No. 12,359,258, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 1)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 1, 3)
treated genomic DNA derived from the sample (claim 1, 9-11)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF).
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 6-10, 12-15, 17, 18, 22, 26, 29-32, 37, and 39 of co-pending Application No. 18/116,196, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 1, 7)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 1)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF). Although the reference does not explicitly require a treated genomic DNA derived from the sample, it would be obvious to one with ordinary skill in the art to use treated DNA for methylation analysis (Zhang: par. 139). This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, 7, 9-11, 14, 15, 20, 24, 26-28, 33, 38, 40, 42, 43, 45, 48, 52 of co-pending Application No. 18/555,639, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 1)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 1, 2)
treated genomic DNA derived from the sample (claim 3, 5)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF). This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 20, 21, 23, 26-28, 34-35, 49, 54, 61, 69, and 72 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 43-58, 62-65 of co-pending Application No. 18/684,140, in view of Zhang (published September 27, 2018; Patent Application Publication No. US 20180274039) and Illumina (publicly available May 23, 2013; accessed from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html; relevant entries summarized in attached PDF).
Although the claims at issue are not identical, they are not patentably distinct from one another. Both sets of claims are drawn to methods. Both sets of claims require:
a method of generating a biomarker profile from a sample obtained from an individual, wherein the biomarker profile comprises a methylation profile comprising data of one or more CpG sites (claim 43, 44)
determining a methylation status for each of the one or more CpG sites of the methylation profile from and generating the methylation profile based on the methylation status of the one or more CpG site of the methylation profile to generate the biomarker profile (claim 44)
Although the reference does not explicitly require that the CpG sites encompass the elected species – either the range of MIR2 (chr17:57918627-57918698) or the explicitly claimed range of chr17:57915773-57915774 – it would be obvious to incorporate CpG sites such as those required by the instant claims, using a tools such as the Infinium 450K Methylation Array (Zhang: par. 196) which includes said CpG sites (see Illumina PDF). Although the reference does not explicitly require a treated genomic DNA derived from the sample, it would be obvious to one with ordinary skill in the art to use treated DNA for methylation analysis (Zhang: par. 139). This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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