Patent SG-11201903858X-A (SG)
Title: Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing
Inventor: HAHM MARK
IPC: G06F21/76
Filed: 2017-10-27
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property :::` , 1111111111111011101111111111101111101111111111111101111111100111111101111111111 Organization International Bureau (10) International Publication Number 03 (43) International Publication Date ......°' WO 2018/081654 Al 03 May 2018 (03.05.2018) W I P0 I P C T (51) International Patent Classification: (72) Inventors: HAHM, Mark, David; 3344 North Torrey GOOF 19/28 (2011.01) G06F 21/76 (2013.01) Pines Court, Plaza Level, La Jolla, CA 92037 (US). DE GOOF 19/22 (2011.01) BEER, Jacobus; 3344 North Torrey Pines Court, Plaza (21) International Application Number: Level, La Jolla, CA 92037 (US). JAIN, Varun; 3344 North PCT/US2017/058890 Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (US). MEHIO, Rami; 3344 North Torrey Pines Court, La Jolla, (22) International Filing Date: CA 92037 (US). OJARD, Eric; 3344 North Torrey Pines 27 October 2017 (27.10.2017) Court, Plaza Level, La Jolla, CA 92037 (US). RUEHLE, Michael; 3344 North Torrey Pines Court, Plaza Level, La (25) Filing Language: English Jolla, CA 92037 (US). PTASHEK, Amnon; 3344 North (26) Publication Language: English Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (US). (30) Priority Data: CATREUX, Severine; 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (US). VISVANATH, 62/414,637 28 October 2016 (28.10.2016) US Arun; 3344 North Torrey Pines Court, Plaza Level, La Jol- (71) Applicant: EDICO GENOME, CORP. [US/US]; 3344 la, CA 92037 (US). North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (US). Title: BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PROCESSING 500 -Ns 1007 20- FIG. : A system, method a genomics analysis platform for executing or more of a first integrated one or more software algorithms analysis pipeline. Additionally, programmable gate array (FPGA), interconnected by a plurality of physical the set of hardwired digital of genomic processing steps. (54) TERTIARY (57) Ot sequence cz pipeline, 500a 500b 500c Active regions PERFORMING SECONDARY AND/OR 11 a 11b 11c sequence data is provided. Particu- analysis platform includes unit (CPU) that is responsive of genomic processing steps of the second integrated circuit forming a hardwired digital logic circuits that steps of the sequence analysis engines to perform the second The genomics = = = 1007a { Worker threads 20a 20b 20c 20a 4k pages 20b 1007b PC data executing a bioinformatics analysis on genetic sequence first each also provided. interface to le flow and HW/SW interaction overview. 1007c 1 Ar.„/ O Data aggregator thread 20a 20d 20e 20f HMM clusters = — — — _ — --..., = = = Data Distributor /111 711 = = 20b 20c 20d 4 and apparatus for circuit, that logic A shared = /11 = integrated instruct configured to perform a second set of genomic FPGA 20c 9 analysis pipeline is provided. circuit forms a central the CPU to perform circuit is also provided, where each by firmware to arrange being arranged as a set of processing 11 processing a first set a set of processing = the HMM a where each are configured a second integrated FPGA being interconnects circuits of memory is _ Il 7r larly, ir) one - to 0 ----, field WD are 1-1 ei set O [Continued on next page] WO 2018/081654 Al 111111111111111111101010111110111110111011111111111111111111111101111111110111111111111 (74) Agent: CLEARY, James, P. et al.; Mintz Levin Cohn Fer- ris Glovsky and Popeo, P.C., 3580 Cannel Mountain Road, Suite 300, San Diego, CA 92130-6768 (US). (81) Designated States (unless otherwise indicated, for every 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. (84) Designated States (unless otherwise indicated, for every 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). Published: — with international search report (Art. 21(3)) — before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h))