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 .
Interview Summary
The Examiner would like to note the inclusion of the Applicant’s interview summary regarding the video interview on May 28th, 2026. With the inclusion of this summary, the interview record is complete.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on July 2nd, 2026 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Specification Summary
The specification has been amended. The filing of the specific amendments to the specification, as well as the substitute specification, on July 2nd, 2026 is acknowledged.
Response to Amendment
The amendment filed July 2nd, 2026 is acknowledged. Regarding the Office Action mailed March 6th, 2026:
The rejections set forth under 35 U.S.C. 112(b) are withdrawn in view of the amendments and cancellation of claim 65.
The rejection set forth under 35 U.S.C. 112(a) is withdrawn in view of the amendments.
The rejection of claim 65 set forth under 35 U.S.C. 101 is withdrawn in view of the cancellation of the claim.
The rejection of claim 65 set for under 35 U.S.C. 103 is withdrawn in view of the cancellation of the claim.
Maintained, modified, or new rejections are set forth below, as necessitated by the amendments. Responses to arguments, if necessary, follow their respective rejection sections.
Claim Summary
Claims 34-35 and 37 have been amended. Claims 1-33, 36, 38-49, 51, 53-171 have been canceled. Claims 172-187 have been added. Claims 34-35, 37, 50, 52, and 172-187 are pending. Claims 34-35, 37, 50, 52, and 172-187 are under examination and discussed in this Office action.
Claim Rejections - 35 USC § 112(a) – New – Necessitated by Amendment
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 34-35, 37, 50, 52, and 172-187 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
This is a new matter rejection.
Claim 34 recites the limitations “(e) processing said sequencing reads to obtain (i) a plurality of sequencing reads having a genomic feature and (ii) a plurality of sequencing reads not having said genomic feature; (f) processing said plurality of sequencing reads having said genomic feature in (e) to obtain a first size distribution of said plurality of sequencing reads having the genomic feature; (g) processing said plurality of sequencing reads not having said genomic feature in (e) to obtain a second size distribution of said plurality of sequencing reads not having said genomic feature; (h) determining a difference in size between said first size distribution and said second size distribution; and (i) determining that said genomic feature in said sequencing reads is associated with a disease state in said human subject when said plurality of sequencing reads having said genomic feature have a size smaller than said plurality of sequencing reads not having said genomic feature”. As written, and given the previous limitations in the claim, these limitations read that sequencing reads produced from sequencing of a plurality of nucleic acid molecules from one sample are separated into reads comprising a genomic feature and reads not comprising the genomic feature, which are further used to determine size distributions that are compared to each other to determine a disease state. These limitations are not described in the specification such that the Applicant has possession of the claimed limitations.
Turning to the specification, there is no description of sequencing and genomic features related to taking reads from one sequenced sample and obtaining pools of reads having a genomic feature and not having a genomic feature. There is description related to identifying an individual nucleic acid molecule as having a genomic feature (at paragraphs [0007], [0008], [0011], [0045], among others, of the amended specification filed July 2nd, 2026). There is description related to preparing two different single stranded DNA libraries, the first derived from a subject of interest and the second derived from a control, to determine size distributions for the subject and the control, and further a difference in size between those size distributions (see paragraphs [0033] and [0044] of the amended specification filed July 2nd, 2026). There is description of sequencing reads being obtained from sequencing methods (see paragraph [0082] of the amended specification filed July 2nd, 2026). There is no description for “(e) processing said sequencing reads to obtain (i) a plurality of sequencing reads having a genomic feature and (ii) a plurality of sequencing reads not having said genomic feature”. The above cited paragraphs are also considered the most pertinent description related to steps (f)-(i) as cited above. There is no description for “(f) processing said plurality of sequencing reads having said genomic feature in (e) to obtain a first size distribution of said plurality of sequencing reads having the genomic feature; (g) processing said plurality of sequencing reads not having said genomic feature in (e) to obtain a second size distribution of said plurality of sequencing reads not having said genomic feature; (h) determining a difference in size between said first size distribution and said second size distribution; and (i) determining that said genomic feature in said sequencing reads is associated with a disease state in said human subject when said plurality of sequencing reads having said genomic feature have a size smaller than said plurality of sequencing reads not having said genomic feature”, particularly given that they all rely on the sequencing reads from one sequenced sample being grouped based on having a genomic feature or not having a genomic feature as recited in step (e).
Given the lack of description related to taking reads from one sequenced sample and obtaining pools of reads having a genomic feature and not having a genomic feature, the currently claimed “(e) processing said sequencing reads to obtain (i) a plurality of sequencing reads having a genomic feature and (ii) a plurality of sequencing reads not having said genomic feature; (f) processing said plurality of sequencing reads having said genomic feature in (e) to obtain a first size distribution of said plurality of sequencing reads having the genomic feature; (g) processing said plurality of sequencing reads not having said genomic feature in (e) to obtain a second size distribution of said plurality of sequencing reads not having said genomic feature; (h) determining a difference in size between said first size distribution and said second size distribution; and (i) determining that said genomic feature in said sequencing reads is associated with a disease state in said human subject when said plurality of sequencing reads having said genomic feature have a size smaller than said plurality of sequencing reads not having said genomic feature” is considered new matter that is not adequately described in the instant disclosure. Claims 35, 37, 50, 52, and 172-187 are also rejected here for their dependence on claim 34, and therefore also encompassing the identified new matter.
Claim 182 recites the limitation “wherein said difference in size between said first size distribution and said second size distribution obtained using a single-stranded DNA library is increased relative to a difference in size obtained using a double stranded DNA library”. As written, and given claim 34, from which claim 182 depends, this limitation reads that a difference in size between a size distribution of reads with a genomic feature and a size distribution of reads without a genomic feature obtained from one sequenced sample using single stranded library preparation is increased as compared to the difference using a double stranded library preparation. This limitation is not described in the specification such that the Applicant has possession of the claimed invention.
