Patent SG-11201811286S-A (SG)
Title: Synthetic wgs bioinformatics validation
Inventor: VASKE CHARLES
IPC: G16B50/00
Filed: 2017-06-30
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 111111111111111111111111111111111111111111111111111111111111111111111111110111111 Organization International Bureau (10) International Publication Number (43) International Publication Date .....0\"\" WO 2018/006057 Al 04 January 2018 (04.01.2018) W I PO I PCT (51) International Patent Classification: GOOF 19/22 (2011.01) GOOF 19/28 (2011.01) Published: — with international search report (Art. 21(3)) (21) International Application Number: PCT/US2017/040455 (22) International Filing Date: 30 June 2017 (30.06.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/357,282 30 June 2016 (30.06.2016) US (71) Applicant: NANTOMICS, LLC [US/US]; 9920 Jefferson Blvd., Culver City, CA 90232 (US). (72) Inventors: VASKE, Charles; 9920 Jefferson Blvd., Culver City, CA 90232 (US). PARULKAR, Rahul; 9920 Jeffer- son Blvd., Culver City, CA 90232 (US). SANBORN, John, Zachary; 9920 Jefferson Blvd., Culver City, CA 90232 _ (US). BENZ, Stephen; 9920 Jefferson Blvd., Culver City, CA 90232 (US). JOHNSON, Mark; 9920 Jefferson Blvd., — Culver City, CA 90232 (US). = Agent: FESSENMAIR, Martin et al.; Umberg Zipser = (74) LLP, 1920 Main Street, Suite 750, Irvine, CA 92614 (US). Designated States (unless otherwise indicated, for every (81) kind of national protection available): AE, AG, AL, AM, = = AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, = = DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, = HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, = KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, = = SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. = = Designated States (unless otherwise indicated, for every (84) = kind of regional protection available): ARIPO (BW, GH, = GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, = UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, = TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, — EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). = — 1-1 IN kr) (54) Title: SYNTHETIC WGS BIOINFORMATICS VALIDATION © (57) : Systems, methods, and devices for generating synthetic genomic datasets and validating bioinformatic pipelines for 0 --- genomic analysis are disclosed. In preferred embodiments, synthetic maternal and paternal datasets with known variants are used with GC 1-1 matched normal synthetic datasets to validate various bioinformatic pipelines. Bioinformatic pipelines are evaluated using the synthetic © datasets to assess design changes and improvements. Accuracy, PPV, specificity, sensitivity, reproducibility, and limit of detection of N the pipelines in calling variants in synthetic datasets is reported. O