SG11201901620SA - Methods of identifying microsatellite instability - Google Patents

Methods of identifying microsatellite instability

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Publication number
SG11201901620SA
SG11201901620SA SG11201901620SA SG11201901620SA SG11201901620SA SG 11201901620S A SG11201901620S A SG 11201901620SA SG 11201901620S A SG11201901620S A SG 11201901620SA SG 11201901620S A SG11201901620S A SG 11201901620SA SG 11201901620S A SG11201901620S A SG 11201901620SA
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Singapore
Prior art keywords
tyne
international
newcastle
university
wear
Prior art date
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SG11201901620SA
Inventor
John Burn
Mohammed Ghanim Mehdi Alhilal
Franscisco Mauro Santibanez-Koref
Lisa Redford
Michael Stewart Jackson
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Cancer Research Tech Ltd
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Publication date
Application filed by Cancer Research Tech Ltd filed Critical Cancer Research Tech Ltd
Publication of SG11201901620SA publication Critical patent/SG11201901620SA/en

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    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • 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
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/119—Strand displacement amplification [SDA]
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/119—Double strand sequencing
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    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing
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    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
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  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
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  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property :::` , MD HIM 0 11101 010 11111 01 II 0 01111 OHM VIII E IMO MAMIE Organization International Bureau (10) International Publication Number 03 (43) International Publication Date ......°' WO 2018/037231 Al 01 March 2018 (01.03.2018) WIP0 I PCT (51) International Patent Classification: Ghanim Mehdi; District 337, Al- Shaab, Baghdad- Iraq C12Q 1/68 (2018.01) (IQ). SANTIBANEZ-KOREF, Franscisco Mauro; c/o The University of Newcastle Upon Tyne, King's Gate, New- (21) International Application Number: castle Upon Tyne Tyne and Wear NE1 7RU (GB). RED- PCT/GB2017/052488 FORD, Lisa; Likollen 70, 1481 Hagan, Norway (NO). (22) International Filing Date: JACKSON, Michael Stewart; c/o The University of New- 23 August 2017 (23.08.2017) castle Upon Tyne, Institute of Genetic Medicine, Interna- tional Centre for Life Central Parkway, Newcastle Upon (25) Filing Language: English Tyne Tyne and Wear NE1 3BZ (GB). (26) Publication Language: English (74) Agent: HGF LTD; Document Handling (HGF) York, 1 (30) Priority Data: City Walk, Leeds Yorkshire LS11 9DX (GB). 1614474.3 24 August 2016 (24.08.2016) GB (81) Designated States (unless otherwise indicated, for every (71) Applicant: THE UNIVERSITY OF NEWCASTLE UP- kind of national protection available): AE, AG, AL, AM, ON TYNE [GB/GB]; King's Gate, Newcastle Upon Tyne, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, Tyne and Wear NE1 7RU (GB). 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, (72) Inventors: BURN, John; c/o The University of Newcas- HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, tle Upon Tyne, Institute of Genetic Medicine, Internation-KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, al Centre for Life Central Parkway, Newcastle Upon Tyne MG, MK, MN, 1\4W, MX, MY, MZ, NA, NG, NI, NO, NZ, Tyne and Wear NE1 3BZ (GB) ALHILAL, Mohammed — OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, = (54) Title: METHODS OF IDENTIFYING MICROSATELLITE INSTABILITY = = A 1M14 7bp SNP1 B LR20 8bp SNP3 100 100 90 90 r 80 7.S 60 0 8 .. 70 . 60 \\ = 1 3 . 0 50 cp 40 T o ' 50 40 _ ce 30 ,,.) — 30 20 20 10 10 \ \ 0 0 A '\ = -1 0 1 -2 _ = U312T U179 H03 = C 1M65 11bp SNP2 D LR36 12bp SNP2 100 = 90 100 90 870 0 --- 0 -- 80 = w . 60 : 6 _1, - 70 u) 60 • 50 Nrt • = w 7, 3 50 • •• _ ct 40 • ,„. 0 40 7 r • _ 30 • • , — 30 • = 20 10 • , 20 10 .. • • 0 m‘s -0 0 mttA7 V / • —RI _ -4 -3 -2 - 0 1 2 -4 -3 -2 -1 0 1 2 U029T U303T Il ® A ®G .' C 5 T 1-1 FIG. 1 cr) N IN (57) : The present invention relates to methods and kits for identifying microsatellite instability (MSI) in a sample. In particular 0 en it relates to identifying microsatellite instability in a tumor sample, which may be from a subject suspected of having colorectal cancer -- --- GC or Lynch syndrome. The methods and kits can be used to identify mismatch repair defects. More particularly the invention relates to a , 1 panel of markers for a sequencing based MSI test, that can differentiate between MSI-H and MSS CRCs. The invention also allows for 0 determination of biological significance, differentiating between PCR and sequencing errors and MSI induced indels/mutations. N C [Continued on next page] WO 2018/037231 Al MIDEDIMOMOIDEIREEMOOMMEIHMIDEIBUDIMIE 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). Declarations under Rule 4.17: — of inventorship (Rule 4.17(iv)) Published: — with international search report (Art. 21(3)) — with sequence listing part of description (Rule 5.2(a))
SG11201901620SA 2016-08-24 2017-08-23 Methods of identifying microsatellite instability SG11201901620SA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GBGB1614474.3A GB201614474D0 (en) 2016-08-24 2016-08-24 Methods of identifying microsatellite instability
PCT/GB2017/052488 WO2018037231A1 (en) 2016-08-24 2017-08-23 Methods of identifying microsatellite instability