Turning to the specification, the provided description related to differences between single stranded library preparation and double stranded library preparation are performed using a comparison between a sample from a subject of interest and a control sample (see paragraphs [0010], [0033], and [0044] of the amended specification filed July 2nd, 2026, and Figures 1 and 2). There is no indication that single stranded library preparation and double stranded library preparation are compared using sequencing reads that originate from one sequenced sample, as is encompassed given claim 182’s dependence on claim 34. Given the lack of description related to a difference in size between a size distribution of reads with a genomic feature and a size distribution of reads without a genomic feature obtained from one sequenced sample using single stranded library preparation being increased as compared to the difference using a double stranded library preparation, the currently claimed “wherein said difference in size between said first size distribution and said second size distribution obtained using a single-stranded DNA library is increased relative to a difference in size obtained using a double stranded DNA library” is considered new matter that is not adequately described in the instant disclosure.
Claim 187 recites the limitation “using an additional sample obtained subsequent to administering said therapeutic to said human subject for monitoring said human subject for a progression or regression of said disease state, which monitoring is performed based at least in part on a size difference between a third size distribution and a fourth size distribution obtained from sequencing reads derived from nucleic acid molecules obtained from said additional sample”. As written, this limitation reads that the claimed method can be used to monitor disease state based on an additional sample from the subject after receiving a therapeutic and determining third and fourth size distributions. This limitation is not described in the specification such that the Applicant has possession of the claimed invention.
Turning to the specification, the provided description of monitoring reads “the method further comprises using the difference to monitor the subject for a progression or regression of the disease” (see paragraphs [0006]-[0008] and [0043] of the amended specification filed July 2nd, 2026). There is no indication that this is performed on an additional sample, that this additional sample is obtained subsequent to administering a therapeutic, or that there are two different size distributions obtained to determine a difference in size after administering a therapeutic. Given the lack of description related to monitoring disease state based on an additional sample from the subject after receiving a therapeutic and determining third and fourth size distributions, the currently claimed “using an additional sample obtained subsequent to administering said therapeutic to said human subject for monitoring said human subject for a progression or regression of said disease state, which monitoring is performed based at least in part on a size difference between a third size distribution and a fourth size distribution obtained from sequencing reads derived from nucleic acid molecules obtained from said additional sample” is considered new matter that is not adequately described in the instant disclosure.
Claim Rejections - 35 USC § 101 - Modified - Necessitated by Amendment
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 34-35, 37, 50, 52, and 172-187 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon and abstract ideas without significantly more. While the claims are directed to processes, and therefore meet step 1 of the subject matter eligibility test (see MPEP 2106.03), the claims recite the natural correlation between nucleic acid size distribution, genomic features, and disease. Such correlation is a natural phenomenon because it describes a consequence of the human body. The claims further recite the abstract ideas of determining a difference in size and associating a genomic feature with a disease based on size. Such recitations are mental process abstract ideas because both determining a difference in size and associating a genomic feature can reasonably be performed in the human mind after simply looking at data.
Step 2A of the subject matter eligibility test requires a two-pronged analysis. Prong One asks: does the claim recite an abstract idea, law of nature or natural phenomenon? As discussed in MPEP 2106.04(II)(A)(1), the meaning of “recites” is “set forth” or “describes”. That is, a claim recites a judicial exception when the judicial exception is “set forth” or “described” in the claim. In the instant case, the claims describe natural phenomena and abstract ideas: the natural correlation between nucleic acid size distribution, genomic features, and disease, and the abstract ideas of determining a difference in size and associating a genomic feature with a disease based on size.
Prong Two of the analysis under step 2A asks: does the claim recite additional elements that integrate the judicial exception into a practical application of the judicial exception? As discussed in MPEP 2106.04(II)(A)(2), “Because a judicial exception is not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B.” The considerations to be used are set forth at MPEP 2106.05(a) through (c) and (e) through (h). Turning to those sections of the MPEP:
MPEP 2106.05(a) has to do with improvements to the functioning of a computer or to any other technology or technical field. The claims at issue do not improve the functioning of a computer or other technology. While the instant claims recite steps of obtaining a sample comprising cfDNA, extracting nucleic acid molecules, and processing nucleic acid molecules for sequencing (further including denaturing the molecules, and/or ligating adapters to 5’, 3’, or both ends of the molecules with a DNA ligase specific for single-stranded DNA; circularizing the single stranded DNA molecules and further amplifying the circularized molecules; size selection with a size threshold of at most 360 nucleotides; whole genome sequencing; untargeted amplification; specific percentages of double-stranded nucleic acids; no end repair; and no alignment to a reference genome); obtaining sequencing reads with and without a genomic feature (wherein a genomic feature can comprise those seen in claim 50, 52, or 172); processing reads to obtain a first size distribution for molecules having the genomic feature; processing reads to obtain a second size distribution for molecules not having the genomic feature; wherein the first size distribution is on average less that the second; difference in size determined using a single-stranded library is increased relation to a double-stranded library; administering a therapeutic upon determining a genomic feature is associated with a disease state; and monitoring after administering the therapeutic by evaluating a further sample for a third and fourth size distribution, the claims do not improve upon DNA extraction technologies, sequencing technologies, genomic feature detection technologies, or size distribution measurement technologies. The claims merely use existing methods for these steps. Note that MPEP 2106.05(a) indicates that “[u]sing well-known standard laboratory techniques to detect enzyme levels in a bodily sample” is an example that the courts have indicated may not be sufficient to show an improvement to technology.
MPEP 2106.05(b) has to do with whether the claims involve the use of a particular machine. In this case, the claims do not involve the use of a particular machine. While the instant claims recite steps of obtaining a sample comprising cfDNA, extracting nucleic acid molecules, and processing nucleic acid molecules for sequencing (further including denaturing the molecules, and/or ligating adapters to 5’, 3’, or both ends of the molecules with a DNA ligase specific for single-stranded DNA; circularizing the single stranded DNA molecules and further amplifying the circularized molecules; size selection with a size threshold of at most 360 nucleotides; whole genome sequencing; untargeted amplification; specific percentages of double-stranded nucleic acids; no end repair; and no alignment to a reference genome); obtaining sequencing reads with and without a genomic feature (wherein a genomic feature can comprise those seen in claim 50, 52, or 172); processing reads to obtain a first size distribution for molecules having the genomic feature; processing reads to obtain a second size distribution for molecules not having the genomic feature; wherein the first size distribution is on average less that the second; difference in size determined using a single-stranded library is increased relation to a double-stranded library; administering a therapeutic upon determining a genomic feature is associated with a disease state; and monitoring after administering the therapeutic by evaluating a further sample for a third and fourth size distribution, no such machines are required by the claim, and certainly no particular machines. Even if some conventional machine were recited in the claims, like a sequencing apparatus, further considerations such as the particularity or generality of the recited machine must be taken into account, as well as whether the involvement of the machine is merely extra-solution activity. MPEP 2106.05(g) describes “extra-solution activity”, noting that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra-solution activity.
