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 .
Claims Status
Claims 1, 10-13, 15, 17, 18, 21, 23-26, & 31-34 filed on 07/29/2026 are pending. The cancellation of claims 19, 20, & 22 without prejudice or disclaimer in the reply filed 07/29/2026 is acknowledged. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 112
Claims 10-13, 15, 18, 24-26, & 31-34 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 10, the recitation of “further comprising after (a) generating one or more fragment length ratios” in lines 1-2 of the claim is unclear how one or more fragment length ratios can be generated after (a) if determining the length of nucleic acid fragments isn’t recited until step (b). If this is the result of a typographical error should be amended to recite “further comprising after (b) generating one or more fragment length ratios”.
Regarding claim 18, the recitation of “wherein detecting the presence or absence of a population of cells in a subject in (b) is according to the comparison” in lines 1-2 of the claim is unclear how determining the presence or absence of a population of cells in (b) if determining the presence or absence of a population of cells isn’t recited until step (c). If this is the result of a typographical error should be amended to recite “wherein detecting the presence or absence of a population of cells in a subject in (c) is according to the comparison”.
Regarding amended claim 24, the recitation of “of the nucleic acid fragment lengths determined in (a)” in line 3 of the claim is unclear how nucleic acid fragment lengths can be determined in (a) if determining the length of nucleic acid fragments isn’t recited until step (b). If this is the result of a typographical error should be amended to recite “of the nucleic acid fragment lengths determined in (b)”.
Regarding amended claim 26, the recitation of “wherein detecting the presence or absence of a population of cells in a subject in (b)” in lines 1-2 of the claim is unclear how determining the presence or absence of a population of cells in (b) if determining the presence or absence of a population of cells isn’t recited until step (c). If this is the result of a typographical error should be amended to recite “wherein detecting the presence or absence of a population of cells in a subject in (c)”.
Regarding claim 31, the recitation of “according to the presence or absence of the population of cells detected in (b)” in lines 1-2 of the claim is unclear how the presence or absence of a population of cells can be detected in (b) if determining the presence or absence of a population of cells isn’t recited until step (c). If this is the result of a typographical error should be amended to recite “according to the presence or absence of the population of cells detected in (c)”.
Claims 11-13 & 15 are rejected due to their dependence on claim 10, claim 25 is rejected due to its dependence on claim 24, and claims 32-34 are rejected due to their dependence on claim 31.
Claim Rejections - 35 USC § 103
Claim(s) 1, 10, 13, 17, 18, 21, 23-26, 31, & 32 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell (WO 2020/132499 A2, June 2020), as cited on the IDS dated 09/29/2023, in view of Liu (Liu et al.; bioRxiv, pages 1-49, October 2019), as cited in the IDS dated 09/29/2023.
Regarding amended claim 1, Hubbell teaches a method of characterizing a cancer genome in a subject through detection of shifts in cell-free DNA fragment length distributions in a biological fluid sample (test sample from a subject) comprising determining the distribution of cell-free DNA fragment lengths in which it was determined the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments than fragments lengths originating from non-cancerous cells (detecting the presence or absence of a population of cells in a subject according to the nucleic acid fragment lengths determined) (paragraph [0014] lines 6-13; paragraph [00108] lines 1-9; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14). Hubbell also teaches extracting nucleic acids from a subject and preparing a sequencing library for the detection of fragment lengths in the sample for detecting the presence or absence of cancer comprising enriching target DNA sequence from the library (enriching the test sample for one or more genomic regions thereby generating one or more pools of enriched nucleic acid) (paragraph [00180] lines 1-10; paragraph [00181] lines 1-3; paragraph [00182] lines 1-6).
Hubbell does not teach one or more genomic regions are selected according to A/B status.
