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
Applicant’s election without traverse of Group I in the reply filed on September 9, 2025 is acknowledged.
Claims 9 and 14 are withdrawn1 from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on September 9, 2025.
Information Disclosure Statement
The IDS received on August 21, 2023 and October 2, 2023 are proper and are being considered by the Examiner.
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 1-8 and 18-23 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 1 is indefinite because it is unclear what the claim is attempting to achieve. Specifically, claim 1 is directed to a method of identifying that a biological sample comprises a DNA from a cell type. This is construed to mean that the method is directed to the identification of the cell type.
The actual steps of the claim, now amended, recites the phrase, “detecting the methylation status of each of at least four CpG sites of a target DNA fragment in the biological sample … wherein the target DNA fragment is (1) from a human oral, larynx or esophageal epithelial cell …”.
This step now recites that the cell type from which the target DNA fragment has been isolated is already known. Therefore, the intent of the preamble recited in the method is rendered moot as the cell type from which the target DNA fragment is produced is already known.
For the purpose of prosecution, the method has been construed according to the intent of the method as recited (i.e., identifying cell-type from which the target DNA is produced from), wherein the target DNA fragment is identified as the recited cell-types based on their recited methylation profile.
Claim 2 is indefinite for the same reason.
Claims 5-8 and 18-23 are rejected by way of their dependency on claim 1.
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 1-8 and 18-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claims recite a judicial exception of an inherent (or naturally occurring) methylation profile of genomic sequences that are present in cells of different tissue/organ. This judicial exception is not integrated into a practical application because this judicial exception is broadly captured by the generic recitation of a detection step that tantamount to capturing the judicial exception itself.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception based on the analysis under the current Patent Eligibility Guidelines (herein, “PEG”) as discussed below.
Step 1 Inquiry under PEG
Step 1 inquiry under Patent Eligibility Guidelines (herein, “PEG”) determines whether or not the claimed invention is drawn to one of the recognized statutory classes of invention. Claims 1-8 and 18-23 satisfy the present inquiry as being drawn to a product.
Step 2A Inquiry under PEG
A recently revised PEG now performs step 2A inquiry under a 2-prong analysis, and the subject claims analyzed accordingly as follows:
Prong 1:
Prong-1 inquiry under step 2A determines whether the claim(s) recites an abstract idea, a law of nature, or a natural phenomenon. As stated above, the claims recite natural correlation (or phenomenon) which exists between a particular cell type and the methylation profile of the CpG sites therein.
This judicial exception is admitted in the application as filed as reproduced below:
“the methylation status of such CpG sites is different among other cells, thereby enabling the respective cell type(s) to be distinguished from other cell types. Each individual CpG dinucleotide is herein referred to as a ‘CpG site’” (section [0048])
“As demonstrated in the accompanying experimental examples, surprisingly, in every one of a large number of human cell types examined, a sufficient number of CpG clusters can be identified as having statistically different methylation status between a cell type and all other cell types. Such CpG clusters, also referred to as ‘methylation markers,’ allow identification of each cell type based on its DNA methylation status (section [0051])
The specification further evidences that the SEQ ID Numbers from which CpG site is selected or present in (see claim 1, step (1)(a) embodiment or (b) embodiment) are found in portions of genomic DNA sequences:
“It was discovered herein that some genomic locations are uniformly under-methylated or over-methylated in oral, larynx and esophageal cells as compared to all other cell types in the human (see, e.g., Table A). for instance, the genomic sequences as provided in SEQ ID NO: 1-15, 16-90, 91-92, or 102-125 (annotated with start and end locations on the respective chromosome) all have lower than 40% methylation percentages in oral, larynx or esophageal epithelial cells, and higher than 60^ methylation percentages in all other cell types. Likewise, the genomic sequences as provided in SEQ ID NO: 126-133, 134-134, or 135-150 all have relatively higher methylation percentages (>60%) in oral, larynx or esophageal epithelial cells and lower methylation percentages (<40%) in all other cell types” (section [0078])
Therefore, the unique methylation profile of CpG sites that are specific to a cell-type is naturally present (judicial exception) and claimed by recitation in the claim.
Prong 2:
Prong-2 inquiry under step 2A determines whether or not the claims recite additional elements that integrate the judicial exception into a practical application in a manner that imposes a meaningful limit on the judicial exception.
Each of additional elements are addressed separately.
Detection means:
Claims 1 and 2 recite that the detection of the at least four CpG sites for the methylation status is achieved via generically recited means of a) hybridizing one or more polynucleotides to the target DNA fragments (harboring the CpG sites) or to an amplification product thereof within 500 nucleotides of the at least four CpG sites.
