DETAILED CORRESPONDENCE
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This action is in response to the papers filed June 3, 2025. Currently, claims 20, 23-31, 33, 35-45 are pending.
All arguments have been thoroughly reviewed but are deemed non-persuasive for the reasons which follow.
This action is FINAL.
Any objections and rejections not reiterated below are hereby withdrawn.
The terminal disclaimer over ‘784 has been approved.
Priority
This application is a continuation of 17/528,699, filed November 17, 2021 which is a divisional of 15/303,762 which is a 371 of PCT/IL2015/050403, filed April 14, 2015 and claims priority to provisional 61-979,233, filed April 14, 2014.
The provisional application does not support adaptors comprising barcodes, sequences for attaching an amplified DNA molecule to a flow cell or binding sites for sequencing primers. Thus, the claims 43-44 are entitled to the April 14, 2015 priority date.
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.
Claims 20, 23-31, 33, 35-45 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
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, part II.
Based upon consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Question 1
The claimed invention is directed to a process that involves a natural principle and a judicial exception.
Question 2A- Prong 1
The claims recite an abstract idea.
Claim 20 is directed to “a method for quantifying molecules of cell-free DNA of a cell- or tissue- type of interest is present in a sample derived from a subject” by amplifying converted DNA using methylation-independent primers with an adaptor and sequencing to identifying the methylation status of at least 4 methylation sites on a continuous sequence of cell-free DNA where the sequence is 15-250 nucleotides.
Claim 20 is directed to a process that involves the judicial exceptions of an abstract idea (i.e. the abstract steps of “identifying a DNA sequence …wherein the methylation pattern of said at least 4 methylation sites in the cell- or tissue-type of interest is different as compared to the methylation pattern of said at least 4 methylation sites in the same DNA sequence in a second different cell- or tissue-type (see Claim 20 step c)). The comparison and identification are abstract ideas that may be performed mentally.
Claim 30 is directed to “the subject is diagnosed as having or not having the disease based on the methylation pattern of the cell-or tissue-type of interest”. This is a natural correlation between the cell/tissue type and disease.
Claims 33, 35 further provides determining a ratio of the amount of the specific methylation pattern to the second cell or tissue type. Mathematical relationships are considered abstract ideas (see 2106.04(a)(2)(I)(A)).
Question 2A- Prong 2
The claims do not integrate the exception into a practical application of the exception. The additional elements in the claims are converting unmethylated cytosines, amplifying DNA and sequencing each of the amplified sequences. These steps are data gathering steps. These additional elements do not apply, rely on or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
Accordingly, the claims are directed to judicial exceptions.
Question 2B
The second step of Alice involves determining whether the remaining elements, either in isolation or combination with the other non patent ineligible elements, are sufficient to “’transform the nature of the claim’ into a patent eligible application” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
The claims are not sufficiently defined to provide a method which is significantly more from a statement of a natural principle for at least these reasons:
The claims do not include applying the judicial exception, or by use of, a particular machine. The claims do not tie the steps to a “particular machine" and therefore do not meet the machine or transformation test on these grounds. The use of machines generally does not impose a meaningful limit on claim scope.
The claims also do not add a specific limitation other than what is well-understood, routine and conventional in the field. That is, the step of amplifying DNA of a sample using primers that generate DNA comprising at least 4 methylation sites in a 15-250 nucleotide sequence were routine and conventional at the time the invention was made. Amplifying nucleic acid sequences has been recognized by the courts as well-understood, routine and conventional activity (see 2106.05(d)(II)), see also Ariosa and Ambry Genetics).
The steps which are set forth in the claims must be taken or used by others to apply the disclosed law of nature, and they encompass using any of a variety of well-understood techniques in the prior art for detection. The specification teaches that “it has been known for decades that plasma contains small fragments of cell-free circulating DNA (cfDNA)” (see page 1). The specification also teaches that determining the methylation status of a methylation site are known in the art and include the use of bisulfite (see page 30). The specification teaches that amplifying may be effected using techniques such a PCR, PCA, ISSR, MSP. These methods were well known in the art at the time the invention as made (see page 33). The specification cites the 1987 Mullis Patent for supporting PCR is well-known in the art.
Further, Scher teaches detecting DNA methylation in humans using methylation independent primers that flank but do not directly hybridize to methylation sites. The primers of Scher are nucleic acids that would identifying a particular molecule, comprise a sequence that could be attached to a flow cell and could bind sequencing primers. The further steps in the method do not require any use of these adaptors. Adaptors is broadly interpreted to encompass any nucleic acid sequence.