MPEP 2106.05(c) has to do with whether the claims involve a particular transformation. Here, none of the limitations of the claims involve a particular transformation. For example, sequencing DNA molecules does not transform that DNA into something else.
MPEP 2106.05(e) has to do with “other meaningful limitations”. The additional limitations imposed upon the natural correlation between nucleic acid size distribution, genomic features, and disease, and the abstract ideas of determining a difference in size and associating a genomic feature with a disease based on size in the instant case have to do with obtaining a sample comprising cfDNA, extracting nucleic acid molecules, and processing nucleic acid molecules for sequencing (further including denaturing the molecules, and/or ligating adapters to 5’, 3’, or both ends of the molecules with a DNA ligase specific for single-stranded DNA; circularizing the single stranded DNA molecules and further amplifying the circularized molecules; size selection with a size threshold of at most 360 nucleotides; whole genome sequencing; untargeted amplification; specific percentages of double-stranded nucleic acids; no end repair; and no alignment to a reference genome); obtaining sequencing reads with and without a genomic feature (wherein a genomic feature can comprise those seen in claim 50, 52, or 172); processing reads to obtain a first size distribution for molecules having the genomic feature; processing reads to obtain a second size distribution for molecules not having the genomic feature; wherein the first size distribution is on average less that the second; difference in size determined using a single-stranded library is increased relation to a double-stranded library; administering a therapeutic upon determining a genomic feature is associated with a disease state; and monitoring after administering the therapeutic by evaluating a further sample for a third and fourth size distribution. These limitations are not considered “meaningful limitations”. MPEP 2106.05(e) states: “The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements that provide an inventive concept to the claim as a whole.” In addition, as has been discussed, they represent insignificant extra-solution activity, i.e. “data gathering”.
MPEP 2106.05(f) raises the question as to whether the additional elements recited in the claim represent “mere instructions to apply an exception”. Here, the judicial exceptions are the natural correlation between nucleic acid size distribution, genomic features, and disease, and the abstract ideas of determining a difference in size and associating a genomic feature with a disease based on size. The additional elements recited in the claims (i.e. obtaining a sample comprising cfDNA, extracting nucleic acid molecules, and processing nucleic acid molecules for sequencing (further including denaturing the molecules, and/or ligating adapters to 5’, 3’, or both ends of the molecules with a DNA ligase specific for single-stranded DNA; circularizing the single stranded DNA molecules and further amplifying the circularized molecules; size selection with a size threshold of at most 360 nucleotides; whole genome sequencing; untargeted amplification; specific percentages of double-stranded nucleic acids; no end repair; and no alignment to a reference genome); obtaining sequencing reads with and without a genomic feature (wherein a genomic feature can comprise those seen in claim 50, 52, or 172); processing reads to obtain a first size distribution for molecules having the genomic feature; processing reads to obtain a second size distribution for molecules not having the genomic feature; wherein the first size distribution is on average less that the second; difference in size determined using a single-stranded library is increased relation to a double-stranded library; administering a therapeutic upon determining a genomic feature is associated with a disease state; and monitoring after administering the therapeutic by evaluating a further sample for a third and fourth size distribution) does amount to mere instructions to apply the judicial exceptions, since the obtaining samples, extracting nucleic acids, processing nucleic acids for sequencing, performing sequencing, and all additional steps serve as mere conventional steps taken for the purpose of gathering data about the nucleic acid molecules, which any practical use of the judicial exceptions would require.
MPEP 2106.05(g) has to do with whether the additional elements of the claim amount to insignificant extra-solution activity. MPEP 2106.05(g) notes that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra - solution activity. Likewise, MPEP 2106.05(g) notes that “[p]erforming clinical tests on individuals to obtain input for an equation” also represents insignificant extra-solution activity. This aligns closely with the instant claims, where the additional elements of the claims amount to obtaining samples, extracting nucleic acids, processing nucleic acids for sequencing, and performing sequencing.
MPEP 2106.05(h) has to do with whether the additional elements amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use. Here, the recitation of “[a] method for nucleic acid analysis”, is considered a “field of use”. However, as MPEP 2106.05(h) indications, such limiting to a particular “field of use” does not confer patentability on otherwise ineligible subject matter.
In addition, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception (as set forth in step 2B of the subject matter eligibility test; see MPEP 2106-III) because it was routine and conventional in the prior art to obtain samples, extract nucleic acids, process nucleic acids for sequencing, and perform sequencing, as well as all additional steps as claimed.
