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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/29/2025 has been entered.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/104,785 filed 01/18/2015 is acknowledged.
Status of claims
Claims 1-26, 28-30, 32, 36-38 and 40-41 are cancelled.
Claims 27, 31, 33-35, 39 and 42-43 are pending and are examined on the merits.
Withdrawn Rejections/Objections
The objections to claim 27 in the Office action mailed 30 June 2025 is withdrawn in view of the claim amendments filed 29 December 2025.
The rejections to claims 27, 31, 33-35, 39 and 42-43 under 35 U.S.C. §112(b) in the Office action mailed 30 June 2025 is withdrawn in view of the claim amendments filed 29 December 2025.
Claim Rejections - 35 USC § 101
This rejection is maintained from a previous Office action. Modification are necessitated by claim amendments.
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 27, 31, 33-35, 39 and 42-43 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
27, 31, 33-35, 39 and 42-43 are directed to a process, here a "method", with a series functional steps like “obtaining”, “treating”, and “mapping”.
Step 2A Prong One: Identification of Abstract Ideas
The claims recite:
Mapping the sequencing reads to a reference sequence of the human genome using a software tool to determine a methylation status of a biomarker from the cfDNA biological sample from the human individual suspected of having the cancer.
----This step recites the comparison of two sequences and then to draw a conclusion (to determine a methylation status of a biomarker). Although recited as done by a software tool (and implicitly using a computer), nothing can stop human mind from performing such a judgement/decision-making activity based on sequence comparison. Therefore this step equates to an abstract idea of mental processes.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of mapping the sequencing reads to a reference sequence of the human genome using a software tool to determine a methylation status of a biomarker from the cfDNA biological sample from the human individual suspected of having the cancer, which is directed to an abstract idea of mental processes. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses 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; and
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.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
obtaining a cfDNA biological sample from the human individual (claim 27);
treating the cfDNA biological sample from the human individual to obtain a treated cfDNA suitable for methylation analysis (claim 27);
performing a next- generation sequencing technique on the treated cfDNA to generate sequencing reads each comprising a nucleic acid sequence of an associated treated cfDNA (claim 27);
wherein the treated genomic DNA cfDNA is generated from an extracted genomic DNA liquid sample from the human individual and treated with a deaminating agent (claim 31);
wherein the cancer is a solid cancer or a hematologic malignant cancer (claim 33);
wherein the cancer is a metastatic cancer-or a relapsed or refractory cancer (claim 34);
wherein the cancer is lung cancer, colon cancer, breast cancer, or liver cancer (claim 35);
wherein the cfDNA biological sample comprises a circulating tumor DNA sample cfDNA from the cancer (claim 39);
wherein the treating converts unmethylated cytosines to uracil (claim 42);
wherein the liquid sample from the human individual is blood, urine, sera, plasma, or cerebral spinal fluid (claim 43).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the above additional elements are all about sample processing and sequence data acquiring.
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of sample handing and sequence acquiring. Data acquiring is insignificant extra-solution activities because the data gathering/outputting are necessary for data analysis (MPEP 2106.05(g)).
The courts have recognized the following laboratory techniques as well-understood, routine, 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
v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546.
The recites subject matter is about analyzing the methylation profiles in the cfDNA samples. Hence, none of the additional element is significant enough to be significantly more.
Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Applicant’s Argument
In the Remarks filed 12/29/2025, Applicant argued (page 7, paras 2-3) that amended claims recite the mapping step is done “using a software tool” and “thus cannot be performed in the human mind”. Applicant’s argument refers to Step 2A/Prong one in the 101 analysis, relating to whether claims recite abstract ideas or not.
To response, Applicant’s argument is not persuasive. The step recites the comparison of two sequences and then to drawing a conclusion (to determine a methylation status of a biomarker), although recited as done by a software tool (and implicitly using a computer), nothing can stop the human mind from performing such a judgement/decision-making activity based on sequence comparison. The recited steps themselves are generic and embrace only routine and conventional computer/software operations to be used in sequence mapping analysis. Thus these generic computer elements do not present anything significantly more than the abstract idea to be “applied” using a generic computer with software tools.
