Patent SG-11201805562Q-A (SG)
Title: Genomic infrastructure for on-site or cloud-based dna and rna processing and analysis
Inventor: VAN ROOYEN PIETER
IPC: G16B50/30
Filed: 2017-01-11
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property -, Organization 11111111011110111010101111101011111011101110111001110110011111111101111011111 International Bureau 0.. .1 j (10) International Publication Number (43) International Publication Date ..... ....r;,„I WO 2017/123664 Al 20 July 2017 (20.07.2017) WIPO I PCT (51) International Patent Classification: Jolla, CA 92037 (US). MEHIO, Rami; 3344 North Torrey GO6F 19/28 (2011.01) GO6F 19/22 (2011.01) Pines Court, Plaza Level, La Jolla, CA 92037 (US). (21) International Application Number: (74) Agents: CLEARY, James, P. et al.; Mintz Levin Cohn PCT/US2017/013057 Ferris Glovsky and Popeo, P.C., 3580 Cannel Mountain Road, Suite 300, San Diego, CA 92130-6768 (US). (22) International Filing Date: 11 January 2017 (11.01.2017) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (25) Filing Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (26) Publication Language: English 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, (30) Priority Data: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, 62/277,445 11 January 2016 (11.01.2016) US KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, (71) Applicant: EDICO GENOME, CORP. [US/US]; 3344 MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, (US). 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, (72) Inventors: VAN ROOYEN, Pieter; 3344 North Torrey ZA, ZM, ZW. Pines Court, Plaza Level, La Jolla, CA 92037 (US). MC- MILLEN, Robert, J.; 3344 North Torrey Pines Court, (84) Designated States (unless otherwise indicated, for every Plaza Level, La Jolla, CA 92037 (US). RUEHLE, Mi- kind of regional protection available): ARIPO (BW, GH, — chael; 3344 North Torrey Pines Court, Plaza Level, La GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, _ [Continued on next page] = (54) Title: GENOMIC INFRASTRUCTURE FOR ON-SITE OR CLOUD-BASED DNA AND RNA PROCESSING AND ANA- LYSIS = = 100 (57) : A system, method and apparatus for execut- = Local Computing _ = ) ing a sequence analysis pipeline on genetic sequence data in- — dudes a integrated circuit formed of a set of hardwired digit - al logic circuits that are interconnected by physical electrical = = 121 Data Acquisition f interconnects. One of the physical electrical interconnects API I. 3rd Party Analytics forms an input to the integrated circuit connected with an Ht lf . I .7 1 _ , t a gence = = A electronic data source for receiving reads of genomic data. 121a / The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of . 50 r in the the = = 110 150 Computing a subset of the hardwired digital logic circuits to perform one Cloud = or more steps sequence analysis pipeline on reads Data Generation of genomic data. Each subset of the hardwired digital logic = 30/50 x 151 circuits is formed in a wired configuration to perform the one — — Cloud Processing Remote Computing X 300 or more steps in the sequence analysis pipeline. = Genome Pipeline Quantitative/ 152 — — Qualitative Analysis — EPI Genome = Meta Genome 11 700 Joint Genotyping 71' GATKI MuTect2 cr) ei Other Pipeline 11 ....... IN FIG. 10 ,—, © ei O WO 2017/123664 Al IIIIIMEOHIMIIMUMMIOMMENNIMMEHOE# TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, Published: TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, DE, LT, SE, GA, with international search 21(3)) report (Art. GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG).