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WO2018087129A1 - Marqueurs de méthylation du cancer colorectal - Google Patents

Marqueurs de méthylation du cancer colorectal Download PDF

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Publication number
WO2018087129A1
WO2018087129A1 PCT/EP2017/078573 EP2017078573W WO2018087129A1 WO 2018087129 A1 WO2018087129 A1 WO 2018087129A1 EP 2017078573 W EP2017078573 W EP 2017078573W WO 2018087129 A1 WO2018087129 A1 WO 2018087129A1
Authority
WO
WIPO (PCT)
Prior art keywords
colorectal cancer
methylation
group
alx4
sept9
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/EP2017/078573
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English (en)
Inventor
Ole THORLACIUS-USSING
Simon LADEFOGED RASMUSSEN
Henrik BYGUM KRARUP
Poul Henning MADSEN
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Aalborg Universitet AAU
Aalborg Universitetshospital
Original Assignee
Aalborg Universitet AAU
Aalborg Universitetshospital
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 Aalborg Universitet AAU, Aalborg Universitetshospital filed Critical Aalborg Universitet AAU
Publication of WO2018087129A1 publication Critical patent/WO2018087129A1/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/154Methylation markers

Definitions

  • the methylation status is determined in two or more, such as all, of the gene loci
  • age above 50 years such as above 51 years, such as above 52 years, such as above 53, such as above 54 years, such as above 55, such as above 56 years, such as above 57 years, such as above 58 years, such as above 59 years, such as above 60 years, such as above 61 years, such as above 62 years, such as above 63 years, such as above 64 years, such as above 65 years, such as above 66 years, such as above 67 years, such as above 68 years, such as above 69 years, such as above 70 years, such as above 71 years, such as above 72 years, such as above 73 years, such as above 74 years, such as above 75 years, such as above 76 years, such as above 77 years, such as above 78 years, such as above 79 years, such as above 80, is indicative of colorectal cancer, increased risk of colorectal cancer, the prognosis of colorectal cancer, and/or relapse of colorectal cancer, and thus indicates that a given treatment being monitored is indicative of
  • aspects provided herein also relates to methods for determining colorectal cancer or the prognosis of a colorectal cancer in a subject and/or inferring a suitable treatment, as well as for monitoring a colorectal cancer, and in particular monitoring the treatment of a colorectal cancer and/or monitoring relapse of a colorectal cancer.
  • a sample such as a blood sample or a blood or plasma sample from said subject comprising nucleic acid material comprising said gene
  • the amplification product is analysed by melting curve analysis.
  • APC inner primer pair SEQ ID NO: 3 or 4 and/or outer primer pair SEQ ID NO: 63 and 64;
  • Tm 64.9°C + 41 °C x (number of G's and C's in the primer - 16.4)/N, where N is the length of the primer.
  • the annealing temperature should be empirically determined in respect of each specific primer.
  • the primers of the present invention may in one preferred embodiment comprise at least one CpG site and anneal with a higher efficiency to a methylated than to an unmethylated template upon modification of unmethylated cytosine.
  • the primers of the present invention comprise at least one CpG site.
  • the primers comprise also for example two CpG sites.
  • Cytosine are modified to uracil which does not hybridize with the CpG dinucleotide of the oligonucleotide primer or at least hybridize with much lower affinity.
  • the oligonucleotide primers are designed to comprise sufficient nucleotides for specific hybridization to the relevant target nucleic acid sequence.
  • the oligonucleotide primers also comprise one or more CpG dinucleotides, as specified elsewhere herein. These CpG dinucleotides only hybridize with the originally methylated alleles of the nucleic acids.
  • ALX4 inner primer pair SEQ ID NO: 1 or 2 and/or outer primer pair SEQ ID NO: 61 and 62;
  • the at least one oligonucleotide primer hybridizes to a target nucleic acid sequence selected from the group consisting of SEQ ID NO: 151 -180, or the complement thereof.
  • SEPT9 inner primer pair SEQ ID NO: 39 or 40 and/or outer primer pair SEQ ID NO: 99 and 100;
  • the nucleic acid (target) sample is preferably subjected to an agent that converts an unmethylated cytosine to another nucleotide which will distinguish the unmethylated from the methylated cytosine.
  • the agent modifies unmethylated cytosine to uracil.
  • the modifying agent can be sodium bisulphite.
  • uracil will be converted to thymidine.
  • the subsequent PCR amplification converts uracils to thymine.
  • the subsequent analysis can be selected from the group consisting of melting curve analysis, high resolution melting analysis, nucleic acid sequencing, primer extension, denaturing gradient gel electrophoresis, southern blotting, restriction enzyme digestion, methylation-sensitive single-strand conformation analysis (MS-SSCA) and denaturing high performance liquid chromatography (DHPLC).
  • MS-SSCA methylation-sensitive single-strand conformation analysis
  • DPLC denaturing high performance liquid chromatography
  • Reference sequence comprising gene locus RARB: inner primer pair SEQ ID NO: 33 or 34 and/or outer primer pair SEQ ID NO: 93 and 94;...
  • ALX4 hypermethylation was the superior individual marker for the differentiation of CRC patients from the control population. However, with a sensitivity of only 28.5% at 99.0% specificity, the need for at multigene hypermethylation panel in order to raise sensitivity is apparent. ALX4 has been proposed as a blood-based biomarker for CRC in several previous studies, with sensitivities ranging from 46.6% to 83.3%. It was therefore not surprising that it reaches our diagnostic prediction model. However, remarkably NEUROG1 did not. One study showed, that hypermethylation of
  • HIC1 CGCGACGGTCGTCGTTCGGGTTCGCG 126
  • kit according to any of items 12 to 13, wherein said kit comprise at least one oligonucleotide probe which hybridizes to a sequence selected from the group consisting of SEQ ID NO: 151 -180 and/or the complement thereof, wherein said sequence may comprise one or more C to T substitutions.
  • oligonucleotide primers comprising a sequence, which is a subsequence of a gene loci selected from the group consisting of RARB, ALX4, NPTX2, SEPT9, BMP3, SDC2, VIM, SFRP1 , THBD, HIC1 , WIF1 , HLTF, APC, PHACTR3, TFPI2, MGMT, CDKN2A and PPENK or the complement thereof for diagnosing colorectal cancer in a method of any of the preceding items.