For example, Mouliere (Enhanced detection of circulating tumor DNA by fragment size analysis, Science Translational Medicine, November 2018, 10, 1-13; cited on the IDS filed January 17th, 2024, copy with supplement is provided) teaches a method for nucleic acid analysis, comprising: (a) obtaining a sample comprising cell-free deoxyribonucleic acid (DNA) from a human subject (Page 2, column 1, paragraph 3; Page 10, column 2, paragraph 2; Page 1, column 2, paragraph 1: plasma contains ctDNA and cfDNA) and (b) extracting a plurality of nucleic acid molecules from said sample obtained from said human subject, wherein said plurality of nucleic acid molecules comprises single stranded nucleic acid molecules and double stranded nucleic acid molecules (Page 10, column 2, paragraph 2). Mouliere’s methods use cfDNA and ctDNA (which is a fraction of total cell-free DNA, see Mouliere’s introduction) from plasma (Page 2, column 1, paragraph 4 to column 2, paragraph 1). As evidenced by Yang (Cell-Free DNA Comprises the Strand-Specific Characteristic Associated with Transcription and Methylation, Clinical Chemistry, September 2025, 71, 980-992), cfDNA in blood contains both single-stranded and double-stranded DNA (Page 980, column 2, Introduction). Mouliere further teaches (d) sequencing a plurality of nucleic acid molecules or a derivative thereof to obtain sequencing reads (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Supplementary Materials, Page 3); (e) processing sequencing reads to obtain (i) a plurality of sequencing reads having a genomic feature and (ii) a plurality of sequencing reads not having said genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Supplementary Materials, Page 3); (f) processing said plurality of sequencing reads having said genomic feature in (e) to obtain a first size distribution of said plurality of sequencing reads having the genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D); (g) processing said plurality of sequencing reads not having said genomic feature in (e) to obtain a second size distribution of said plurality of sequencing reads not having said genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D); (h) determining a difference in size between said first size distribution and said second size distribution (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D); and (i) determining that said genomic feature in said sequencing reads is associated with a disease state in said human subject when said plurality of sequencing reads having said genomic feature have a size smaller than said plurality of sequencing reads not having said genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D). Mouliere further teaches wherein said genomic feature comprises a single nucleotide variant (SNV) (Supplementary Materials, Page 3, Tam-Seq). Mouliere further teaches the method further comprising, prior to said processing in (c), subjecting said plurality of nucleic acid molecules to size selection to enrich for nucleic acid molecules having sizes less than a size threshold (Page 2, column 2, paragraph 2: “We determined the feasibility of selective sequencing of shorter fragments using in vitro sizes election with a bench-top microfluidic device followed by sWGS…”; Figure 3A). Mouliere further teaches wherein said size threshold is at most 360 nucleic acid bases (Figure 3A: 90-150 bp). Mouliere further teaches wherein said size selection comprises gel purification (Supplementary Materials, Page 3, paragraph 1: DNA loaded on 3% agarose gel). Mouliere further teaches wherein an average of said first size distribution of said plurality of sequencing reads having said genomic feature is less than an average of said second size distribution of said plurality of sequencing reads not having said genomic feature (Figure 2D). Mouliere further teaches wherein said sequencing in (d) comprises whole genome sequencing (Page 2, column 1, paragraph 4 to column 2, paragraph 1).
In a further example, Wang (CLAmp-seq: A Novel Amplicon-Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC, Small Methods, August 2019, 4, 1-10; previously cited) teaches processing a plurality of nucleic acid molecules to obtain a plurality of single stranded nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1) and sequencing a plurality of single stranded nucleic acid molecules to obtain sequencing reads (Page 2, column 2, paragraph 2; Figure 1). As evidenced by Cheng (A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection, Frontiers in Oncology, March 2024, 14, 1-11; previously cited), CLAmp-seq is considered a single-stranded DNA library preparation technique (Page 4, column 2, paragraphs 2-3). Wang further teaches wherein (c) comprises denaturing said plurality of nucleic acid molecules (Page 2, column 2, paragraph 2). Wang further teaches wherein (c) comprises (i) circularizing individual single stranded nucleic acid molecules of said plurality of nucleic acid molecules to form a plurality of circular nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1); and (ii) amplifying said plurality of circular nucleic acid molecules to yield a plurality of amplified nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1). Wang further teaches wherein said processing in (c) comprises untargeted amplification of said plurality of nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1: amplification via primers hybridized to sequencing adapters for PCR amplification). Wang further teaches the method of CLAmp-seq, a single stranded library method (whole document), and therefore can achieve the claimed wherein said plurality of single stranded nucleic acid molecules obtained in (c) comprises at most 5% of said double stranded nucleic acid molecules and the claimed said difference in size between said first size distribution and said second size distribution obtained using a single-stranded DNA library is increased relative to a difference in size obtained using a double stranded DNA library.
In a further example, Lo (US 20170024513 A1; cited on the IDS filed February 16th, 2023; previously cited) teaches on looking at both fragment size and methylation in cell-free DNA fragments to determine informativeness or specificity to a disease (e.g. cancer) (Page 23, paragraph [0294]). Lo further teaches wherein said genomic feature comprises an epigenetic modification, wherein said epigenetic modification comprises methylation (Page 23, paragraph [0294]).
In a further example, Weng (US 20180057871 A1; cited on the IDS filed February 16th, 2023) teaches wherein circularizing is performed under reaction conditions sufficient for self-joining of nucleic acid molecules shorter than a threshold length (Page 16, paragraph [0123]). Weng further teaches wherein said threshold length is at most 5000 nucleotides (Page 16, paragraph [0123]). Weng further teaches wherein processing of sequencing reads can comprise aligning sequencing reads to other sequencing reads (Page 10, paragraph [0091]). Weng further teaches wherein said circularizing is performed using a ligation enzyme, and wherein said ligation enzyme is degraded prior to said amplifying (Pages 13-14, paragraph [0113]). Weng further teaches on processing sequence reads produced from the described methods to obtain reads with the same sequence (Page 10, paragraph [0091]), which may include one of a number of sequence differences that reasonably represent genomic features (Page 11, paragraph [0097]). Weng further teaches that the methods further comprise diagnosing and optionally treating based on sequence variants (Page 11, paragraph [0098]). Weng later reasserts that the methods described may have therapeutic applications, including diagnosis of a condition, informing the selection of therapies, and actual treatment of a subject based on the methods (Page 33, paragraph [0198]). These teachings reasonably suggest a method further comprising administering a therapeutic to a human subject upon determining that a genomic feature in sequencing reads is associated with a disease state. Weng further teaches using described methods to monitor treatment efficacy by comprising patient ctDNA samples from before, during, and after treatment (Page 51, paragraph [0209]).
In a final example, Troll (A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos, BMC Genomics, December 2019, 20, 1-14) teaches on processing a plurality of nucleic acid molecules to obtain a plurality of single stranded nucleic acid molecules (Page 2, column 2, paragraph 4) with no end repair (Page 2, column 2, paragraph 2; Page 5, column 1, paragraph 2).