The use of such highly general language of using a polynucleotide to anneal to the target or its amplification product is not deemed to impose any meaningful limit on the judicial exception, but tantamount to “applying” the judicial exception itself as discussed by the Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories (566 U.S. 66 (2012)).2
Claims 3-8 further recites that he detection is for an elevated amount of cell-free DNA fragment while tying this phenomenon to a abnormal death of cell death of the cell type, or disease relating to the cell type (claim 3), or the identification that the subject has an injury, inflammation, or cancer of the tissue from which the cell-type is determined (claim 4), where the disease is pancreatic disease or condition (claim 7), or where the disease is diabetes, inflammation, or cancer. However, these are not additional element that impose a limitation to the judicial exception discussed above.
Rather, these are recitation of additional judicial exception pertaining to cell-free DNA that are known to be released when cell goes through apoptosis in normal, abnormal, or diseased conditions.
“Small fragments of nucleic acids, e.g., DNA, circulate freely in the peripheral blood of healthy and diseased individuals. These cell-free nucleic acids, such as DNA (cfDNA) molecules may originate from dying or damaged cells and thus reflect ongoing cell death or injuries taking place in the body. In recent years, such understanding has led to the emergence of diagnostic tools, which are impacting multiple areas of medicine. For instance, next-generation sequencing of fetal DNA circulating in maternal blood has allowed non-invasive prenatal testing of fetal chromosomal abnormalities; detection of donor-derived DNA in the circulation of organ transplant recipients can be used for early identification of graft rejection; and the evaluation of mutated DNA in circulation can be used to detect genotype and monitor cancer (section [0004])
Therefore, the present combination of one judicial exception with another judicial exception do not result in a meaningful limit on either/both of the judicial exceptions.
Claims 18-23 recite the additional elements of detecting genetic variations in the target DNA fragment (from which cell-type is identified, claim 18), or the one of more polynucleotides involved in the detection is one or more probe (claim 20), or primer (claim 21), or that the detection means is rendered via array/sequencing (claim 22), and that the methylation detection is detected via bisulfite means (which deaminates non-methylated cytosines, claims 23).
The recitation of a genetic variant to a condition is deemed a judicial exception, and does not add to the judicial exceptions presently discussed, and the usage of a general language “probes” and “primers” for detecting a nucleic acid sequence is not deemed significant nor impose any meaningful limit as such detection means are necessarily involved conventionally in array/amplification/sequencing reactions. Lastly, methylation detection also conventionally requires the deamination step with a bisulfite, converting unmethylated cytosine to uracil, and therefore is not deemed to meaningfully limit the judicial exception.
Step 2B Inquiry under PEG
Step 2B inquiry of the PEG determines whether or not additional elements are provided and whether such elements amount to significantly more than the judicial exception in the claims.
Presently, the additional elements are deemed routine and conventionally employed techniques in the art of molecule diagnostics.
For example, the means of detecting methylated CpG sites utilizing bisulfite-treatment in a PCR or array hybridization is well-known in the art as evidenced by Lee et al. (Cancer Letters, 2013, vol. 340, pages 171-178):
“methylation status of DNA can be analyzed by many different methods which utilize three basic principles … bisulfite treatment can convert unmethylated cytosine into uracil while leaving methylated cytosine unchanged. These principles have been integrated into high-throughput analytical applications such as microarray and next-generation sequencing (NGS) platforms” (page 172, 1st column, 1st para)
Lastly, claim 19 recites the additional element of “treating the subject for the disease by resection, surgery, radiation therapy, chemotherapy, or immunotherapy”. However, theses steps are not specific to any of the judicial exceptions recited. Rather, they are generalized concept of treating any patient that has a condition. Because the claimed judicial exception is not specifically tied and/or apply to the treatment step, this is not a specific and meaningful application of the judicial exception.
For these reasons, the additional elements recited in the claims are not deemed significantly more than just inclusion of means which are commonly used, routine and conventional in the art.
Therefore, the present claims lack patent eligibility.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-8 and 18-23 are rejected under 35 U.S.C. 103 as being unpatentable over Dor et al. (WO 2015/159292 A2, published October 2015, IDS ref) in view of Fortin et al. (Bioinformatics, 2017, vol. 33, no. 4, pages 558-560).