Liu teaches a method for determining correlation between fragment length in cell free DNA and chromatin organization relating to A/B compartments (A/B status) in cancer patients in which fragment lengths for each 500 kb bin (genomic region) was calculated and correlated to A/B compartments in chromatin organization to determine differences and cell types from cancer versus non-cancer samples (one or more genomic region is selected according to A/B status for a chosen cell type) in which the cells are prepared for Hi-C analysis (A/B compartments mapped for a given cell type using spatial proximity analysis) through enrichment of the sample (enriching a test sample for one or more genomic regions selected by identifying A/B status for a chosen cell type thereby generating one or more pools of enriched nucleic acid) (abstract lines 1-12; pg. 4 1st full paragraph lines 1-20; pg. 9 1st full paragraph lines 1-5; pg. 9 2nd full paragraph lines 1-12; pg. 9-11 paragraph bridging pg. 9 & 11 lines 1-33; pg. 21 1st full paragraph lines 1-10). Liu also teaches that this method provides a noninvasive method monitoring genome organization and accurate quantification of cell death in different clinical conditions through cell-free DNA samples from cancer patients and healthy individuals (abstract lines 8-12).
Hubbell and Liu are considered to be analogous to the claimed invention because they are all in the same field of nucleic acid fragment length analysis in cancer samples. Therefore, 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 have modified the method the method of characterizing a cancer genome in a cancer subject through detection of shifts in cell-free DNA fragment length distributions in windows of the genome in Hubbell to incorporate the selecting of one or more genomic regions according to A/B status through enriching one or more genomic regions by identifying A/B status for a chosen cell type as taught in Liu because Liu teaches that doing so would provide a noninvasive method monitoring genome organization and accurate quantification of cell death in different clinical conditions through cell-free DNA samples from cancer patients and healthy individuals.
Regarding claim 10, Hubbell teaches determining the distribution of cell-free DNA fragment lengths, filtered to 210 nucleotides or less, in which it was determined the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments (fragment length ratios) than fragments lengths (fragment length ratios) originating from non-cancerous cells (detecting the presence or absence of a population of cells in a subject according to the nucleic acid fragment length ratios determined) (paragraph [0014] lines 6-13; paragraph [00108] lines 1-9; paragraph [00161] lines 1-6; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14).
Regarding claim 13, Hubbell teaches measuring a ratio of the amount of nucleic acid fragments according to aligning to a particular region in the genome comprising in a window of the genome (one or more fragment length ratios are generated from one or more genomic portions) (paragraph [00161] lines 1-14).
Regarding claim 17, Hubbell teaches the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments than fragments lengths originating from non-cancerous cells (control samples) (comparing the nucleic acid fragment lengths for the test (cancerous) sample to one or more control (non-cancerous) samples) (paragraph [0014] lines 6-13; paragraph [0043] lines 1-3; paragraph [00108] lines 1-9; paragraph [00125] lines 1-9; paragraph [00161] lines 1-6; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14).
Regarding claim 18, Hubbell teaches the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments than fragments lengths originating from non-cancerous cells (control samples) (presence or absence of a population of cells in a subject is according to the comparison) (paragraph [0014] lines 6-13; paragraph [0043] lines 1-3; paragraph [00108] lines 1-9; paragraph [00125] lines 1-9; paragraph [00161] lines 1-6; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14).
Regarding amended claim 21, Liu teaches a method for determining correlation between fragment length in cell free DNA and chromatin organization relating to A/B compartments (A/B status) in cancer patients in which fragment lengths for each 500 kb bin (genomic region) was calculated and correlated to A/B compartments in chromatin organization to determine differences and cell types from cancer versus non-cancer samples (one or more genomic region is selected according to A/B status differences between diseased (cancer) and non-diseased (non-cancer) cell) (abstract lines 1-12; pg. 4 1st full paragraph lines 1-20; pg. 9 1st full paragraph lines 1-5; pg. 9 2nd full paragraph lines 1-12; pg. 9-11 paragraph bridging pg. 9 & 11 lines 1-33).
Regarding claim 23, Hubbell teaches that during enrichment hybridization (capture) probes are used to target and pull down nucleic acid fragments informative for the presence or absence of cancer (enriching comprises hybridizing capture probes to nucleic acid fragments in the test sample, wherein the capture probes are specific to the one or more selected genomic regions) (paragraph [00180] lines 1-10; paragraph [00181] lines 1-3; paragraph [00182] lines 1-6).
Regarding amended claims 24 & 26 and claim 25, Hubbell does not teach identifying an A/B status of the genome for a test sample according to the nucleic acid fragment lengths.