Having considered the factors discussed in MPEP 2106.05 (a)-(c) and (e)-(h), as well as the well-understood, routine, and conventional nature of what is claimed given the examples of Mouliere, Wang, Lo, Weng, and Troll, it is clear that the additional elements recited in the claims, whether considered individually or as a combination, do not integrate the judicial exception into a practical application of that exception in such a way as to provide meaningful limits on the use of the judicial exception. Therefore, claims 34-35, 37, 50, 52, and 172-187 are rejected here under 35 U.S.C. 101.
Response to Arguments
Applicant's arguments filed July 2nd, 2026 have been fully considered but they are not persuasive.
The Applicant first states that claim 34 has been amended to clarify the claimed subject matter and is now eligible under Step 2A and Step 2B (Page 11 of the Remarks filed July 2nd, 2026). With respect to Step 2A, prong two, the Applicant includes the full recitation of claim 34, stating that the elements of amended claim 34 integrates the alleged judicial exception into a practical application of identifying a disease associated genomic feature in a human subject from single stranded sequencing reads (Pages 11-12 of the Remarks filed July 2nd, 2026). The Applicant argues that the invention improves disease detection by enabling identification of disease-associated genomic features and can detect previously unknown features and associate them with a disease state in a human subject (Page 12 of the Remarks filed July 2nd, 2026). With respect to Step 2B, the Applicant includes part of claim 34 with added emphasis, stating that the amendments recite a combination of elements that were not routine or conventional at the time of filing and the cited references do not meet all elements of the claim (Pages 12-13 of the Remarks filed July 2nd, 2026). The Applicant argues that the rejection of claim 34 should be withdrawn, and given claims 35, 37, 50, and 52 depend from claim 34, the rejection of these claims should also be withdrawn (Page 13 of the Remarks filed July 2nd, 2026).
In response to these arguments, it is noted that the amended elements of claim 34 do not serve to integrate the judicial exceptions into a practical application given the above presented 101 analysis. Briefly, the limitations are not considered “meaningful limitations” because they do not provide an inventive concept given the well-understood, routine and conventional nature of what is claimed. In addition, they represent insignificant extra-solution activity, i.e. “data gathering”. Therefore, the additional limitations as presented in the amended claim 34 do not represent integration of a practical application. In addition, it is specifically noted that the emphasized statement of “amended claim 34 can detect previously unknown features” is not an aspect of the invention that is currently claimed. Therefore, it cannot serve as the practical application of the invention. Furthermore, given the above presented 101 analysis, the amended claim 34 is found to be routine and conventional given the presented art citations. Therefore, the arguments are not considered persuasive.
Claim Rejections - 35 USC § 103 – Modified – Necessitated by Amendment and the Addition of New Claims
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 34-35, 37, 52, 173-176, and 179-182 are rejected under 35 U.S.C. 103 as being unpatentable over Mouliere (Enhanced detection of circulating tumor DNA by fragment size analysis, Science Translational Medicine, November 2018, 10, 1-13; cited on the IDS filed January 17th, 2024, copy with supplement is provided; previously cited), in view of Wang (CLAmp-seq: A Novel Amplicon-Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC, Small Methods, August 2019, 4, 1-10; previously cited), as evidenced by Yang (Cell-Free DNA Comprises the Strand-Specific Characteristic Associated with Transcription and Methylation, Clinical Chemistry, September 2025, 71, 980-992; previously cited) and Cheng (A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection, Frontiers in Oncology, March 2024, 14, 1-11; previously cited).
Regarding instant claim 34, Mouliere teaches a method for nucleic acid analysis, comprising: (a) obtaining a sample comprising cell-free deoxyribonucleic acid (DNA) from a human subject (Page 2, column 1, paragraph 3; Page 10, column 2, paragraph 2; Page 1, column 2, paragraph 1: plasma contains ctDNA and cfDNA) and (b) extracting a plurality of nucleic acid molecules from said sample obtained from said human subject, wherein said plurality of nucleic acid molecules comprises single stranded nucleic acid molecules and double stranded nucleic acid molecules (Page 10, column 2, paragraph 2). Mouliere’s methods use cfDNA and ctDNA (which is a fraction of total cell-free DNA, see Mouliere’s introduction) from plasma (Page 2, column 1, paragraph 4 to column 2, paragraph 1). As evidenced by Yang, cfDNA in blood contains both single-stranded and double-stranded DNA (Page 980, column 2, Introduction). Mouliere further teaches (d) sequencing a plurality of nucleic acid molecules or a derivative thereof to obtain sequencing reads (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Supplementary Materials, Page 3); (e) processing sequencing reads to obtain (i) a plurality of sequencing reads having a genomic feature and (ii) a plurality of sequencing reads not having said genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Supplementary Materials, Page 3); (f) processing said plurality of sequencing reads having said genomic feature in (e) to obtain a first size distribution of said plurality of sequencing reads having the genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D); (g) processing said plurality of sequencing reads not having said genomic feature in (e) to obtain a second size distribution of said plurality of sequencing reads not having said genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D); (h) determining a difference in size between said first size distribution and said second size distribution (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D); and (i) determining that said genomic feature in said sequencing reads is associated with a disease state in said human subject when said plurality of sequencing reads having said genomic feature have a size smaller than said plurality of sequencing reads not having said genomic feature (Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D).
Mouliere does not teach (c) processing said plurality of nucleic acid molecules to obtain a plurality of single stranded nucleic acid molecules or a derivative thereof or (d) sequencing a plurality of specifically single stranded nucleic acid molecules or a derivative thereof to obtain sequencing reads.
Wang, in a reasonably pertinent field, teaches processing a plurality of nucleic acid molecules to obtain a plurality of single stranded nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1) and sequencing a plurality of single stranded nucleic acid molecules to obtain sequencing reads (Page 2, column 2, paragraph 2; Figure 1). As evidenced by Cheng, CLAmp-seq is considered a single-stranded DNA library preparation technique (Page 4, column 2, paragraphs 2-3).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere with the library preparation of Wang. Since Wang teaches on library preparation for sequencing of cell-free DNA, which is reasonably pertinent to Mouliere, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because the preparation technique of Wang utilizes concatemer error correction to suppress sequencing errors as well as polymerase errors introduced during PCR amplification (Page 2, column 1, paragraph 2).