Regarding claim 1, Dor et al. teach a well-known known means of typing a cell/tissue based on the cell’s/tissue’s unique methylation pattern:
“Despite having an identical nucleotide sequence, the DNA of each cell type in the body carries unique epigenetic marks correlating with its gene expression profile … Methylation patterns are unique to each cell type, conserved among cells of the same type in the same individual and between individuals, and are highly stable under physiologic or pathologic conditions. Therefore, it may be possible to use the DNA methylation pattern of cfDNA to determine its tissue of origin and hence to infer cell death in the source organ” (page 1, line 31 to page 2, line 5)
“detecting death of a cell type or tissue in a subject comprising determining whether cell-free DNA comprised in a fluid sample of the subject is derived from the cell type or tissue, wherein the determining is effected by ascertaining the methylation status of at least four methylation sites on a continuous sequence of the cell-free DNA, the sequencing comprising no more than 300 nucleotides, wherein a methylation status of each of the at least four methylation sites on the continuous sequence of the DNA characteristic of the cell type or tissue is indicative of death of the cell type or tissue” (page 2, line 29 to page 3, line 4)
In determining the methylation status, the method employs “methylation-dependent oligonucleotide” to hybridize to at least one of the four methylation sites (page 4, lines 22-24), or via use of primers (“amplifying the continuous sequence of DNA using oligonucleotides that hybridize to a nucleic acid sequence adjacent to the first and last of the at least four methylation sites on the continuous sequence of the DNA”, page 5, lines 5-7; “typical amplification reaction is carried out by contacting a forward and reverse primer pair (a primer pair)”, page 32, lines 5-6).
With regard to claim 3, the biological sample comprises, “blood, plasma, sperm, milk, urine, saliva and cerebral spinal fluid” (page 4, lines 18-19)
With regard to claim 4, the target DNA fragment is a cell-free DNA fragment (“the invention is cell-free DNA”, page 4, line 7).
With regard to claim 5, the artisans teach determining the amount of cell-free DNA from the cell type or tissue (“method further comprises analyzing the amount of cell-free DNA derived from the cell type or tissue”, page 5, lines 12-13; “when the amount of cell free DNA derived from the cell type or tissue is above the predetermined level, it is indicative that there is a predetermined level of cell death … level of cell death is above a predetermined level, it is indicative that the subject has the disease or pathological state”, page 47, lines 15-18).
With regard to claim 6, the artisans further teach identifying the subject human as having cancer, inflammation, or cancer (“a wide variety of pathologies, including but not limited to cancers, trauma …”, page 14, lines 1-2).
With regard to claims 20 and 22, the detection means is via hybridization to a DNA array which comprises probes or sequenced (“DNA may be sequenced using any methods known in the art”, page 36, lines 24-25; “Illumina 450k array”, page 55, line 32, see also page 61, lines 10-11).
With regard to claim 21, the artisans teach amplifying the at least for CpG sites (“amplifying the continuous sequence of DNA using oligonucleotides that hybridize to a nucleic acid sequence adjacent to the first and last of the at least four methylation sites on the continuous sequence of the DNA”, page 5, lines 5-7).
With regard to claim 23, the target DNA fragment comprises one or more deaminated cytosines (i.e., cytosines are deaminated to uracil when treated with bisulfite, “[m]ethods of determining the methylation status of a methylation site are known in the art and includes the use of bisulfite … which converts cytosine residues to uracil … but leaves 5-methylcytosine residues unaffected …”, page 30, lines 21-25).
Dor et al. teach a plurality of SEQ ID Numbers of interest containing CpG sites, sequences of which expand to 1496 different SEQ ID Numbers (pages 16-28_, some of which are discussed below:
“SEQ ID NO: 1-27 and 1241-1244 comprise sequences which include at least 4 methylation sites in a continuous sequence of no more than 300 nucleotides that are unmethylated in pancreatic beta cells and methylated in other cells” (page 16, lines 27-29)
SEQ ID NO: 28-50 comprise sequences which include at least 4 methylation sites in continuous sequence of no more than 300 nucleotides that are methylated in pancreatic beta cells and unmethylated in other cells (page 17, lines 1-3)
SEQ ID NO: 51-100 comprise sequences which include at least 4 methylation sites in a continuous sequence of no more than 300 nucleotides that are unmethylated in pancreatic ductal cells and methylated in other cells (page 17, lines 12-14)
Due to the nature of the claims and the disclosure, actual SEQ ID Numbers of the disclosure and instant SEQ ID Numbers do not match, despite having the same assignee.
