Status of the Claims
Claims 1-17, 19-21 and 189 are pending and examined herein.
It is noted the claim 189 is a probable typo and is likely meant to be claim 18. However, for the purposes of examination, the claims will be referred to as written. Correction of the claim number is invited if determined appropriate by Applicant.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Interpretation
Claim 17 recites that the assay described therein is “to detect minimal residual disease in the subject.” As written, this constitutes an intended use and, as there are no positive method steps recited to further limit the claim and the use does not impose any manipulative difference to the method, the intended use is non-limiting.
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 2, 7, 10, and 21 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.
Regarding claim 2, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 2 recites the broad recitation "at least about 700 base-pairs", and the claim also recites "preferably at least about 800 base-pairs" which is the narrower statement of the range/limitation. The claim is considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. For the purpose of examination, this claim will be interpreted as being limited by the broad recitation (700 base-pairs). This rejection may be overcome by removing one of the recited ranges, or otherwise clearly specifying the required range. Other solutions are possible.
Regarding claims 7, 10, and 21, each of these claims recite a limitation with regards to a “bead:DNA amplicon ratio”, but the type of ratio is not specified as to whether it is a molar, volume, mass, or other type of ratio. For the purpose of examination, these limitations will be interpreted as volume ratios. This rejection may be resolved by providing the type of ratio in the claim language. Other solutions are possible.
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 11-16 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to abstract ideas without significantly more.
Claim 11 recites “validating an average size of the amplicons”.
Claims 12 and 13 recite “performing a first mapping”, “performing a second mapping”, and “merging the first mapping with the second mapping”.
Claims 14-16 recite “analyzing the sequence reads” and “filtering the putative SVs” and claim 16 further recites “designing, by computer software, at least one primer pair”.
The listed limitations are all abstract ideas, specifically mental processes that could be performed in the human mind, or by a human using a pen and paper.
These judicial exceptions are not integrated into a practical application because the additional elements recited are insignificant extra-solution activity and there are no steps recited that apply or use the judicial exception. Specifically, the additional elements of “measuring a concentration” of claim 11 and “sequencing the amplicons” of claims 12-16 are simply data gathering steps required to use the judicial exceptions and do not add a meaningful limitation to the method. Additionally, regarding the computer-implemented “designing” limitation of claim 16, the inclusion of a generic computer does not add a meaningful limitation to the abstract idea because it amounts to simply implementing the abstract idea on a computer.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements are well-understood, routine, and conventional. Specifically, the limitations of claim 1 recite steps for isolating DNA from formalin-fixed, paraffin-embedded tissue, including extraction, fragmentation, adaptor ligation, size-selection, and amplification. These are all standard steps for isolating DNA from FFPE tissue, and are recapitulated in several publications including So et al. (Gen. Med. (2018), 3: 2; cited in IDS of 2/22/2024) and Hartwig et al. (WO 2019/070598; cited in IDS of 2/22/2024). In the instant specification, applicant argues that recited fragment size “of at least about 500 base-pairs” amounts to an inventive concept. However, these fragment sizes are well-known in the art, as evidenced by the above publications as well as the instructions of commercially available kits for standard NGS library prep such as TruSeq®Nano DNA Library Prep (Illumina, 2015) or those specific to isolating DNA from FFPE tissue such as the Covaris truXTRAC™ FFPE DNA microTUBE Kit (Covaris, 2019). Therefore, the recited limitations of claim 1 do not amount to significantly more, indicating that claims 11-16 are directed to ineligible subject matter.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
So et al.
Claims 1, 3-4, 9, and 11-15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by So et al. (Gen. Med. (2018), 3: 2; cited in IDS of 2/22/2024) as evidenced by Promega (Technical Manual, 2015).
Regarding claim 1, So discloses a library preparation method comprising: extracting DNA from an FFPE tissue sample (p.2, “Overview of in-solution OS-Seq”; p. 7, “DNA Samples and Preparation”); fragmenting the DNA into fragments with an average fragment size of 550 bp (Fig. 1; p. 2, “Overview…”); ligating adaptors to the fragments (Fig. 1; p. 2, “Overview…”); isolating selected adaptor-ligated fragments with an average size within a range of about 500 to 1000 bp from unwanted material (p. 2, “Overview…”: size-selective bead purification); and amplifying the selected adaptor-ligated fragments to obtain amplicons (Fig.1 description: “the sequence library is expanded by PCR”).