It is noted by the Examiner that the recitation of “processing said sequencing reads to obtain (i) a plurality of sequencing reads having a genomic feature and (ii) a plurality of sequencing reads not having said genomic feature” and further references to said genomic feature have been interpreted such that the genomic feature is previously known to be associated with a disease, unless claimed otherwise. This interpretation is based on descriptions from the instant specification at paragraphs [0066], [0074], and [0075]. Given this interpretation, the difference in size distribution serves as confirmation that the genomic feature is associated with the disease given that it appears in a different nucleic acid size distribution than nucleic acid molecules that lack the genomic feature.
Regarding instant claim 35, Mouliere, in view of Wang, teaches the method of claim 34. Wang further teaches wherein (c) comprises denaturing said plurality of nucleic acid molecules (Page 2, column 2, paragraph 2).
Regarding instant claim 37, Mouliere, in view of Wang, teaches the method of claim 34. Wang further teaches wherein (c) comprises (i) circularizing individual single stranded nucleic acid molecules of said plurality of nucleic acid molecules to form a plurality of circular nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1); and (ii) amplifying said plurality of circular nucleic acid molecules to yield a plurality of amplified nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1).
Regarding instant claim 52, Mouliere, in view of Wang, teaches the method of claim 34. Mouliere further teaches wherein said genomic feature comprises a single nucleotide variant (SNV) (Supplementary Materials, Page 3, Tam-Seq).
Regarding instant claim 173, Mouliere, in view of Wang, teaches the method of claim 34. Mouliere further teaches the method further comprising, prior to said processing in (c), subjecting said plurality of nucleic acid molecules to size selection to enrich for nucleic acid molecules having sizes less than a size threshold (Page 2, column 2, paragraph 2: “We determined the feasibility of selective sequencing of shorter fragments using in vitro sizes election with a bench-top microfluidic device followed by sWGS…”; Figure 3A).
Regarding instant claim 174, Mouliere, in view of Wang, teaches the method of claim 173. Mouliere further teaches wherein said size threshold is at most 360 nucleic acid bases (Figure 3A: 90-150 bp).
It is noted that the courts have found “[i]n the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990)”. Thus, the range as taught in the art is obvious given it falls below the claimed threshold.
Regarding instant claim 175, Mouliere, in view of Wang, teaches the method of claim 173. Mouliere further teaches wherein said size selection comprises gel purification (Supplementary Materials, Page 3, paragraph 1: DNA loaded on 3% agarose gel).
Regarding instant claim 176, Mouliere, in view of Wang, teaches the method of claim 34. Mouliere further teaches wherein an average of said first size distribution of said plurality of sequencing reads having said genomic feature is less than an average of said second size distribution of said plurality of sequencing reads not having said genomic feature (Figure 2D).
Regarding instant claim 179, Mouliere, in view of Wang, teaches the method of claim 34. Mouliere further teaches wherein said sequencing in (d) comprises whole genome sequencing (Page 2, column 1, paragraph 4 to column 2, paragraph 1).
Regarding instant claim 180, Mouliere, in view of Wang, teaches the method of claim 34. Wang further teaches wherein said processing in (c) comprises untargeted amplification of said plurality of nucleic acid molecules (Page 2, column 2, paragraph 2; Figure 1: amplification via primers hybridized to sequencing adapters for PCR amplification).
Regarding instant claim 181, Mouliere, in view of Wang, teaches the method of claim 34.
It is noted that the subject matter of a properly construed claim is defined by the terms that limit its scope. It is this subject matter that must be examined. As a general matter, the grammar and intended meaning of terms used in a claim will dictate whether the language limits the claim scope. Language that suggests or makes optional but does not require steps to be performed or does not limit a claim to a particular structure does not limit the scope of a claim or claim limitation. “Wherein” clauses are examples of language that may raise a question as to the limiting effect of the language in a claim. See MPEP 2103 I.C. and MPEP § 2111.04. It is also noted that a “wherein” clause, such as that in claim 181, must give “meaning and purpose to the manipulative steps.” See, MPEP § 2111.04. The claimed “wherein said plurality of single stranded nucleic acid molecules obtained in (c) comprises at most 5% of said double stranded nucleic acid molecules” does not serve to add meaning and purpose to the manipulative steps as it describes an outcome of performing the method rather than further limiting the method itself. Therefore, the rejection of claim 34 can also be said to sufficiently reject claim 181.
In addition, as described in provided example in the specification, the CLAmp-seq method is performed for single strand based technology (Paragraphs [00107]-[00115] of the amended specification filed July 2nd, 2026). Given this being the only specific method exemplified in the specification, it is therefore reasonable that CLAmp-seq can achieve the claimed at most 5% of said double stranded nucleic acid molecules. Wang serves to teach the method of CLAmp-seq, a single stranded library method (whole document). Therefore, it would be obvious that CLAmp-seq as taught by Wang can achieve the claimed wherein said plurality of single stranded nucleic acid molecules obtained in (c) comprises at most 5% of said double stranded nucleic acid molecules.
Finally, it is further noted that the courts have found that “where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See MPEP 2144.05 II. Thus, the claimed “at most 5%” merely represents routine optimization of the method of the cited prior art.
Regarding instant claim 182, Mouliere, in view of Wang, teaches the method of claim 34.
It is reiterated that the subject matter of a properly construed claim is defined by the terms that limit its scope. It is this subject matter that must be examined. As a general matter, the grammar and intended meaning of terms used in a claim will dictate whether the language limits the claim scope. Language that suggests or makes optional but does not require steps to be performed or does not limit a claim to a particular structure does not limit the scope of a claim or claim limitation. “Wherein” clauses are examples of language that may raise a question as to the limiting effect of the language in a claim. See MPEP 2103 I.C. and MPEP § 2111.04. It is also noted that a “wherein” clause, such as that in claim 181, must give “meaning and purpose to the manipulative steps.” See, MPEP § 2111.04. The claimed “said difference in size between said first size distribution and said second size distribution obtained using a single-stranded DNA library is increased relative to a difference in size obtained using a double stranded DNA library” does not serve to add meaning and purpose to the manipulative steps as it describes an outcome of performing the method rather than further limiting the method itself. Therefore, the rejection of claim 34 can also be said to sufficiently reject claim 182.
