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1. 发明专利

SG10201913208QA BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING 未知
公开(公告)号：SG10201913208QA
公开(公告)日：2020-02-27
申请号：SG10201913208Q
申请日：2017-10-27
申请人： ILLUMINA INC
发明人： HAHM MARK , DE BEER JACOBUS , JAIN VARUN , MEHIO RAMI , OJARD ERIC , RUEHLE MICHAEL , PTASHEK AMNON , CATREUX SEVERINE , VISVANATH ARUN
摘要： Systems, methods, and computer programs for analyzing genetic sequence data is disclosed. In one aspect, the system can include one or more of a first integrated circuit, with each first integrated circuit forming a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of a sequence analysis pipeline. Additionally, the system can include one or more second integrated circuits, with each second integrated circuit forming a field programmable gate array (FPGA). The FPGA can be configured by firmware to arrange a set of hardwired digital logic circuits to perform a second set of genomic processing stages of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing stages.

2. 发明专利

AU2022252718A1 Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing 未知
公开(公告)号：AU2022252718A1
公开(公告)日：2022-11-03
申请号：AU2022252718
申请日：2022-10-11
申请人： ILLUMINA INC
发明人： VAN ROOYEN PIETER , RUEHLE MICHAEL , MEHIO RAMI , STONE GAVIN , HAHM MARK , OJARD ERIC , PTASHEK AMNON
IPC分类号： G16B20/00 , G16B30/10 , G16B50/30
摘要： Abstract A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

3. 发明专利

AU2017277636A1 Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing 未知
公开(公告)号：AU2017277636A1
公开(公告)日：2018-12-13
申请号：AU2017277636
申请日：2017-06-07
申请人： ILLUMINA INC
发明人： VAN ROOYEN PIETER , RUEHLE MICHAEL , MEHIO RAMI , STONE GAVIN , HAHM MARK , OJARD ERIC , PTASHEK AMNON
IPC分类号： G06F19/28
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit(CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

4. 发明专利

CA3042239A1 BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING 未知
公开(公告)号：CA3042239A1
公开(公告)日：2018-05-03
申请号：CA3042239
申请日：2017-10-27
申请人： ILLUMINA INC
发明人： HAHM MARK DAVID , DE BEER JACOBUS , JAIN VARUN , MEHIO RAMI , OJARD ERIC , RUEHLE MICHAEL , PTASHEK AMNON , CATREUX SEVERINE , VISVANATH ARUN
IPC分类号： G16B50/30 , G16B20/00 , G16B30/00 , G16B50/00 , H03K19/177
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

5. 发明专利

AU2017348382A1 Bioinformatics systems, apparatuses, and methods for performing secondary and/or tertiary processing 未知
公开(公告)号：AU2017348382A1
公开(公告)日：2019-06-20
申请号：AU2017348382
申请日：2017-10-27
申请人： ILLUMINA INC
发明人： HAHM MARK DAVID , DE BEER JACOBUS , JAIN VARUN , MEHIO RAMI , OJARD ERIC , RUEHLE MICHAEL , PTASHEK AMNON , CATREUX SEVERINE , VISVANATH ARUN
IPC分类号： G06F21/76
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

6. 发明专利

SG11201903858XA BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING 未知
公开(公告)号：SG11201903858XA
公开(公告)日：2019-05-30
申请号：SG11201903858X
申请日：2017-10-27
申请人： ILLUMINA INC
发明人： HAHM MARK , DE BEER JACOBUS , JAIN VARUN , MEHIO RAMI , OJARD ERIC , RUEHLE MICHAEL , PTASHEK AMNON , CATREUX SEVERINE , VISVANATH ARUN
IPC分类号： G06F21/76
摘要： 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))

7. 发明专利

CA3026644A1 BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING 未知
公开(公告)号：CA3026644A1
公开(公告)日：2017-12-14
申请号：CA3026644
申请日：2017-06-07
申请人： ILLUMINA INC
发明人： VAN ROOYEN PIETER , RUEHLE MICHAEL , MEHIO RAMI , STONE GAVIN , HAHM MARK , OJARD ERIC , PTASHEK AMNON
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit(CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

8. 发明专利

AU2017277636B2 Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing 未知
公开(公告)号：AU2017277636B2
公开(公告)日：2022-07-14
申请号：AU2017277636
申请日：2017-06-07
申请人： ILLUMINA INC
发明人： VAN ROOYEN PIETER , RUEHLE MICHAEL , MEHIO RAMI , STONE GAVIN , HAHM MARK , OJARD ERIC , PTASHEK AMNON
IPC分类号： G16B20/00 , G16B30/10 , G16B50/30
摘要： A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit(CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

9. 发明专利

SG10201913534QA BIOINFORMATICS SYSTEMS, APPARATUSES, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING 未知
公开(公告)号：SG10201913534QA
公开(公告)日：2020-03-30
申请号：SG10201913534Q
申请日：2017-06-07
申请人： ILLUMINA INC
发明人： VAN ROOYEN PIETER , RUEHLE MICHAEL , MEHIO RAMI , STONE GAVIN , HAHM MARK , OJARD ERIC , PTASHEK AMNON
摘要： A system, method and acomputer-readable storage device for improving the accuracy of a variant call by jointly evaluating reads that map to two or more regions of a reference sequence that are homologous are disclosed. The method comprises accessing a joint-pileup including a first pileup of sequence reads that have been aligned to a first region of the reference sequence and at least a second pileup of reads that have been aligned to a second region of the reference sequence, wherein the first region and the second region are homologous with each other; determining a set of candidate variants from the joint-pileup; defining a connection matrix that defines an order of processing of the candidate variants; evaluating, by the one or more computers, each of the candidate variants from the set of candidate variants based on the defined processing order; and generating variant call file that identifies one or more of the candidate variants.

10. 发明专利

SG11201810734YA BIOINFORMATICS SYSTEMS, APPARATUS, AND METHODS FOR PERFORMING SECONDARY AND/OR TERTIARY PROCESSING 未知
公开(公告)号：SG11201810734YA
公开(公告)日：2018-12-28
申请号：SG11201810734Y
申请日：2017-06-07
申请人： ILLUMINA INC
发明人： VAN ROOYEN PIETER , RUEHLE MICHAEL , MEHIO RAMI , STONE GAVIN , HAHM MARK , OJARD ERIC , PTASHEK AMNON
摘要： A system, method and acomputer-readable storage device for improving the accuracy of a variant call by jointly evaluating reads that map to two or more regions of a reference sequence that are homologous are disclosed. The method comprises accessing a joint-pileup including a first pileup of sequence reads that have been aligned to a first region of the reference sequence and at least a second pileup of reads that have been aligned to a second region of the reference sequence, wherein the first region and the second region are homologous with each other; determining a set of candidate variants from the joint-pileup; defining a connection matrix that defines an order of processing of the candidate variants; evaluating, by the one or more computers, each of the candidate variants from the set of candidate variants based on the defined processing order; and generating variant call file that identifies one or more of the candidate variants.

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