Therefore this step equates to an abstract idea of mental processes.
In the Remarks filed 12/29/2025, Applicant argued (page 7, 4th para through page 9, 2nd para) that amended claims present a technological improvement to the technical field of cfDNA methylation profiling assays. Applicant’s argument refers to Step 2A/Prong two in the 101 analysis, relating to whether claims are integrated into a practical application or not.
To response, Applicant’s argument is not persuasive. At Step 2A/Prong two in the 101 analysis, additional elements other than the judicial exceptions are searched. To integrate claims into a practical application, additional elements will apply, capture and reflect the judicial exceptions. In the instant claims, such an additional element (or the combination of additional elements) are not identified.
Therefore, the 1010 rejection is maintained.
Claim Rejections - 35 USC § 103
The instant rejection is maintained from the previous Office Action filed 6/30/2025 and modified in view of Applicant’s amendments filed 12/29/2025.
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 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 27, 31, 33-34, 39 and 42-43 are rejected under 35 U.S.C. 103 as being unpatentable over Lo et al.: (“Non-invasive determination of methylome of fetus or tumor from plasma”, US 2014/0080715 A1, published 3/20/2014. Cited on the 02/14/2018 IDS), in view of Zhai et al. (“Genome-wide DNA Methylation Profiling of Cell-Free Serum DNA in Esophageal Adenocarcinoma and Barrett Esophagus”, Neoplasia, Volume 14, Issue 1, 2012, Pages 29-IN4. Previously cited).
Claim 27 is drawn to a method for determining a methylation status of a biomarker in a cell-free DNA (cfDNA) biological sample from an individual. Similar to the claim limitations, Lo teaches the method steps of claim 27 as follows:
With respect to: “A method of detecting a methylation profile from a cell-free DNA (cfDNA) biological sample from a human individual suspected of having a cancer, wherein the methylation profile comprises data of a biomarker”, Lo provides detecting human methylation profiles, using cell free DNA (cfDNA), including for the analysis of the presence or absence of cancer (tumors). (Abstract).
With respect to: “the method comprising: obtaining a cfDNA biological sample from the human individual;” Lo provides the use of plasma, or serum, from a human individual, at [0047, et al.].
With respect to: “treating the cfDNA biological sample from the human individual to obtain a treated cfDNA suitable for methylation analysis;” Lo provides treating the cell-free sample to obtain a treated cfDNA “suitable for analysis” at [0059-0064], Fig 1, [0070-0087] et al..
With respect to “performing a next generation sequencing technique on the treated cfDNA to generate sequencing reads”, Lo provides sequence reads and the sequencing depth achieved per sample. (Fig. 21B, Fig. 27I, [032, 038, 049]).
With respect to: “mapping the sequencing reads from the next-generation sequencing technique to a reference sequence of the human genome to determine a methylation status of the biomarker and”, Lo provides mapping the sequence read to a reference sequence to determine a methylation status at least at [0049, 0066-0067, 086, 0188, 0242, 0356].
Lo does not clearly describe the loci for the biomarkers in cg terms. However, Lo employs the Illumina Infinium HumanMethylation 450K beadchip sequencing array. [0082, 0360], and bisulfite sequencing on plasma and tissue samples of a hepatocellular carcinoma (HCC) patient [0267]. Lo’s “massively parallel sequencing” [0267] is interpreted as the next-generation sequencing under a broadest reasonable interpretation (BRI). Lo’s “Methy-Pipe” (P. Jiang, et al. Methy-Pipe: An integrated bioinformatics data analysis pipeline for whole genome methylome analysis, paper presented at the IEEE International Conference on Bioinformatics and Biomedicine Workshops, Hong Kong, 18 to 21 Dec. 2010) anticipates the “software tool” in claim 27.