Liu teaches a method for determining correlation between fragment length in cell free DNA and chromatin organization relating to A/B compartments (A/B status) in cancer patients in which fragment lengths for each 500 kb bin (genomic region) was calculated and correlated to A/B compartments in chromatin organization to determine differences and cell types present in cancer samples compared to non-cancer samples (identifying an A/B status of the genome for the test sample according to nucleic acid fragment lengths and comparing to the A/B status to a control and further detecting presence or absence of a population of cells according to the A/B status comparison) (abstract lines 1-12; pg. 4 1st full paragraph lines 1-20; pg. 9 1st full paragraph lines 1-5; pg. 9 2nd full paragraph lines 1-12; pg. 9-11 paragraph bridging pg. 9 & 11 lines 1-33). Liu also teaches that this method provides a noninvasive method monitoring genome organization and accurate quantification of cell death in different clinical conditions through cell-free DNA samples from cancer patients and healthy individuals (abstract lines 8-12).
Hubbell and Liu are considered to be analogous to the claimed invention because they are all in the same field of nucleic acid fragment length analysis in cancer samples. Therefore, 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 have modified the method the method of characterizing a cancer genome in a cancer subject through detection of shifts in cell-free DNA fragment length distributions in windows of the genome in Hubbell to incorporate the identifying an A/B status of the genome compared to a control genome to determine differences between a cancer (diseased) and non-diseased (non-cancer) cell as taught in Liu because Liu teaches that doing so would provide a noninvasive method monitoring genome organization and accurate quantification of cell death in different clinical conditions through cell-free DNA samples from cancer patients and healthy individuals.
Regarding claims 31 & 32, Hubbell teaches a method of characterizing a cancer genome in a subject through detection of shifts in cell-free DNA fragment length distributions in a biological fluid sample (test sample from a subject) comprising determining the distribution of cell-free DNA fragment lengths in which it was determined the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments than fragments lengths originating from non-cancerous cells (detecting a presence or absence of a disease comprising cancer according to the presence or absence of a population of cells in a subject according to the nucleic acid fragment lengths determined) (paragraph [0014] lines 6-13; paragraph [00108] lines 1-9; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14).
Claim(s) 11 & 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell (WO 2020/132499 A2, June 2020), as cited on the IDS dated 09/29/2023, and Liu (Liu et al.; bioRxiv, pages 1-49, October 2019), as cited in the IDS dated 09/29/2023, as applied to claims 1, 10, 13, 17, 18, 21, 23-26, 31, & 32 above, and further in view of Cristiano (Cristiano et al.; Nature Letter, Vol. 570, pages 385-404, June 2019), as cited in the IDS dated 09/29/2023, and Zhao (EP 3175000 B1, July 2020).
The teachings of Hubbell and Liu with respect to claims 1 & 10 are discussed above.
Regarding claims 11 & 12, Hubbell teaches determining the distribution of cell-free DNA fragment lengths, filtered to 210 nucleotides or less, in which it was determined the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments (short fragment counts) than fragments lengths (medium to long fragment counts) originating from non-cancerous cells (paragraph [0014] lines 6-13; paragraph [00108] lines 1-9; paragraph [00161] lines 1-6; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14).
Hubbell and Liu does not teach wherein each of the one or more fragment length ration is chosen from short fragment counts, comprising length of about 0 bp to about 99 bp, medium fragment counts, comprising length of about 100 bp to about 149 bp, or long fragment counts, comprising length about 150 bp to 220 bp.
Cristiano teaches a method of analyzing cell-free DNA fragmentation profiles in patients with cancer compared to non-cancer cells in which the fraction of small cfDNA fragments from 100-150 bp (medium fragment counts comprising length of about 100 bp to about 149 bp) to larger cfDNA fragments from 151-220 bp (long fragment counts comprising length of about 150 bp to about 220 bp) (abstract lines 1-21; pg. 386 column 1 1st full paragraph lines 1-4; pg. 386 paragraph bridging column 1 & 2 lines 1-11; pg. 386 column 2 1st full paragraph lines 10-17). Cristiano also teaches that this method provides an approach for screening and early detection and monitoring for human cancer (abstract lines 18-21).