Publications (1)

Publication Number Publication Date
SG11201901620SA true SG11201901620SA (en) 2019-03-28

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US (1) US11519021B2 (en)
EP (1) EP3504341A1 (en)
JP (1) JP7198199B2 (en)
AU (1) AU2017316709B2 (en)
CA (1) CA3034758A1 (en)
GB (1) GB201614474D0 (en)
SG (1) SG11201901620SA (en)
WO (1) WO2018037231A1 (en)

Families Citing this family (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019074963A1 (en) * 2017-10-09 2019-04-18 Strata Oncology, Inc. Microsatellite instability characterization
EP3815092A2 (en) * 2018-06-29 2021-05-05 F. Hoffmann-La Roche AG Detection of microsatellite instability
JP7514224B2 (en) * 2018-09-14 2024-07-10 レクセント バイオ， インコーポレイテッド Methods and systems for assessing microsatellite instability - Patent Application 20070123633
WO2021019197A1 (en) 2019-07-31 2021-02-04 University Of Newcastle Upon Tyne Methods of identifying microsatellite instability
CN110599462B (en) * 2019-08-23 2023-04-07 东南大学 Urinary sediment detection method based on unbalanced local Fisher discriminant analysis
CN110910957B (en) * 2019-12-31 2023-06-27 求臻医学科技(浙江)有限公司 Single-tumor-sample-based high-throughput sequencing microsatellite instability detection site screening method
EP3863019A1 (en) 2020-02-07 2021-08-11 Sophia Genetics S.A. Methods for detecting and characterizing microsatellite instability with high throughput sequencing
CN111304303B (en) * 2020-02-18 2023-05-05 福建和瑞基因科技有限公司 Method for predicting microsatellite instability and application thereof
WO2023281117A1 (en) * 2021-07-09 2023-01-12 Hubro Therapeutics As A Primer
GB202114136D0 (en) 2021-10-01 2021-11-17 Cancer Research Tech Ltd Microsatellite markers
CN114220483B (en) * 2021-12-03 2022-11-15 广州达安临床检验中心有限公司 Marker, application, method and device for detecting stability state of microsatellite
WO2024105220A1 (en) * 2022-11-17 2024-05-23 Universite De Poitiers Method for determining microsatellite instability status, kits and uses thereof
CN115595371B (en) * 2022-12-07 2023-04-11 元码基因科技（北京）股份有限公司 Method for determining MSI state of colorectal cancer patient and application

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CA2584741A1 (en) 2004-10-22 2006-05-04 Marijo Kent-First Methods and kits for detecting germ cell genomic instability
US20120295267A1 (en) 2011-05-16 2012-11-22 Baylor Research Institute Detecting DNA Mismatch Repair-Deficient Colorectal Cancers
EP3998347A1 (en) 2012-04-10 2022-05-18 Vib Vzw Novel markers for detecting microsatellite instability in cancer and determining synthetic lethality with inhibition of the dna base excision repair pathway
US10633707B2 (en) * 2012-04-10 2020-04-28 Vib Vzw Markers for detecting microsatellite instability in cancer and determining synthetic lethality with inhibition of the DNA base excision repair pathway
US20160040254A1 (en) 2014-07-31 2016-02-11 Virginia Tech Intellectual Properties, Inc. Prognostic and diagnostic methods based on quantification of somatic microsatellite variability
MX2017010122A (en) 2015-02-06 2018-06-06 Quest Diagnostics Invest Llc Compositions and methods for determining endometrial cancer prognosis.

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Publication number Publication date
US20190194731A1 (en) 2019-06-27
WO2018037231A1 (en) 2018-03-01
JP7198199B2 (en) 2022-12-28
CA3034758A1 (en) 2018-03-01
US11519021B2 (en) 2022-12-06
AU2017316709B2 (en) 2024-01-04
AU2017316709A1 (en) 2019-03-21
GB201614474D0 (en) 2016-10-05
EP3504341A1 (en) 2019-07-03
JP2019528076A (en) 2019-10-10

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