SG11201910070PA - Universal short adapters for indexing of polynucleotide samples - Google Patents

Universal short adapters for indexing of polynucleotide samples

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Publication number
SG11201910070PA
SG11201910070PA SG11201910070PA SG11201910070PA SG 11201910070P A SG11201910070P A SG 11201910070PA SG 11201910070P A SG11201910070P A SG 11201910070PA SG 11201910070P A SG11201910070P A SG 11201910070PA
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SG
Singapore
Prior art keywords
index
california
international
rule
san diego
Prior art date
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Tatjana Singer
Ryan Kelley
Gordon Bean
Eric Vermaas
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Illumina Inc
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Application filed by Illumina Inc filed Critical Illumina Inc
Publication of SG11201910070PA publication Critical patent/SG11201910070PA/en

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    • 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
    • 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • 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
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • 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)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)

Abstract

17 index primer 222 220 218 204 15 index primer 202 214 Short universal adapter (Y-shaped) 223 216 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 15 November 2018 (15.11.2018) WIPO I PCT omit VIII °nolo Holommoillionomom oimIE (10) International Publication Number WO 2018/208699 Al (51) International Patent Classification: C12Q 1/6869 (2018.01) Cl 2N 15/10 (2006.01) GOOF 19/22 (2011.01) (21) International Application Number: PCT/US2018/031459 (22) International Filing Date: 07 May 2018 (07.05.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/503,272 08 May 2017 (08.05.2017) US 62/524,390 23 June 2017 (23.06.2017) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, California 92122 (US). (72) Inventors: SINGER, Tatjana; 5200 Illumina Way, San Diego, California 92122 (US). KELLEY, Ryan; 5200 Il- lumina Way, San Diego, California 92122 (US). BEAN, Gordon; 5200 Illumina Way, San Diego, California 92122 (US). VERMAAS, Eric; 5200 Illumina Way, San Diego, California 92122 (US). (74) Agent: ZHOU, Feng et al.; WEAVER AUSTIN VIL- LENEUVE & SAMPSON LLP, P. 0. BOX 70250, OAK- LAND, California 94612-0250 (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). = (54) Title: UNIVERSAL SHORT ADAPTERS FOR INDEXING OF POLYNUCLEOTIDE SAMPLES Figure 2C (57) : The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides. [Continued on next page] W O 20 18/ 208699 Al WO 2018/208699 Al MIDEDIMOMOIDEIRDERIHNOIREIHRIONVOIMIE Declarations under Rule 4.17: as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(11)) as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) 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)) with sequence listing part of description (Rule 5.2(a))
SG11201910070P 2017-05-08 2018-05-07 Universal short adapters for indexing of polynucleotide samples SG11201910070PA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762503272P 2017-05-08 2017-05-08
US201762524390P 2017-06-23 2017-06-23
PCT/US2018/031459 WO2018208699A1 (en) 2017-05-08 2018-05-07 Universal short adapters for indexing of polynucleotide samples

Publications (1)

Publication Number Publication Date
SG11201910070PA true SG11201910070PA (en) 2019-11-28

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SG11201910070P SG11201910070PA (en) 2017-05-08 2018-05-07 Universal short adapters for indexing of polynucleotide samples
SG10202113017YA SG10202113017YA (en) 2017-05-08 2018-05-07 Universal short adapters for indexing of polynucleotide samples

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Country Status (7)

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US (2) US11028436B2 (en)
EP (1) EP3622089A1 (en)
CN (1) CN110832087A (en)
AU (1) AU2018266377B2 (en)
CA (1) CA3062174A1 (en)
SG (2) SG11201910070PA (en)
WO (1) WO2018208699A1 (en)

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CN110832087A (en) 2020-02-21
US11814678B2 (en) 2023-11-14
US20210262026A1 (en) 2021-08-26
CA3062174A1 (en) 2018-11-15
EP3622089A1 (en) 2020-03-18
US20180334712A1 (en) 2018-11-22
AU2018266377B2 (en) 2024-06-20
AU2018266377A1 (en) 2019-11-14
SG10202113017YA (en) 2021-12-30
US11028436B2 (en) 2021-06-08
WO2018208699A1 (en) 2018-11-15

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