Regarding claims 3 and 9, So discloses that the extracting step was performed using the ReliaPrep FFPE gDNA Miniprep System from Promega (p. 7, “DNA samples and preparation”), which teaches emulsifying paraffin from the sample into a buffer (p. 7, “Deparaffinization” – steps 1-2); centrifuging the buffer to form a DNA pellet (p. 7, “Deparaffinization” – steps 7-10); rehydrating the pellet with lysis buffer (p. 7, “Lysis” – step 1); capturing the DNA from the lysis buffer onto a column (p.8, “Nucleic Acid Binding” – steps 4-5); and eluting the DNA from the column (p. 5, “Column Washing and Elution” – steps 9-10). Additionally, Promega discloses the use of microcentrifuge tubes.
Regarding claim 4, So further discloses that the fragmenting step comprises sonicating the eluate (p. 7, “DNA samples and preparation”, last ¶).
Regarding claim 11, So further discloses measuring the concentration of the amplicons (p. 8, “Targeting assay”, end of 2nd ¶). Furthermore, though not explicitly stated, there is reason to believe the amplicons would have an average size with a peak between about 600 and 800 bp. So teaches that the original fragments were sheared to 550 bp, after which adapters were ligated to both ends and then subjected to amplification (Fig. 1). Because of the length addition by the adapters, the resulting amplicons would fall within about 600 and 800 bp.
Regarding claim 12, So further discloses sequencing the amplicons (p. 8, “Targeting assay”, last sentence) and performing and merging two mappings of the reads to a reference by two algorithms (p. 8, “Alignment and performance metrics”).
Regarding claim 13, So further discloses using a first algorithm for assembling then traversing a genomic graph to build an alignment (p. 8, “Alignment and performance metrics”: BWA). Additionally So discloses using a second algorithm to identify indels in the reads when compared to a reference (p. 8, “Variant calling in NA12878 and matched samples”: MuTect).
Regarding claims 14 and 15, So further discloses sequencing the amplicons (p. 8, “Targeting assay”, last sentence); identifying putative structural variants; and filtering the putative structural variants by comparing them to a database of known germline structural variants and removing the matching ones (p. 8, “Variant calling in NA12878 and matched samples”: MuTect).
Hartwig et al.
Claims 1, 3-4, 6, and 9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hartwig et al. (WO 2019/070598; cited in IDS of 2/22/2024) as evidenced by Schroer et al. (Qiagen, 2017).
Regarding claim 1, Hartwig discloses a library preparation method comprising: extracting DNA from an FFPE tissue sample (p. 8, ¶[36]); fragmenting the DNA into fragments with an average fragment size of 500-600 bp (p. 8, ¶[37]); ligating adaptors to the fragments (p. 10-11, ¶[45]); isolating selected adaptor-ligated fragments with an average size within a range of about 500 to 1000 bp from unwanted material (p. 12, ¶[42]); and amplifying the selected adaptor-ligated fragments to obtain amplicons (p. 13, ¶[54]).
Regarding claims 3 and 9, Hartwig discloses that the extracting step was performed using “commercially available kits (e.g., those sold by Qiagen or Covaris)” (p. 8, ¶[36]). One such kit is the Qiagen AllPrep DNA/RNA FFPE Kit, as evidenced by Schroer, which teaches emulsifying paraffin from the sample into a buffer; centrifuging the buffer to form a DNA pellet; rehydrating the pellet with lysis buffer; capturing the DNA from the lysis buffer onto a column; and eluting the DNA from the column (Fig. 1, below). Additionally, Schroer discloses the use of microcentrifuge tubes.
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Regarding claims 4 and 6, Hartwig discloses that the fragmenting step comprises sonicating an eluate (p. 8, ¶[39]) and reverse transcribing RNA from a supernatant (p. 8, ¶[36]; also see Schroer Fig. above).
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.
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.
So et al. and Rudd et al.
Claims 2 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over So et al. in view of Rudd et al. (Covaris Application Note, 2016).
Regarding claim 2, So discloses the limitations of claim 1, as discussed previously, but does not disclose that the average fragment size is at least about 700 base-pairs. Rudd discloses several average fragment sizes for FFPE-extracted DNA (Fig. 2 and 4), ranging from 150 bp to >5,000 bp. Additionally, Rudd teaches that fragmentation is “tunable to specific sizes” depending on the downstream application and that “the size of genomic fragments is highly dependent upon the handling of the tissue prior to its embedding in paraffin” (p. 2). This indicates that the fragmentation size can be easily controlled depending on the desired outcome, and therefore discovering an optimum range is considered routine optimization (see MPEP § 2144.05(II)). Therefore, it would have been obvious to one of ordinary skill in the art to perform the method of So with an average fragment size of at least about 700 bp because it constitutes optimization achievable by routine experimentation.
