SG11201810734YA - Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing - Google Patents

Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing

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Publication number
SG11201810734YA
SG11201810734YA SG11201810734YA SG11201810734YA SG11201810734YA SG 11201810734Y A SG11201810734Y A SG 11201810734YA SG 11201810734Y A SG11201810734Y A SG 11201810734YA SG 11201810734Y A SG11201810734Y A SG 11201810734YA SG 11201810734Y A SG11201810734Y A SG 11201810734YA
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SG
Singapore
Prior art keywords
plaza
jolla
level
pipeline
international
Prior art date
Application number
SG11201810734YA
Inventor
Rooyen Pieter Van
Michael Ruehle
Rami Mehio
Gavin Stone
Mark Hahm
Eric Ojard
Amnon Ptashek
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Illumina Inc
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Publication date
Priority claimed from US15/404,146 external-priority patent/US10847251B2/en
Priority claimed from US15/497,149 external-priority patent/US10068183B1/en
Application filed by Illumina Inc filed Critical Illumina Inc
Priority claimed from PCT/US2017/036424 external-priority patent/WO2017214320A1/en
Publication of SG11201810734YA publication Critical patent/SG11201810734YA/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

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  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Data Mining & Analysis (AREA)
  • Molecular Biology (AREA)
  • Artificial Intelligence (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
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  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
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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.
SG11201810734YA 2016-06-07 2017-06-07 Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing SG11201810734YA (en)

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US201662347080P 2016-06-07 2016-06-07
US201662399582P 2016-09-26 2016-09-26
US201662414637P 2016-10-28 2016-10-28
US15/404,146 US10847251B2 (en) 2013-01-17 2017-01-11 Genomic infrastructure for on-site or cloud-based DNA and RNA processing and analysis
US201762462869P 2017-02-23 2017-02-23
US201762469442P 2017-03-09 2017-03-09
US15/497,149 US10068183B1 (en) 2017-02-23 2017-04-25 Bioinformatics systems, apparatuses, and methods executed on a quantum processing platform
PCT/US2017/036424 WO2017214320A1 (en) 2016-06-07 2017-06-07 Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing

Publications (1)

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SG11201810734YA true SG11201810734YA (en) 2018-12-28

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EP (3) EP3982368B1 (en)
JP (2) JP7046840B2 (en)
KR (3) KR102638677B1 (en)
CN (2) CN109416928B (en)
AU (2) AU2017277636B2 (en)
BR (1) BR112018075407A2 (en)
CA (1) CA3026644A1 (en)
MX (1) MX2018014579A (en)
RU (1) RU2750706C2 (en)
SG (2) SG10201913534QA (en)

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