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

Abstract

La présente invention concerne une méthode permettant de déterminer un cancer colorectal, ou le pronostic d'un cancer colorectal chez un sujet, ladite méthode consistant à déterminer, dans un échantillon provenant dudit sujet, l'état de méthylation d'un panel de marqueurs d'un gène spécifique.
PCT/EP2017/078573 2016-11-08 2017-11-08 Marqueurs de méthylation du cancer colorectal Ceased WO2018087129A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP16197722 2016-11-08
EP16197722.8 2016-11-08

Publications (1)

Publication Number Publication Date
WO2018087129A1 true WO2018087129A1 (fr) 2018-05-17

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PCT/EP2017/078573 Ceased WO2018087129A1 (fr) 2016-11-08 2017-11-08 Marqueurs de méthylation du cancer colorectal

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Cited By (24)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN108796080A (zh) * 2018-06-06 2018-11-13 苏州唯善生物科技有限公司 用于结直肠癌诊断、检测或筛查的引物和探针组
CN110699437A (zh) * 2019-11-11 2020-01-17 益善生物技术股份有限公司 人sdc2基因甲基化检测试剂盒
WO2020081549A1 (fr) * 2018-10-15 2020-04-23 The Regents Of The University Of California Procédés et matériels pour évaluer et traiter le cancer
CN111560435A (zh) * 2020-05-20 2020-08-21 深圳市新合生物医疗科技有限公司 一种用于结直肠癌检测的dna甲基化试剂盒及使用方法、应用
CN112063712A (zh) * 2019-10-28 2020-12-11 北京康美天鸿生物科技有限公司 基于高分辨率熔解曲线检测septin9基因甲基化的特异引物对和试剂盒
WO2021004215A1 (fr) * 2019-07-11 2021-01-14 广州市康立明生物科技有限责任公司 Réactif de détection combiné multigénique
KR20210044923A (ko) * 2019-10-15 2021-04-26 사회복지법인 삼성생명공익재단 대장암 진단을 위한 대장암 특이적 메틸화 바이오마커
CN112752763A (zh) * 2018-05-23 2021-05-04 杭州诺辉健康科技有限公司 筛查结直肠癌和晚期腺瘤的试剂盒及其应用
KR20210055281A (ko) * 2019-11-07 2021-05-17 (주)지노믹트리 대장암 검출 방법
CN113403393A (zh) * 2021-05-06 2021-09-17 江苏为真生物医药技术股份有限公司 一种癌症和/或癌前病变检测试剂盒
WO2021209161A1 (fr) * 2020-04-17 2021-10-21 Universal Diagnostics, S.L. Détection d'un adénome avancé et/ou d'un cancer colorectal de stade précoce
EP3792362A4 (fr) * 2018-01-23 2021-11-17 Excellen Medical Technology Co., Ltd. Méthode et kit pour identifier l'état d'un cancer colorectal
WO2022002424A1 (fr) * 2020-06-30 2022-01-06 Universal Diagnostics, S.L. Systèmes et procédés de détection de plusieurs types de cancer
WO2022139581A1 (fr) * 2020-12-24 2022-06-30 Stichting Vumc Détection de marqueurs d'acide nucléique dans l'urine à l'aide d'une analyse de méthylation de l'adn
US11396679B2 (en) 2019-05-31 2022-07-26 Universal Diagnostics, S.L. Detection of colorectal cancer
CN114807373A (zh) * 2022-05-31 2022-07-29 益善生物技术股份有限公司 人bmp3和ndrg4基因甲基化检测试剂盒
US20220267859A1 (en) * 2019-07-22 2022-08-25 Wuhan Ammunition Life-Tech Co., Ltd. Use of detection reagent for detecting methylation of genes associated with colorectal cancer, and kit
WO2022222146A1 (fr) * 2021-04-23 2022-10-27 华大数极生物科技(深圳)有限公司 Composition, kit et application pour la détection du cancer colorectal
EP3963095A4 (fr) * 2019-05-03 2023-01-25 Cornell University Marqueurs pour l'identification et la quantification d'une mutation, d'une expression, d'un variant d'épissage, d'une translocation, d'un nombre de copies ou de changements de méthylation de séquence d'acides nucléiques
CN116121387A (zh) * 2023-01-19 2023-05-16 深圳市人民医院 一种用于结直肠癌检测的组合标志物及其应用
US11821045B2 (en) 2021-04-13 2023-11-21 Geninus Inc. Colorectal cancer-specific methylation biomarkers for diagnosing colorectal cancer
US11898199B2 (en) 2019-11-11 2024-02-13 Universal Diagnostics, S.A. Detection of colorectal cancer and/or advanced adenomas
CN117551762A (zh) * 2023-10-19 2024-02-13 嘉兴允英医学检验有限公司 作为结直肠肿瘤标志物的dna甲基化位点组合及其应用
US12467096B2 (en) 2020-05-15 2025-11-11 Universal Diagnostics, S.A. Methods and systems for identifying methylation biomarkers

