SG11201905640XA - Oncogenic splice variant determination - Google Patents

Oncogenic splice variant determination

Info

Publication number
SG11201905640XA
SG11201905640XA SG11201905640XA SG11201905640XA SG11201905640XA SG 11201905640X A SG11201905640X A SG 11201905640XA SG 11201905640X A SG11201905640X A SG 11201905640XA SG 11201905640X A SG11201905640X A SG 11201905640XA SG 11201905640X A SG11201905640X A SG 11201905640XA
Authority
SG
Singapore
Prior art keywords
junctions
sample
illumina
baseline
splice
Prior art date
Application number
SG11201905640XA
Inventor
June Snedecor
Han-Yu Chuang
Gwenn Berry
Xiao Chen
Original Assignee
Illumina Inc
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.)
Filing date
Publication date
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of SG11201905640XA publication Critical patent/SG11201905640XA/en

Links

Classifications

    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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

Abstract

Retrievethe sample junctions [ Retrieve the baseline junctions DIA Remove sample junctions with baseline junction overlap o the sample junctions overlap with the baseline junctions? RIR ..1 Yes Collect as filtered sample junctions Rid Collect as overlap sample junctions 1122 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 26 July 2018 (26.07.2018) WIP0 I PCT Iiiimmomiolollmonolomoilloolloomomomovoimill (10) International Publication Number WO 2018/136416 Al (51) International Patent Classification: GOOF 19/18 (2011.01) GOOF 19/22 (2011.01) (21) International Application Number: PCT/US2018/013864 (22) International Filing Date: 16 January 2018 (16.01.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/447,382 17 January 2017 (17.01.2017) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, CA 92122 (US). (72) Inventors: SNEDECOR, June; C/o Illumina, Inc., 5200 Il- lumina Way, San Diego, CA 92122 (US). CHUANG, Han- yu; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). BERRY, Gwenn; C/o Illumina, Inc., 5200 Il- lumina Way, San Diego, CA 92122 (US). CHEN, Xiao; C/ o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). (74) Agent: FULLER, Michael, L.; Knobbe, Martens, Olson & Bear LLP, 2040 Main Street, Fourteenth Floor, Irvine, CA 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, (54) Title: ONCOGENIC SPLICE VARIANT DETERMINATION FIG. 8 Verify unctions I Store filtered sample junctions R_0 00 O O (57) : Presented herein are systems and methods for identifying splice variants. The techniques include determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample, retrieving a set of baseline splice junctions determined from a plurality of healthy RNA samples and comparing the one or more sample splice junctions to the set of baseline splice junctions to identify one or more filtered sample splice junctions comprising sample splice junctions that do not overlap with the baseline splice junctions, wherein the one or more filtered sample splice junctions are candidate oncogenic events. [Continued on next page] WO 2018/136416 Al MIDEDIMOMOIDEIREEMOMMIMINHEMEOMEHOIMI 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). 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))
SG11201905640XA 2017-01-17 2018-01-16 Oncogenic splice variant determination SG11201905640XA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762447382P 2017-01-17 2017-01-17
PCT/US2018/013864 WO2018136416A1 (en) 2017-01-17 2018-01-16 Oncogenic splice variant determination

Publications (1)

Publication Number Publication Date
SG11201905640XA true SG11201905640XA (en) 2019-08-27

Family

ID=61148514

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201905640XA SG11201905640XA (en) 2017-01-17 2018-01-16 Oncogenic splice variant determination

Country Status (10)

Country Link
US (1) US20200090784A1 (en)
EP (1) EP3571613A1 (en)
JP (2) JP6806909B2 (en)
KR (1) KR102326612B1 (en)
CN (1) CN110178184B (en)
AU (1) AU2018210316A1 (en)
BR (1) BR112019014042A2 (en)
CA (1) CA3045498C (en)
SG (1) SG11201905640XA (en)
WO (1) WO2018136416A1 (en)

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US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
EP3665308A1 (en) 2017-08-07 2020-06-17 The Johns Hopkins University Methods and materials for assessing and treating cancer
JP6931860B2 (en) * 2019-02-08 2021-09-08 株式会社Ｚｅｎｉｃｋ Pre-mRNA analysis method, information processing device, computer program
JPWO2021172315A1 (en) * 2020-02-25 2021-09-02
US20240102099A1 (en) * 2020-11-20 2024-03-28 H. Lee Moffitt Cancer Center And Research Institute, Inc. Methods and compositions relating to a novel epidermal growth factor receptor (egfr) splice variant

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Also Published As

Publication number Publication date
CN110178184B (en) 2024-04-19
EP3571613A1 (en) 2019-11-27
WO2018136416A1 (en) 2018-07-26
CA3045498C (en) 2021-07-13
BR112019014042A2 (en) 2020-02-04
CA3045498A1 (en) 2018-07-26
KR20190098233A (en) 2019-08-21
KR102326612B1 (en) 2021-11-15
CN110178184A (en) 2019-08-27
JP6806909B2 (en) 2021-01-06
JP2021036895A (en) 2021-03-11
AU2021201007B2 (en) 2023-02-23
US20200090784A1 (en) 2020-03-19
AU2021201007A1 (en) 2021-03-11
AU2018210316A1 (en) 2019-06-27
JP2020506684A (en) 2020-03-05

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