Regarding claim 5, So discloses all limitations of claim 4, as discussed previously. So does not disclose performing sonication until an average fragment size of at least about 800 bp, but performing the method of So with a fragment size of at least about 800 bp is considered routine optimization, as evidenced by Rudd and discussed above. Additionally, So does not disclose sonicating until the eluate reaches an optical density indicating the desired average fragment size. However, regardless of what the desired fragment size is, the optical density will inherently indicate that average fragment size if that is what is targeted by the fragmentation method. In other words, if the eluate is sonicated to an average fragment size of 800 bp, then the optical density would indicate that the average fragment size is 800 bp. Therefore, the limitations of claim 5 are considered obvious as routine optimization over So, as evidenced by Rudd.
So et al. and Beckman Coulter
Claims 7 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over So et al., as evidenced by NEB (FAQ, 2020) in view of Beckman Coulter (User Guide, 2012).
Regarding claim 7, So discloses all limitations of claim 1, as discussed previously. Additionally, So discloses repairing the fragments enzymatically (p. 8, “Targeting assay”: NEB repair) and purifying the fragments with magnetic beads (“The repaired DNA was then purified using… sREP+ beads”) after fragmentation and prior to ligation. So does not disclose using a bead:DNA fragment ratio of less than about 1.
Beckman Coulter discloses a range of bead:DNA fragment ratios from 1.2 to 0.4 (p. 1-3 and 1-5). It also indicates that the ratio of beads:DNA can be optimized to isolate the desired size selection range and “can be adjusted to suit the application and platform used” (p. 1-1). Therefore, it would be routine optimization for one of ordinary skill in the art to perform the method of So using a bead:DNA fragment ratio of less than about 1.
Regarding claim 8, So further discloses that the NEBNext FFPE DNA Repair Mix was used to perform the repairing step (p. 8, “Targeting assay”). As evidenced by NEB, this repair mix contains a polymerase and a ligase.
So et al. and Lucero et al.
Claims 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over So et al. in view of So et al. (US 2014/0287937) – herein referred to as Lucero. So disclosed all limitations of claim 14, as discussed above, but does not disclose designing a primer pair to amplify a target SV, nor using the primer pair to perform digital PCR on cell-free DNA. However, Lucero discloses designing primer pairs (p. 1, ¶[0008]; p. 20, ¶[0236]) to amplify a target SV (p. 18, ¶[0211]; p. 23, ¶[0258]), performing an assay (p. 9, ¶[0132]; Fig. 1: 140) on a sample from a subject from whom the FFPE tissue sample was obtained (Fig. 1), where the assay comprises digital PCR (p. 23, ¶[0258]) on cell-free DNA from blood (Fig. 1: 130). Additionally, Lucero teaches that this method is able to “improve the monitoring and treatment of a subject suffering from a disease” (p. 9, ¶[0130]). Therefore, it would have been obvious to one of ordinary skill in the art by the effective filing date to apply the method from Lucero to the FFPE DNA extraction method of So, yielding the predictable result of a method for assessing cancer with improved monitoring.
So et al., Rudd et al., and Beckman Coulter
Claims 19-21 are rejected under 35 U.S.C. 103 as being unpatentable over So et al. in view of Rudd et al. and Beckman Coulter.
Regarding claim 19, So discloses a method of preparing a sequencing library comprising fragmenting FFPE-DNA into fragments (Fig. 1; p. 2, “Overview…”); ligating adaptors to the fragments (Fig. 1; p. 2, “Overview…”); isolating selected adaptor-ligated from unwanted material (p. 2, “Overview…”: size-selective bead purification); and amplifying the selected adaptor-ligated fragments to obtain amplicons (Fig.1 description: “the sequence library is expanded by PCR”). So does not disclose fragmenting the DNA into fragments at least 800 bp in length on average, nor that the size selection enriched for fragments with a size of about 600 to about 900 bp. However, these would both be considered routine experimentation, as discussed above with regards to claim 2 via Rudd and claim 7 via Beckman Coulter. Therefore, it would have been obvious to one of ordinary skill in the art by the effective filing date to fragment the DNA to 800 bp and size select to about 600 to 900 bp.
Regarding clam 20, So further discloses that the method further comprises sonicating the sample to emulsify paraffin, centrifuging and resuspending the sample in lysis buffer to liberate the DNA, and purifying the DNA onto a column, as discussed with regards to claim 3.
Regarding claim 21, So further discloses purifying the fragments with magnetic beads and performing a clean-up on the amplicons, as discussed with regards to claim 7. So does not disclose a bead:DNA fragment ratio in a range of about 0.5 to 0.7. However, it would be routine optimization for one of ordinary skill in the art to perform the method of So using this bead:DNA fragment ratio and is therefore considered obvious.
Conclusion
No claims are allowed.
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/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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