Patent SG-11201810734Y-A (SG)
Title: Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing
Inventor: VAN ROOYEN PIETER
Filed: 2017-06-07
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) -., (19) World Intellectual Property 1 MI 1411 0 11101 010 11111 010 1111 1 0 01 01 010 11111 001 010 110 11110 MAMIE Organization . International Bureau (10) International Publication Number 03 (43) International Publication Date ......°' WO 2017/214320 Al 14 December 2017 (14.12.2017) W I PO I PCT (51) International Patent Classification: 15/497,149 25 April 2017 (25.04.2017) US GOOF 19/28 (2011.01) (71) Applicant: EDICO GENOME, CORP. [US/US]; 3344 (21) International Application Number: North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 PCT/US2017/036424 (US). (22) International Filing Date: (72) Inventors: VAN ROOYEN, Pieter; 3344 North Tor- 07 June 2017 (07.06.2017) rey Pines Court, Plaza Level, La Jolla, CA 92037 (US). (25) Filing Language: English RUEHLE, Michael; 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (US). MEHIO, Rami; 3344 (26) Publication Language: English North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (30) Priority Data: (US). STONE, Gavin; 3344 North Torrey Pines Court, 62/347,080 07 June 2016 (07.06.2016) US Plaza Level, La Jolla, CA 92037 (US). HAHM, Mark; 62/399,582 26 September 2016 (26.09.2016) US October 2016 (28.10.2016) US 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA 92037 (US). OJARD, Eric; 3344 North Torrey Pines Court, 62/414,637 28 15/404,146 11 January 2017 (11.01.2017) US 23 February 2017 (23.02.2017) US Plaza Level, La Jolla, CA 92037 (US). PTASHEK, Am- 62/462, 869 non; 3344 North Torrey Pines Court, Plaza Level, La Jolla, 62/469,442 09 March 2017 (09.03.2017) US CA 92037 (US). _ (54) Title: BIOINFORMATICS SYSTEMS, APPARATUS, AND METHODS FOR PERFORMING SECONDARY AND/OR _ TERTIARY PROCESSING = = 900 = EMR Data Precision FDA Annotation Other Data = 600 = = Cloud I Application API Cloud = = Developer 1 Environment NIPT N a) Cancer L DT AgB io Other I Genomic Medicine app Store , = Pipeline API = = = Genome , 'se' Epigenome Metagenome Join \/ G MuTect ATKi 2 I Other Pipelines 700 Pipeline Pipeline ., . Pipeline Genotyping Pipelines = Platf om API 0o o — HMM Smith-Water Compress Sort Dedup Convert o ..- 600 = = Speed I Accuracy I Flexibility Onsite, Cloud or Hybrid Cloud = 500 .-----..., Scheduler Analytics Compare Graphs Releases Other = _ FIG. 43A ,-, C:::;) (57) : A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particu- M larly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes 7 1. one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit(CPU) that is responsive Il to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the e• 1 sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a --.... IN field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that 1-1 c::::) are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis ei pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second o [Continued on next page] WO 2017/214320 Al IMEDIMOM0101011MMEM00110101EDIMMEMOMMEN (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, 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)) set of genomic processing steps. A shared memory is also provided.