SG11201908893UA - Signature-hash for multi-sequence files - Google Patents

Signature-hash for multi-sequence files

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Publication number
SG11201908893UA
SG11201908893UA SG11201908893UA SG11201908893UA SG 11201908893U A SG11201908893U A SG 11201908893UA SG 11201908893U A SG11201908893U A SG 11201908893UA SG 11201908893U A SG11201908893U A SG 11201908893UA
Authority
SG
Singapore
Prior art keywords
international
hash
california
boulevard
culver city
Prior art date
Application number
Inventor
John Zachary Sanborn
Stephen Charles Benz
Rahul Parulkar
Original Assignee
Nantomics Llc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Publication date
Application filed by Nantomics Llc filed Critical Nantomics Llc
Publication of SG11201908893UA publication Critical patent/SG11201908893UA/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/22—Indexing; Data structures therefor; Storage structures
    • G06F16/2228—Indexing structures
    • G06F16/2255—Hash tables
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/40—Encryption of genetic data
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • 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

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  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Chemical & Material Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Bioethics (AREA)
  • Databases & Information Systems (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Artificial Intelligence (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Medicinal Preparation (AREA)

Abstract

e229ap014319EESKS1911919E£1,9199 , 9123: • 851 , 9189121991..12292.3, : 01E12111119992 :•• 212919121 , 009•59931010i2A2,3,1;;; 11201H.1681E1196F11991E...WEI , • . 11111009919A91211.EF1.AinatiVX29 40,49 , E.1991.91.1.2910982F.19129 . 18£12/0 , , •51F.4119.4...: 3b,0b9h.2122:3s. lelf)e 51 mmiter§ .7040.M.80-9416.50.100 • : : : MILE 21.11494R:111•21,3S.11.1.1•19.1 :261. •IEEEEZ 219341 191/.3.11:: IOW • • •0911111a919EF.P , 9115E99M , 22:00.8: 1.1.10142.92/.1M18061G1193.11F • 19101081.11E29103.13078221.1112181.1:19F8181.6111.121: .1.1119.SEEIE81122212 • 9P.3/4.12171rtlif IF119.94.3E1DBE211111.121Af.£112142112512293.919 133f 42100,300=050000201110.30..000.001111.•94141121119110.9F1991a, . , 19 A.2, , ,Z1211212202103A291126611W1191 , 1021SRAE: 8600291 1E012 il<101.A1OPS11.1 22 ..... 611RZAtilla1:504119399091A2a9603318213222224, F?Fi..9111.1311FEADEM12.2.922211.61.132.16 7,1.11.1.9111121.1.A12993FEIAir 101199E2112999SP 120 122 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 04 October 2018 (04.10.2018) W I PO I PCT oimiolollm °nolo mol imam ono OII IIII (10) International Publication Number WO 2018/183493 Al (51) International Patent Classification: GOOF 19/22 (2011.01) C12Q 1/6888 (2018.01) GOOF 19/18 (2011.01) (21) International Application Number: PCT/US2018/024838 (22) International Filing Date: 28 March 2018 (28.03.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/478,531 29 March 2017 (29.03.2017) US (71) Applicant: NANTOMICS, LLC [US/US]; 9920 Jefferson Boulevard, Culver City, California 90232 (US). (72) Inventors: SANBORN, John Zachary; 9920 Jefferson Boulevard, Culver City, California 90232 (US). BENZ, Stephen Charles; 9920 Jefferson Boulevard, Culver City, California 90232 (US). PARULKAR, Rahul; 9920 Jeffer- son Boulevard, Culver City, California 90232 (US). (74) Agent: FESSENMAIER, Martin et al.; UMBERG ZIPSER LLP, 1920 Main Street, Suite 750, Irvine, Califor- nia 92614 (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, (54) Title: SIGNATURE-HASH FOR MULTI-SEQUENCE FILES 130 1-1 co 00 O C ..2.= •1WS911S11,_ . .16.301 , 11911297. 9LillA1402190RF1/81,1 ... • 12469891219919211% • .58921.“121ADITII,V12- .. ;;;. i•OFRA711 , 91 . 11F112EFAA121 IMEKkI , J.9829181191-51... • 123 EFAle1193n192MF01819.C... J420,1$E \"*.114.10.11020AESLANMEIAAOSIAEE31632FA.48xMlek._:_, i 110.3101220FERF1.911819111M8.92321A001.0 SICAE9N1103641A1.1F.1.1.RE... 11227711023E110.EIM11101 • • • • . • • • • +111111` .1133322. i111111WW1011112111111E11 !101111111' 2111111..1110111211111W```` • • • :MI I lz •2111222223.1190311131121331311311::0. ill111.1.110.1.11:211111.22 ... • 1211181 111111121111111105 . ...\" ,. • , 11319\",..611191111000111122111150 . ::1132 L111 .....11.12! ..311991191.1211100:.: ....... : .. 111......1112•12 1.1.123.11.3.1.212.0.132 iC003.81.111.3.3.1 .1M1 . ,.1.1.1.111.102111 .1.21.1.1.0.1101 • Ini1112111121111011..1 UMW. .. .1.1111111111112r • • ..,10111111111111411. 104 -, 111 t121111111111111111111 '11111111 .11000113311 '13Z0.111111111181 I IWI , EamYeiiinn 111211.111E11MM 1330 . 11121A11,0991 • '11.22€12 • 1,1111122112102 ...MAW '1E111 ' 1.9.1111111... . ‘ ..1.1.1.111%. 9 1 ' 'n1110121:11 1 ,1210.111111:111 111111`• 11111= .. ..'..;111 .31211 .00.100 ,, Di1.10•31M , EFFFFIEM£3330MEEEFEIF012322.i112.1E21401,: MEMS142.343E111.1.2ENTEYMPF12111112.11120,2 11 , 113.£ , MIMEFIN Figure 1 (57) : A unique hash representing patient omics data is constructed using results for known SNP positions and their respective allele frequencies in the patient's omics data. In most preferred aspects, the known SNP positions are selected for specific factors (e.g., ethnicity, sex, etc.) and the allele fraction is represented in values of a non-linear scale. Typically, the hash comprises a header/metadata relating to the known SNP positions and non-linear scale and further includes the actual hash string. [Continued on next page] WO 2018/183493 Al MIDEDIMOIMEMIHINOMOINIIIMIBIMMOVOIMIE 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)) with amended claims (Art. 19(1))
SG11201908893U 2017-03-29 2018-03-28 Signature-hash for multi-sequence files SG11201908893UA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762478531P 2017-03-29 2017-03-29
PCT/US2018/024838 WO2018183493A1 (en) 2017-03-29 2018-03-28 Signature-hash for multi-sequence files