In addition, as described in provided example in the specification, the CLAmp-seq method is performed for single strand based technology (Paragraphs [00107]-[00115] of the amended specification filed July 2nd, 2026). Given this being the only specific method exemplified in the specification, it is therefore reasonable that CLAmp-seq can achieve the claimed difference in size between said first size distribution and said second size distribution obtained using a single-stranded DNA library is increased relative to a difference in size obtained using a double stranded DNA library. Wang serves to teach the method of CLAmp-seq, a single stranded library method (whole document). Therefore, it would be obvious that CLAmp-seq as taught by Wang can achieve the claimed said difference in size between said first size distribution and said second size distribution obtained using a single-stranded DNA library is increased relative to a difference in size obtained using a double stranded DNA library.
In addition,
Response to Arguments
Applicant's arguments filed July 2nd, 2026 have been fully considered but they are not persuasive.
The Applicant first states that claim 34 has been amended to clarify certain differences between the claimed subject matter and the cited art (Page 13 of the Remarks filed July 2nd, 2026). The Applicant argues that claim 34 is non-obvious over the combinations of Mouliere, Wang, Yang, and Cheng because they do not meet all elements of the claim (Page 13 of the Remarks filed July 2nd, 2026). The Applicant then provides an example of Mouliere not teaching claim 34, including the entire recitation of claim 34 as amended with particular emphasis added, and further providing citations from Mouliere that allegedly show that it does not teach amended claim 34 (Pages 13-14 of the Remarks filed July 2nd, 2026). The Applicant further states that Wang, as evidenced by Yang and Cheng, does not cure the deficiencies of Mouliere, further restating a part of claim 34 that is allegedly not taught (Pages 14-15 of the Remarks filed July 2nd, 2026). The Applicant further states that claims 35, 37, and 52 depend from claim 34 and recite additional elements of particular advantage and utility, and given that the afore mentioned references do not meet the limitations of claim 34, they also do not meet the limitations of claims 35, 37, and 52.
In response to these arguments, it is noted that as currently analyzed above, it is found the Mouliere, in view of Wang and as evidenced by Yang and Cheng, teaches all claimed limitations recited in claims 34-35, 37, and 52. Therefore, the arguments presented are not persuasive.
Claims 50 and 172 are rejected under 35 U.S.C. 103 as being unpatentable over Mouliere (Enhanced detection of circulating tumor DNA by fragment size analysis, Science Translational Medicine, November 2018, 10, 1-13; cited on the IDS filed January 17th, 2024, copy with supplement is provided; previously cited) and Wang (CLAmp-seq: A Novel Amplicon-Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC, Small Methods, August 2019, 4, 1-10; previously cited), as applied to claims 34-35, 37, 52, 173-176, and 179-182 above, and further in view of Lo (US 20170024513 A1; cited on the IDS filed February 16th, 2023; previously cited).
Regarding instant claim 50, Mouliere, in view of Wang, teaches the method of claim 34.
Neither reference teaches wherein said genomic feature comprises an epigenetic modification selected from the group consisting of methylation, phosphorylation, ubiquitination, sumoylation, acetylation, ribosylation, citrullination, and fragmentation.
Lo, in the same field of endeavor, teaches on looking at both fragment size and methylation in cell-free DNA fragments to determine informativeness or specificity to a disease (e.g. cancer) (Page 23, paragraph [0294]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, with the genomic feature of Lo. Since both Mouliere, in view of Wang, and Lo are in the same field of endeavor (e.g. cfDNA fragmentation pattern as it relates to tumors), one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because using multiple disease associated parameters increases specificity in identification of informative fragments (Lo, Page 23, paragraph [0294]).
Regarding instant claim 172, Mouliere, in view of Wang and Lo, teaches the method of claim 50. Lo further teaches wherein said genomic feature comprises an epigenetic modification, wherein said epigenetic modification comprises methylation (Page 23, paragraph [0294]).
Response to Arguments
Applicant's arguments filed July 2nd, 2026 have been fully considered but they are not persuasive.
The Applicant argues that claim 50 is not obvious over the combination of Mouliere, Wang, and Lo given that it depends from claim 34 (Page 15 of the Remarks filed July 2nd, 2026). The Applicant argues that Mouliere and Wang do not meet all the elements of claim 34, much less the elements of claim 50, and Lo does not cure the deficiencies of Mouliere and Wang related to claim 34 (Page of the Remarks filed July 2nd, 2026).
In response to these arguments, it is noted that as currently analyzed above, it is found the Mouliere, in view of Wang and as evidenced by Yang and Cheng, teaches all claimed limitations recited in claims 34. Mouliere, in combination with Wang and Lo, teach all claimed limitations recited in claim 50. Therefore, the arguments presented are not persuasive.
Claims 177-178 and 184-187 are rejected under 35 U.S.C. 103 as being unpatentable over Mouliere (Enhanced detection of circulating tumor DNA by fragment size analysis, Science Translational Medicine, November 2018, 10, 1-13; cited on the IDS filed January 17th, 2024, copy with supplement is provided; previously cited) and Wang (CLAmp-seq: A Novel Amplicon-Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC, Small Methods, August 2019, 4, 1-10; previously cited), as applied to claims 34-35, 37, 52, 173-176, and 179-182 above, and further in view of Weng (US 20180057871 A1; cited on the IDS filed February 16th, 2023).
Regarding instant claim 177, Mouliere, in view of Wang, teaches the method of claim 37.
Neither reference teaches wherein said circularizing is performed under reaction conditions sufficient for self-joining of nucleic acid molecules shorter than a threshold length.
Weng, in a reasonably pertinent field, teaches wherein circularizing is performed under reaction conditions sufficient for self-joining of nucleic acid molecules shorter than a threshold length (Page 16, paragraph [0123]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, with the circularizing conditions of Weng. Since Weng teaches on amplification and sequencing of nucleic acids, which is reasonably pertinent to the method of Mouliere, in view of Wang, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because the methods of Weng “provide for highly sensitive detection of rare or low frequency nucleic acid sequence variants” (Weng, Page 1, paragraph [0006]).