In the same field of methylome analysis of DNA, Zhai disclosed a genome-wide DNA methylation profiling of cell-free serum DNA study, a subject matter that reads on the instant claim. More specifically, Zhai teaches the Illumina Infinium HumanMethylation27 BeadChip (Illumina, San Diego, CA) to analyze DNAm profiles. The BeadChip contains 27,578 highly informative CpG loci covering more than 14,495 genes [31] (last para, col 1, pg. 30). The Illumina Infinium HumanMethylation27 BeadChip has some the biomarkers (such as cg10590292, cg20261167).
Zhai provides “We used the Illumina Infinium HumanMethylation27 BeadChip
(Illumina, San Diego, CA) to analyze DNAm profiles. The BeadChip contains 27,578 highly informative CpG loci covering more than 14,495 genes [31]. DNA samples were bisulfite converted, then whole-genome amplified (WGA), enzymatically fragmented, and hybridized to the array” (last para, col 1, pg. 30), which teaches methylation profiling using bisulfite treated sample and biomarkers.
Regarding claim 31, Zhai provides “We used the Illumina Infinium HumanMethylation27 BeadChip (Illumina, San Diego, CA) to analyze DNAm profiles. The BeadChip contains 27,578 highly informative CpG loci covering more than 14,495 genes [31]. DNA samples were bisulfite converted, then whole-genome amplified (WGA), enzymatically fragmented, and hybridized to the array” (last para, col 1, pg. 30), which teaches treating the genomic DNA with a deaminating agent.
Lo also taught bisulfite sequencing for detecting CpG methylation status plasma and tissue samples of a hepatocellular carcinoma (HCC) patient (par. [0267]).
Regarding claim 33, Lo does not specify solid cancer or hematological cancer. Zhai teaches the solid tumors (“esophageal adenocarcinoma (EA) and Barrett esophagus”, Title and Abstract, pg. 29).
Regarding claim 34, Lo does not specify metastatic cancer or relapsed or refractory cancer. Zhai provides “Matched serum and tissue samples were obtained from eight randomly selected EA patients. Additional serum samples were collected from 10 BE patients and 10 healthy controls [28,29]. EA and BE were
incident cases of histologically confirmed patients, and all subjects were recruited from Massachusetts General Hospital (Boston, MA). EA is defined as a tumor center located at or above the gastroesophageal junction and had at least two-thirds of the bulk tumor located in the esophagus; and BE is defined as pathologically confirmed intestinal metaplasia [30]” (penultimate para, lines 1-9, col 1, pg. 30), which teaches metastatic cancer.
Regarding claim 39, Lo is not explicit on cfDNA from cancer. Zhai provides “Matched serum and tissue samples were obtained from eight randomly selected EA patients. Additional serum samples were collected from 10 BE patients and 10 healthy controls [28,29]. EA and BE were coincident cases of histologically confirmed patients, and all subjects were recruited from Massachusetts General Hospital (Boston, MA). EA is defined as a tumor center located at or above the gastroesophageal junction and had at least two-thirds of the bulk tumor located in the esophagus; and BE is defined as pathologically confirmed intestinal metaplasia [30]” (penultimate para, lines 1-9, col 1, pg. 30) and “Peripheral venous blood sample was drawn for each subject, and the serum sample was separated within 2 hours. The serum was isolated by centrifugation at 2000 rpm for 10 minutes at 40°C and stored at −80°C until analysis. CfDNA was extracted from 800-μl aliquots of serum using the Maxwell 16 blood DNA kit (Promega, Madison, WI)” (penultimate para, lines 14-19, col 1, pg. 30), which teaches circulating tumor DNA sample.
Regarding claim 42, Lo provides “The DNA samples extracted from the plasma and tissue samples were analyzed using massively parallel sequencing with and without prior bisulfite treatment. The plasma DNA from four healthy individuals without cancer was also analyzed as controls. The bisulfite treatment of a DNA sample would convert the unmethylated cytosine residues to uracil” ([0267]), which teaches treating converts unmethylated cytosines to uracil.