Zhao teaches a method analyzing nucleic acid fragment lengths in cancer samples and selected multiple fragment lengths through normalizing the nucleic acid fragment lengths with a reference in which the nucleic acid sample may be enriched for a particular length or range of lengths for a length-based separation method (paragraph [0005] lines 15-28; paragraph [0010] lines 1-12; paragraph [0101] lines 1-13). Zhao also teaches that nucleic acids fragments of 100 bp, 90 bp, 50 bp, or 30 bp and under may be referred to as short fragments and fragments of 150 bp, 175bp, or 200 bp and over may be considered long fragments in which the fragments ranging from about 10 bp to about 100 bp may be enriched for and retained (short fragment counts comprising length of about 0 bp to about 99 bp) (paragraph [0102] lines 1-19). Zhao also teaches that this method can aid in diagnosis of and facilitate medical decisions in treatments for a medical condition comprising cancer (paragraph [0017] lines 6-11).
Hubbell, Liu, Cristiano, and Zhao are considered to be analogous to the claimed invention because they are all in the same field of nucleic acid fragment length analysis in cancer samples. Therefore, 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 have modified the method of characterizing a cancer genome in a cancer subject through detection of shifts in cell-free DNA fragment length distributions in Hubbell to incorporate analysis of one or more fragment length ratio comprising medium fragment counts comprising length of about 100 bp to about 149 bp and long fragment counts comprising length of about 150 bp to about 220 bp as taught in Cristiano because Cristiano teaches that doing so would provide an approach for screening and early detection and monitoring for human cancer and to incorporate analysis of one or more fragment length ratio comprising of short fragment counts comprising 10 bp to 100 bp (about 0 bp to about 99 bp) as taught in Zhao because Zhao teaches that doing so would provide a method that can aid in diagnosis of and facilitate medical decisions in treatments for a medical condition comprising cancer.
Claim(s) 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell (WO 2020/132499 A2, June 2020), as cited on the IDS dated 09/29/2023, and Liu (Liu et al.; bioRxiv, pages 1-49, October 2019), as cited in the IDS dated 09/29/2023, as applied to claims 1, 10, 13, 17, 18, 21, 23-26, 31, & 32 above, and further in view of Cristiano (Cristiano et al.; Nature Letter, Vol. 570, pages 385-404, June 2019), as cited in the IDS dated 09/29/2023.
The teachings of Hubbell and Liu with respect to claims 1, 10, & 13 are discussed above.
Regarding claim 15, Hubbell and Liu does not teach that the one or more genomic portions are about 250 kb in length.
Cristiano teaches a method of analyzing cell-free DNA fragmentation profiles in patients with cancer compared to non-cancer cells in which genomic portions can be analyzed in windows ranging in a size from thousands to millions of bases and in which 5 megabase (Mb) (5,000 kb) windows were used to evaluate cell-free DNA fragmentation patterns (one or more genomic portions are about 250 kb in length) (abstract lines 1-21; pg. 386 column 1 1st full paragraph lines 1-16; pg. 386 paragraph bridging column 1 & 2 lines 1-11; pg. 386 column 2 1st full paragraph lines 10-17). Cristiano also teaches that this method provides an approach for screening and early detection and monitoring for human cancer (abstract lines 18-21).
Hubbell, Liu, and Cristiano are considered to be analogous to the claimed invention because they are all in the same field of nucleic acid fragment length analysis in cancer samples. Therefore, 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 have modified the method of characterizing a cancer genome in a cancer subject through detection of shifts in cell-free DNA fragment length distributions in windows of the genome in Hubbell to incorporate one or more genomic portions (windows) about 250 kb in length as taught in Cristiano because Cristiano teaches that doing so would provide an approach for screening and early detection and monitoring for human cancer.
Claim(s) 33 & 34 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell (WO 2020/132499 A2, June 2020), as cited on the IDS dated 09/29/2023, and Liu (Liu et al.; bioRxiv, pages 1-49, October 2019), as cited in the IDS dated 09/29/2023, as applied to claims 1, 10, 13, 17, 18, 21, 23-26, 31, & 32 above, and further in view of Gupta (Gupta; Hematopathology, Springer, pages 491-502, August 2019).
The teachings of Hubbell and Liu with respect to claims 1, 31, & 32 are discussed above.