Regarding instant claim 178, Mouliere, in view of Wang and Weng, teaches the method of claim 177. Weng further teaches wherein said threshold length is at most 5000 nucleotides (Page 16, paragraph [0123]).
Regarding instant claim 184, Mouliere, in view of Wang, teaches the method of claim 34.
Neither reference teaches said processing in (e) does not comprise aligning or mapping said sequencing reads to a reference genome.
Weng, in a reasonably pertinent field, teaches processing of sequencing reads comprises aligning sequencing reads to other sequencing reads (Page 10, paragraph [0091]). Thus, Weng teaches known techniques wherein processing sequencing reads comprises aligning to other sequencing reads instead of aligning with a reference genome.
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, with the alignment methods of Weng. Since Weng teaches on amplification and sequencing of nucleic acids, which is reasonably pertinent to the method of Mouliere, in view of Wang, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because the methods of Weng “provide for highly sensitive detection of rare or low frequency nucleic acid sequence variants” (Weng, Page 1, paragraph [0006]).
Regarding instant claim 185, Mouliere, in view of Wang, teaches the method of claim 37.
Neither reference teaches wherein said circularizing is performed using a ligation enzyme, and wherein said ligation enzyme is degraded prior to said amplifying.
Weng, in a reasonably pertinent field, teaches wherein said circularizing is performed using a ligation enzyme, and wherein said ligation enzyme is degraded prior to said amplifying (Pages 13-14, paragraph [0113]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, with the circularizing conditions of Weng. Since Weng teaches on amplification and sequencing of nucleic acids, which is reasonably pertinent to the method of Mouliere, in view of Wang, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because the methods of Weng “provide for highly sensitive detection of rare or low frequency nucleic acid sequence variants” (Weng, Page 1, paragraph [0006]).
Regarding instant claim 186, Mouliere, in view of Wang, teaches the method of claim 34.
Neither reference teaches the method further comprising administering a therapeutic to said human subject upon determining that said genomic feature in said sequencing reads is associated with said disease state.
Weng, in a reasonably pertinent field, teaches on processing sequence reads produced from the described methods to obtain reads with the same sequence (Page 10, paragraph [0091]), which may include one of a number of sequence differences that reasonably represent genomic features (Page 11, paragraph [0097]). Weng further teaches that the methods further comprise diagnosing and optionally treating based on sequence variants (Page 11, paragraph [0098]). Weng later reasserts that the methods described may have therapeutic applications, including diagnosis of a condition, informing the selection of therapies, and actual treatment of a subject based on the methods (Page 33, paragraph [0198]). These teachings reasonably suggest a method further comprising administering a therapeutic to a human subject upon determining that a genomic feature in sequencing reads is associated with a disease state.
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, with the treatment step of Weng. Since Weng teaches on amplification and sequencing of nucleic acids, which is reasonably pertinent to the method of Mouliere, in view of Wang, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because treating “refers to an approach for obtaining beneficial or desired results including but not limited to a therapeutic benefit and/or a prophylactic benefit.” (Weng, Page 33, paragraph [0199]).
Regarding instant claim 187, Mouliere, in view of Wang and Weng, teaches the method of claim 186. Weng further teaches on using described methods to monitor treatment efficacy using patient ctDNA samples from before, during, and after treatment (Page 51, paragraph [0209]).
None of the cited references specifically teach the aspect of monitoring performed based at least in part on a size difference between a third size distribution and a fourth size distribution obtained from sequencing reads derived from nucleic acid molecules obtained from said additional sample. However, given the teachings of Mouliere, in view of Wang, regarding a first and second distribution (Mouliere, Page 2, column 1, paragraph 4 to column 2, paragraph 1; Figure 2D) and the teachings of Weng regarding monitoring by performing the same methods on samples over time (Weng, Page 51, paragraph [0209]), it would be obvious that the method of Mouliere, in view of Wang, could be performed on a later sample to determine a third and fourth size distribution in the same way as described for the first and second size distribution.
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, to include a further step of monitoring after treatment using the same method as taught by Weng. Since Weng teaches on treatment of disease based on genomic features, which is reasonably pertinent to the method of Mouliere, in view of Wang, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because it can track treatment efficacy (Weng, Page 51, paragraph [0209]).
Claim 183 is rejected under 35 U.S.C. 103 as being unpatentable over Mouliere (Enhanced detection of circulating tumor DNA by fragment size analysis, Science Translational Medicine, November 2018, 10, 1-13; cited on the IDS filed January 17th, 2024, copy with supplement is provided; previously cited) and Wang (CLAmp-seq: A Novel Amplicon-Based NGS Assay with Concatemer Error Correction for Improved Detection of Actionable Mutations in Plasma cfDNA from Patients with NSCLC, Small Methods, August 2019, 4, 1-10; previously cited), as applied to claims 34-35, 37, 52, 173-176, and 179-182 above, and further in view of Troll (A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos, BMC Genomics, December 2019, 20, 1-14).
Regarding instant claim 183, Mouliere, in view of Wang, teaches the method of claim 34.
Neither reference teaches wherein said processing in (c) does not comprise end repair.
Troll, in a reasonably pertinent field, teaches on processing a plurality of nucleic acid molecules to obtain a plurality of single stranded nucleic acid molecules (Page 2, column 2, paragraph 4) with no end repair (Page 2, column 2, paragraph 2; Page 5, column 1, paragraph 2).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Mouliere, in view of Wang, with no end repair of Troll. Since Troll teaches on single strand library preparation, which is reasonably pertinent to the method of Mouliere, in view of Wang, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because using the native termini of fragments allows for examining the base composition at the exact 5’ and 3’ ends of each fragment (Troll, Page 5, column 1, paragraph 2).
Conclusion
All claims stand rejected.
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 Allison E Schloop whose telephone number is (703)756-4597. The examiner can normally be reached Monday-Friday 8:30-5 ET.
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/ALLISON E SCHLOOP/Examiner, Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
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