Herold teaches analysis of methylation DNA patterns in plasma samples.
Kadam et al. (J. of Molecular Diagnostics, Vol. 14, No. 4, July 2012) teaches quantitative measurement of cell-free plasma DNA for detecting tumor methylation.
Varley et al. (Genome Research, Vol. 20, pages 1279-1287, 2010) teaches bisulfite patch PCR enables multiplexed sequencing of promoter methylation across cancer samples. The method quantifies the methylation pattern in a cis pattern (page 1279, col. 2). Varley teaches restriction digesting the human genomic DNA, adding patch oligos, bisulfite treatment and amplifying. Varley teaches the restriction fragments were between 125bp and 600bp and contained at least three CpG positions (page 1285). The samples were then subjected to the 454 Life Sciences (Roche) FLX sequencer for obtaining reads and aligning the sequences. Figure 2 illustrates the length of the amplicons includes 15-250. Figure 4 illustrates the segments of DNA had more than 4 methylated positions (see Figure 4, page 1283).
Warton et al. (BMC Genomics, Vol. 15, No. 476, pages 1-13, June 15, 2014) also teaches deep sequence of methylation sequences in free circulating DNA. Warton teaches the high-quality methylated fcDNA, library preparation and downstream genome-wide Next-generation sequencing in serum and plasma. Thus, it was routine and conventional to deep sequence bisulfite treated sequences in cell free samples.
The claims do not impose meaningful limits on the claim scope such that others are not substantially foreclosed from using the judicial exceptions. Particularly, the claims are set forth at a high level of generality.
The amplifying step is a mere data gathering step that amounts to extra solution activity to the judicial exception. It merely tells the users to determine the methylation of four or more CpG sites in a sample without further specification as to how the sample should be analyzed. The claim does not recite a new, innovative method for such determination. The determining step essentially tells users to determine the methylation pattern through whatever known processes they wish to use.
For these reasons the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to Arguments
The response traverses the rejection. The response asserts Claim 20
Contains limitations that can not be practically performed in the human mind because the claim requires high-throughput sequencing to produce thousands of sequence reads”. This argument has been reviewed but is not persuasive. As provided in MPEP 2106 “The courts consider a mental process (thinking) that “can be performed in the human mind, or by a human using a pen and paper” to be an abstract idea. CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372, 99 USPQ2d 1690, 1695 (Fed. Cir. 2011). As the Federal Circuit explained, “methods which can be performed mentally, or which are the equivalent of human mental work, are unpatentable abstract ideas the ‘basic tools of scientific and technological work’ that are open to all.’” 654 F.3d at 1371, 99 USPQ2d at 1694 (citing Gottschalk v. Benson, 409 U.S. 63, 175 USPQ 673 (1972)). See also Mayo Collaborative Servs. v. Prometheus Labs. Inc., 566 U.S. 66, 71, 101 USPQ2d 1961, 1965 (2012)” Here, the quantifying or counting of a thousand sequence reads may be performed in the human mind using a pen and paper. The calculations required to count the quantity of methylation in 1000 sequencing reads is not impractical. Applicant alleges the quantification of thousands of sequence reads would require years or lifetimes to conduct. There is no argument to support this assertion. Counting methylation patterns in 15-250bp for 1,000 sequencing reads would not consume a year of human effort. Thus, claim recites an abstract idea.
The response argues the additional elements provide for an improvement to the technical field of determining the tissue or cell origin of DNA. This argument has been reviewed but is not persuasive. The newly issued 101 Examples (July 2024), Example 49, claim 1 discusses improvements. Example 49, claim 1 state there is no improvement to the functioning of a computer nor to any other technology. At best, the claimed combination amounts to an improvement to the abstract idea of identifying a sequence that is characteristic of a cell/tissue type of interest compared to a second different cell/tissue type rather than an improvement to any technology. There is no improvement to the amplification or sequencing technology. See MPEP 2106.05(a). The response argues the signal to noise of the assay is increased but the claims do not reflect any of these improvements to the technology. The claims are minimally directed to using methylation independent primers, this was well understood, routine and conventional in the art at the time the invention was made (see Weisenberger). Thus, there is no integration of the recited exception into a practical application.
The response does not separately address Claims 30, 33, 35 which are also directed to different judicial exceptions.
Thus, for the reasons above and those already of record, the rejection is maintained.
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.