Regarding claim 43, Lo provides “we analyzed the plasma and tissue samples of a hepatocellular carcinoma (HCC) patient. Blood samples were collected from the HCC patient before and at 1 week after surgical resection of the tumor” ([0267]), which teaches the liquid sample from human individual is blood and plasma.
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Applying the KSR standard of obviousness to Lo and Zhai and Illumina, the Examiner concluded that the combination of the listed cg biomarkers, provided by Zhai and Illumina, with the method of Lo, for the purpose of analyzing a cell free sample of Human DNA, suspected of having cancer, is an illustration of the reasoning that it would have been “obvious to try" choosing from a finite number of identified, predictable solutions to achieve the claimed process.
The Zhai disclosure and the Illumina disclosures provided a plurality of differentially methylated biomarkers useful in the analysis of human samples. The use of the Illumina BeadChip as designated by Lo would have been predicted to have provided a methylation status result for at least one of the markers as claimed. Carrying out the 450K beadchip analysis on cell-free DNA samples would have been reasonably predictable, as Lo teaches how to obtain, treat, and analyze cell-free DNA samples from humans, using that the 450K beadchip.
The analysis, determining the status of the biomarker is taught in the analysis of Lo. The 450K beadchip, though large, provides a finite list of differentially methylated loci of the human genome, merely requiring the application of the sample at hand. The prior art, as summarized by Lo and Zhai had recognized the obstacles to be overcome in development of assays to determine methylation profiles in cell-free DNA samples, and had suggested a finite number of ways to overcome those obstacles, particularly the use of the Illumina 450K beadchip array.
Carrying out the method of the claims would have been obvious to one of skill in the art, because the art provides multiple strategies for treating, testing, and analyzing samples from humans suspected of having cancer, and a finite list of biomarker loci. Merely identifying one or more cg biomarker/ loci status using these elements represents a choice from a finite number of identified, and predictable solutions.
When there is motivation to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to anticipated success, it is likely the product not of innovation but of ordinary skill and common sense."
The skilled artisan would have had reason to try these methods with the reasonable expectation that at least one would be successful. Thus, carrying out the analysis of Lo using the cg loci of Zhai and Illumina as claimed was "the product not of innovation but of ordinary skill and common sense”
Such a combination is merely a "predictable use of prior art elements according to their established functions." KSR Int’l 7, 127 S. Ct. at 1740.
Claim 35 is rejected under 35 U.S.C. 103 as being unpatentable over Lo and Zhai, as applied to claims 27, 31, 33-34, 39 and 41 above, in view of Hansen et al. ("Increased methylation variation in epigenetic domains across cancer types." Nature genetics 43.8 (2011): 768-775. Newly cited).
Lo and Zhai are applied to claims 27, 31, 33-34, 39 and 42-43 above.
Lo and Zhai both disclosed genome-wide DNA methylation profiling of cell-free serum DNA studies, through bisulfite sequencing or through Illumina Chip.
Regarding claim 35, neither Lo nor Zhai does not teach sampling the lung, colon, breast or the liver cancer.
Hansen provides “We sought to increase the precision of DNA methylation measurements over our previous tiling array-based approach, termed CHARM6, analyzing 151 colon cDMRs. We designed a custom nucleotide-specific Illumina bead array of 384 probes covering 139 regions. We studied 290 samples, including cancers from colon, lung, breast, thyroid and Wilms’ tumor, with matched normal tissues to 111 of these 122 cancers, along with 30 colon premalignant adenomas and 27 additional normal samples (Online Methods). (last para, col 2, pg. 768 through 1st para, col 1, pg. 769), which teaches sampling colon cancer.
An invention would have been prima facie obvious to one of ordinary skill in the art if some motivation would have led that person to substitute prior art teachings to arrive at the claimed invention. Prior to the time of invention, said person would have been motivated to modify the methylation biomarker research samples for hepatocellular carcinoma (HCC) and esophageal adenocarcinoma (EA) cancers as taught by Lo and Zhai, with the colon cancer taught by Hansen, because cancer-specific differentially DNA-methylated regions (cDMRs) are identified in colon cancers (Hansen: Section Abstract lines 1-2, pg. 768).