Regarding claims 33 & 34, Hubbell teaches a method of characterizing a cancer genome in a subject through detection of shifts in cell-free DNA fragment length distributions in a biological fluid sample comprising determining the distribution of cell-free DNA fragment lengths in which it was determined the presence of a variant allele originating from a cancer cell comprise shorter cell-free DNA fragments than fragments lengths originating from non-cancerous cells (paragraph [0014] lines 6-13; paragraph [00108] lines 1-9; paragraph [00323] lines 1-12; paragraph [00327] lines 1-14). Hubbell also teaches that determining nucleic acid fragment sequences comprises sequencing methods comprising next generation sequencing (NGS) (paragraph [00177] lines 1-7; paragraph [00178] lines 1-3).
Hubbell and Liu does not teach that the disease is MDS-RS-MLD.
Gupta NGS techniques and processes comprising fragmentation of DNA and further sequencing of the prepared library in which the application of NGS in hematologic disorders provides new insights to disease initiation, progression, and therapy outcome comprising use of NGS to identify MDS-RS-MLD to augment clinic-pathological prognostic tools for this specific type of cancer (pg. 491 column 1 1st full paragraph lines 1-26; pg. 492-493 paragraph bridging pg. 492 & 493 lines 5-18; pg. 495 column 1 1st full paragraph lines 1-14; pg. 496-497 paragraph bridging pg. 496 & 497 lines 1-16; pg. 497 column 1 1st full paragraph lines 21-26).
Hubbell, Liu, and Gupta are considered to be analogous to the claimed invention because they are all in the same field of detection of cancer using NGS techniques. Therefore, 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 have modified the method of determining lengths of nucleic acid fragment sequences comprising next generation sequencing (NGS) in cancer samples in Hubbell to incorporate the use of NGS to determine specific cancer types comprising MDS-RS-MLD as taught in Gupta because Gupta teaches that doing so would augment clinic-pathological tools for disease initiation, progression, and therapy outcome in MDS-RS-MLD.
Response to Arguments
The response traverses the rejection. The response asserts that Liu does not teach or suggest the claimed feature of enriching a test sample from a subject for one or more selected genomic regions, where he one or more genomic regions are selected by identifying A/B status for a chosen cell type and that the only mention of enrichment in Liu is at page 21 first paragraph. Further, the response also asserts that the enrichment in Liu does not mention any selection of genomic regions based on A/B status and accordingly, Hubbel in combination with Liu does not teach or suggest all elements of the claimed subject matter. This argument has been thoroughly reviewed but was not found persuasive. First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Further, Hubbell teaches extracting nucleic acids from a subject and preparing a sequencing library for the detection of fragment lengths in the sample for detecting the presence or absence of cancer comprising enriching target DNA sequence from the library (enriching the test sample for one or more genomic regions thereby generating one or more pools of enriched nucleic acid) (paragraph [00180] lines 1-10; paragraph [00181] lines 1-3; paragraph [00182] lines 1-6). In addition, Liu teaches a method for determining correlation between fragment length in cell free DNA and chromatin organization relating to A/B compartments (A/B status) in cancer patients in which fragment lengths for each 500 kb bin (genomic region) was calculated and correlated to A/B compartments in chromatin organization to determine differences and cell types from cancer versus non-cancer samples (one or more genomic region is selected according to A/B status for a chosen cell type) in which the cells are prepared for Hi-C analysis (A/B compartments mapped for a given cell type using spatial proximity analysis) through enrichment of the sample (enriching a test sample for one or more genomic regions selected by identifying A/B status for a chosen cell type thereby generating one or more pools of enriched nucleic acid) (abstract lines 1-12; pg. 4 1st full paragraph lines 1-20; pg. 9 1st full paragraph lines 1-5; pg. 9 2nd full paragraph lines 1-12; pg. 9-11 paragraph bridging pg. 9 & 11 lines 1-33; pg. 21 1st full paragraph lines 1-10). Therefore, Hubbell in combination with Liu teaches all of the elements of the claimed subject matter.
The response also asserts that the other cited references do not cure the deficiencies of Hubbell ana Liu. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 1, 10-13, 15, 17, 18, 21, 23-26, & 31-34 are 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 BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