Claims 20, 23-31, 33, 35-45 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 20 has been amended to quantifying molecules of cell-free DNA having methylation pattern of any ONE of a plurality of cell -or tissue types. Claim 20 then concludes by requiring “for each of the plurality of cell-or tissue-types of interest”. It is unclear whether the claim requires quantifying one or a plurality of cell- or tissue types. Clarification is required.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
N Claims 20, 23-31, 33, 35-45 are is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Herold et al. (US 2014-0256574, September 11, 2014).
Herold teaches methods for diagnosing disease and disorders associated with beta cell death. Herold teaches the presence of hypomethylated B-cell DNA outside of the pancreas of a subject is indicative of B cell death (abstract). Herold teaches the method may be used to diagnose a subject with a disease or disorder associated with B-cell death by detecting hypomethylated B cell insulin DNA including diabetes (para 8)(limitations of Claims 27, 30). The method relies upon detecting hypomethylated B cell insulin DNA in a biological sample of a subject by obtaining a sample from the subject, where the biological sample is obtained from outside of the subject’s pancreas and where the biological sample contains B cell insulin DNA, determining the methylation status of at least one of the CpG dinucleotides in the B cell insulin DNA, where when at least one of the CpG dinucleotides in the B cell insulin DNA is determined to be unmethylated the hypomethylated B cell insulin is detected (abstract)(limitations of Claims 36, 37). Example 1 is directed to detection of B cell death in diabetes using differentially methylated circulating DNA (para 101).
The sample may be blood, serum or plasma (para 28, para 57)(limitations of Claim 38). Herold teaches the sample may be processed to enhance access to nucleic acids (para 68). Herold further teaches DNA extraction may be performed on fresh or fixed biological samples (para 92).
The first PCR generated a product of 204bp that was gel-extracted to improve real-time PCR efficiency (para 118). The primers used by Herold are methylation independent and do not overlap the methylation sites for analysis (see Figure 2 and 8). Herold teaches using a nested PCR design to detect low amounts of circulating DNA in serum (see para 118). Herold teaches the second PCR was methylation site-specific primers used in a methylation specific real-time PCR analysis followed by sequencing (para 118). Real-time PCR relies upon labeled probes to the methylated sites (para 83, 84)(limitations of Claim 23-25). Herold teaches the CpG dinucleotides at positions 255, 273, 303, 329, 364, 370, 396 and 399 are hypomethylated in insulin DNA (para 56)(limitations of Claim 20). The sequence of 255-399 is less than 170bp in length (limitations of Claim 42). Figure 6 illustrates the 8 methylation sites in Beta cells and Kidney cells, identifying and amplifying the 8 sites across a 144 bp sequence in 10 Beta cell clones and 12 kidney cell clones (see also para 22).
The methylation may be analyzed using methylation specific PCR, methylation specific DNA microarray, bisulfite sequencing, pyrosequecing of bisulfite treated DNA (para 56). Herold teaches primers may be designed that are strand-specific as well as bisulfite-specific (para 73). Herold also teaches methylation specific PCR can be designed to either methylated nucleotides or unmethylated nucleotides (para 75). Figures 8-10 further illustrates the methylated and unmethylated forward and reverse primers. The hybridization probe may be used that anneal to the target (para 80).
Herold teaches the amount of hypomethylated B cell DNA detected outside the pancreas of the subject is compared with a comparator such as a negative or positive control (para 57, 65). Herold also teaches that the DNA may be detected by methylated specific quantitative PCR analysis (para 118). Herold teaches the ratio between two DNA species was analyzed (Figure 5)(limitations of Claims 33).
Response to Arguments
The response traverses the rejection. The response asserts Claim 20 has been amended to require “for each of the plurality of cell- or tissue types of interest” and Herold fails to teach this limitation. This argument has been considered but is not convincing because, as noted in the 112B rejection above, the claim is not clear what is required. Claim 20 requires “any one” in the preamble and “each of the plurality” in step d. It is not clear what is required to perform the claimed method. As admitted by the response Harold provides results for pancreatic marker which meets the limitations of the preamble.
Further, the response cites para 118 to demonstrate Herold illustrates multiple CpG’s are not collectively characterized. This argument has been reviewed but is not persuasive. Herold teaches performing nested PCR that comprises methylation-insensitive primers to amplify a region between the CpG dinucleotide of interest. This meets the limitation of step (b). The claims do not exclude additional steps such as further analysis with methylation specific primers.
Thus for the reasons above and those already of record, the rejection is maintained.
Conclusion
No claims allowable.
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 JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682 August 28, 2025