Zhai teaches the methylation profiling in cfDNA has good correlation with the methylation profiling in tissue samples (Zhai: Section Abstract, pg. 29), and Hansen teaches colon cancers have differential DNA methylation (Hansen: Section Abstract lines 1-2, pg. 768). We can reasonably expect the success as Zhai “suggest that genome-wide cfDNAm profiles are highly consistent with DNAm profiles detected in corresponding tumor tissues” (Zhai: Section Abstract, pg. 29), suggesting other cancers in different tissue may indicate cfDNAm profiles, such as the colon cancer investigated by Hansen.
Response to Applicant’s Arguments
In the Remarks filed 29 December 2025, Applicant argued (page 9, penultimate para through page 10, 2nd para) that Lo and Zhai based on a two-bead system missed the bisulfite sequencing and corresponding methylation analysis methods (two-bead system does not require bisulfite treatment to the sample and hence the downstream methylation analysis will be different).
In response, Applicant’s arguments with respect to claim 27 have been considered but are not persuasive. As demonstrated above in the 103 rejection, Lo taught the NGS sequencing. The most convincing evidence comes from the following paragraph by Lo (emphasis added):
[0267] In this example, we analyzed the plasma and tissue samples of a hepatocellular carcinoma (HCC) patient. Blood samples were collected from the HCC patient before and at 1 week after surgical resection of the tumor. Plasma and buffy coat were harvested after centrifugation of the blood samples. The resected tumor and the adjacent non-tumor liver tissue were collected. The DNA samples extracted from the plasma and tissue samples were analyzed using massively parallel sequencing with and without prior bisulfite treatment. The plasma DNA from four healthy individuals without cancer was also analyzed as controls. The bisulfite treatment of a DNA sample would convert the unmethylated cytosine residues to uracil. In the downstream polymerase chain reaction and sequencing, these uracil residues would behave as thymidine. On the other hand, the bisulfite treatment would not convert the methylated cytosine residues to uracil. After massively parallel sequencing, the sequencing reads were analyzed by the Methy-Pipe (P. Jiang, et al. Methy-Pipe: An integrated bioinformatics data analysis pipeline for whole genome methylome analysis, paper presented at the IEEE International Conference on Bioinformatics and Biomedicine Workshops, Hong Kong, 18 to 21 Dec. 2010), to determine the methylation status of the cytosine residues at all CG dinucleotide positions, i.e CpG sites.
The “massively parallel sequencing” in this paragraph is interpreted as the next-generation sequencing, under a BRI.
Hence bisulfite treatment of a sample, next-generation sequencing, and the corresponding methylation mapping analysis, are all taught.
Examiner mentioned that Lo employs the Illumina Infinium HumanMethylation 450K beadchip sequencing array and Zhai employs the Illumina Infinium HumanMethylation27 BeadChip (Illumina, San Diego, CA) together, is to prepare the rational why these references are combined. Clearly, Lo taught more than the 450K beadchip.
In the Remarks, Applicant argued (page 10, 3rd para through page 11, 1st para) that the Xu Declaration praised the claimed biomarkers at paragraphs 5-6, and “surprising finding” provides strong evidence of non-obviousness of the amendment claims.
To response, Applicant’s arguments are not persuasive. The claims are obviousness over the prior art. Xu’s Declaration of having a “surprising finding” is not supported by evidence. Under a BRI, claim 27 reads on a method to do bisulfite sequencing of a single biomarker. Claim 27 is broad. The mapping step “to determine a methylation status” of one of the listed biomarkers is also an intended use or result of the mapping.
Therefore, the 103 rejection is maintained.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GUOZHEN LIU whose telephone number is (571)272-0224. The examiner can normally be reached Monday-Friday 8-5.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635