Publications (1)

Publication Number Publication Date
SG11201908893UA true SG11201908893UA (en) 2019-10-30

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US (2) US20180293348A1 (en)
EP (1) EP3602361A4 (en)
JP (1) JP2020515978A (en)
KR (1) KR20190126930A (en)
CN (1) CN110476215A (en)
AU (1) AU2018244373A1 (en)
CA (1) CA3058413A1 (en)
IL (1) IL269731A (en)
SG (1) SG11201908893UA (en)
WO (1) WO2018183493A1 (en)

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* Cited by examiner, † Cited by third party
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EP3049444A4 (en) * 2013-09-26 2017-06-07 Five3 Genomics, LLC Systems, methods, and compositions for viral-associated tumors
WO2020076474A1 (en) * 2018-10-12 2020-04-16 Nantomics, Llc Prenatal purity assessments using bambam

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US6703228B1 (en) * 1998-09-25 2004-03-09 Massachusetts Institute Of Technology Methods and products related to genotyping and DNA analysis
JP2001290822A (en) * 2000-04-05 2001-10-19 Iyaku Bunshi Sekkei Kenkyusho:Kk Device giving priority to candidate gene
US20030211504A1 (en) * 2001-10-09 2003-11-13 Kim Fechtel Methods for identifying nucleic acid polymorphisms
US7303879B2 (en) * 2003-07-31 2007-12-04 Applera Corporation Determination of SNP allelic frequencies using temperature gradient electrophoresis
WO2008079374A2 (en) * 2006-12-21 2008-07-03 Wang Eric T Methods and compositions for selecting and using single nucleotide polymorphisms
EP2332082A1 (en) * 2008-07-23 2011-06-15 Translational Genomics Research Institute Method of characterizing sequences from genetic material samples
EP2748801B1 (en) * 2011-08-26 2020-04-29 Life Technologies Corporation Systems and methods for identifying an individual
WO2013097048A1 (en) * 2011-12-29 2013-07-04 深圳华大基因科技服务有限公司 Method and device for labelling single nucleotide polymorphism sites in genome
KR20150055002A (en) * 2012-09-11 2015-05-20 테라노스, 인코포레이티드 Information management systems and methods using a biological signature
US9792403B2 (en) * 2013-05-10 2017-10-17 Foundation Medicine, Inc. Analysis of genetic variants
US10191929B2 (en) * 2013-05-29 2019-01-29 Noblis, Inc. Systems and methods for SNP analysis and genome sequencing
JP2015035212A (en) * 2013-07-29 2015-02-19 アジレント・テクノロジーズ・インクＡｇｉｌｅｎｔ Ｔｅｃｈｎｏｌｏｇｉｅｓ， Ｉｎｃ． Method for finding variants from targeted sequencing panels
WO2015027085A1 (en) * 2013-08-22 2015-02-26 Genomoncology, Llc Computer-based systems and methods for analyzing genomes based on discrete data structures corresponding to genetic variants therein
AU2014348566B2 (en) * 2013-11-13 2019-02-28 Five3 Genomics, Llc Systems and methods for transmission and pre-processing of sequencing data
CN107735787A (en) * 2014-09-05 2018-02-23 南托米克斯有限责任公司 System and method for introduces a collection measure
US10069627B2 (en) * 2015-07-02 2018-09-04 Qualcomm Incorporated Devices and methods for facilitating generation of cryptographic keys from a biometric

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Publication number Publication date
WO2018183493A1 (en) 2018-10-04
EP3602361A4 (en) 2020-12-16
JP2020515978A (en) 2020-05-28
IL269731A (en) 2019-11-28
CA3058413A1 (en) 2018-10-04
AU2018244373A1 (en) 2019-10-24
US20200104285A1 (en) 2020-04-02
KR20190126930A (en) 2019-11-12
US20180293348A1 (en) 2018-10-11
EP3602361A1 (en) 2020-02-05
CN110476215A (en) 2019-11-19

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