While the Dor et al. further teach that the amount of cell death in a particular cell population can be used to diagnose a particular pathological state (e.g., disease) or condition (e.g., trauma) (see page 45, line 28 to page 46, line 2, also “when the amount of cell free DNA derived from the cell type or tissue is above the predetermined level, it is indicative that there is a predetermined level of cell death … level of cell death is above a predetermined level, it is indicative that the subject has the disease or pathological state”, page 47, lines 15-18), the artisans do not explicitly teach that the increase in the cell-free DNA is linked to pancreatic cell type, wherein disease is diabetes, inflammation, or cancer (claims 7 and 8).
Dor et al. teach that their method is used for the detection of conditions, and monitoring treatment (“death of the cell type is associated with a pathological process, the method further comprise diagnosing the pathological process, page 4, lines 5-7; “method can be used for diagnosis, monitoring disease progression and assessment of response to therapy”, page 14, lines 2-3), but do not explicitly teach that genetic mutation is examined (claim 18) or that treatment of surgery, resection, radiation therapy, chemotherapy, or immunotherapy is administered (claim 19).
Fortin et al. teach a well-known commercial availability of methylation detection assays, such as HumanMethylation 450, or “450k” solid via Illumina®.
“In 2015, Illumina released their next generation methylation array, the HumanMethylationEPIC (‘EPIC’) array … We have extended … to convert EPIC array to a virtual 450k array …” (page 558)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Dor et al. with Fortin et al. and the suggestions mad by Dor et al., thereby arriving at the invention as claimed for the following reasons.
As discussed above, Dor et al. already teach that methylation profiles of DNA (in particular cell-free DNA) from samples are cell-type specific and can be used to identify the origin from which the cell-free DNA was released. And as discussed above, the artisans explicitly list thousands of target DNA fragments (by SEQ ID Numbers) comprising at least 4 CpG sites thereon. However, as noted above, the nature of the application and the prior art is that the thousands of SEQ ID numbers disclosed by Dor et al. and instant application, the comparison of such sheer numbers of SEQ ID numbers cannot be made. However, the Office notes the analysis of determining cell-type specific methylation patterns employed by Dor et al. and instant application employed the same commercially available platform, Illumina 450k array (see above). Therefore, the Office asserts that at least one of the target DNA fragment sequences represented in the instant claim is represented in the thousands of cell-free DNA fragments containing CpG sites disclosed by Dor et al., absent evidence to the contrary.
And based on this rationale, one of ordinary skill in the art would have had a reasonable motivation to identify a cell type based on the methylation pattern observed in the many of the target DNA fragments harboring CpG sites disclosed by Dor et al.
With regard to identifying that the increased cell-free DNA is an indication of a pancreatic disease such as diabetes, one of ordinary skill in the art would have been clearly capable of concluding and arriving at such an application because Dor et al. explicitly teach that the list of cell-free DNA is related back to the original source being a hepatocyte (see page 5, line 18). Because Dor et al. teach that the increased cell-free DNA above a predetermined level is indicative of cell death and disease (“when the amount of cell free DNA derived from the cell type or tissue is above the predetermined level, it is indicative that there is a predetermined level of cell death … level of cell death is above a predetermined level, it is indicative that the subject has the disease or pathological state”, page 47, lines 15-18), one of ordinary skill in the art would have been motivated and would have had a reasonable expectation of success at concluding that the rise of cell-free DNA level that originated from hepatocytes would be reason for screening for diabetes.
As to the detection of genetic variation in cell-free DNA for mutations that relate to diseases such as cancer, and concluding that proper treatment is applied (such as surgery, radiation therapy, etc.), such a conclusion would have also been obvious as such a practice has been long precited in the art of molecular diagnostics, where mutation markers are detected to render a diagnosis, followed by an appropriate treatment, requiring no more than a common sense.
In KSR International Co. v. Teleflex Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007), the Supreme Court held that “obvious to try” was a valid rationale for an obviousness finding, for example, when there is a “design need” or “market demand” and there are a “finite number” of solutions. 550 U.S. at 421, 82 USPQ2d at 1397 (“The same constricted analysis led the Court of Appeals to conclude, in error, that a patent claim cannot be proved obvious merely by showing that the combination of elements was ‘[o]bvious to try.’ ... When there is a design need or market pressure 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 the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show that it was obvious under §103.”).
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YOUNG J KIM/Primary Examiner
Art Unit 1637 November 12, 2025
/YJK/
1 Applicants’ election canceled claims 10-13 and 15-17, dependent on the independent claims 9 and 14, respectively.
2 “to transform an unpatentable law of nature into a patentable eligible application of such a law, a patent
must to more than simply state the law of nature while adding the words ‘apply it.’ See, e.g.,
Gottschalk v. Benson, 409, U.S. 63, 71-72. It must limit its reach to a particular, inventive application
of the law.” (Id. at 60)