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EP3792362A4 (fr) * 2018-01-23 2021-11-17 Excellen Medical Technology Co., Ltd. Méthode et kit pour identifier l'état d'un cancer colorectal
CN112752763A (zh) * 2018-05-23 2021-05-04 杭州诺辉健康科技有限公司 筛查结直肠癌和晚期腺瘤的试剂盒及其应用
EP3797112A4 (fr) * 2018-05-23 2022-03-23 Hangzhou New Horizon Health Technology Co., Ltd. Kit de dépistage du cancer colorectal et d'adénome avancé et son application
WO2019233102A1 (fr) * 2018-06-06 2019-12-12 苏州唯善生物科技有限公司 Ensemble d'amorce et de sonde pour le diagnostic, la détection, ou le criblage du cancer colorectal
CN108796080B (zh) * 2018-06-06 2022-06-07 苏州唯善生物科技有限公司 用于结直肠癌诊断、检测或筛查的引物和探针组
EP3744860A4 (fr) * 2018-06-06 2021-05-19 Suzhou Versabio Technologies, Inc. Ensemble d'amorce et de sonde pour le diagnostic, la détection, ou le criblage du cancer colorectal
CN108796080A (zh) * 2018-06-06 2018-11-13 苏州唯善生物科技有限公司 用于结直肠癌诊断、检测或筛查的引物和探针组
WO2020081549A1 (fr) * 2018-10-15 2020-04-23 The Regents Of The University Of California Procédés et matériels pour évaluer et traiter le cancer
EP3963095A4 (fr) * 2019-05-03 2023-01-25 Cornell University Marqueurs pour l'identification et la quantification d'une mutation, d'une expression, d'un variant d'épissage, d'une translocation, d'un nombre de copies ou de changements de méthylation de séquence d'acides nucléiques
US11396679B2 (en) 2019-05-31 2022-07-26 Universal Diagnostics, S.L. Detection of colorectal cancer
WO2021004215A1 (fr) * 2019-07-11 2021-01-14 广州市康立明生物科技有限责任公司 Réactif de détection combiné multigénique
US20220267859A1 (en) * 2019-07-22 2022-08-25 Wuhan Ammunition Life-Tech Co., Ltd. Use of detection reagent for detecting methylation of genes associated with colorectal cancer, and kit
US11767565B2 (en) * 2019-07-22 2023-09-26 Wuhan Ammunition Life-Tech Co., Ltd. Use of detection reagent for detecting methylation of genes associated with colorectal cancer, and kit
KR20210044923A (ko) * 2019-10-15 2021-04-26 사회복지법인 삼성생명공익재단 대장암 진단을 위한 대장암 특이적 메틸화 바이오마커
KR102440245B1 (ko) * 2019-10-15 2022-09-07 사회복지법인 삼성생명공익재단 대장암 진단을 위한 대장암 특이적 메틸화 바이오마커
CN112063712A (zh) * 2019-10-28 2020-12-11 北京康美天鸿生物科技有限公司 基于高分辨率熔解曲线检测septin9基因甲基化的特异引物对和试剂盒
KR20210055281A (ko) * 2019-11-07 2021-05-17 (주)지노믹트리 대장암 검출 방법
KR102261606B1 (ko) * 2019-11-07 2021-06-07 (주)지노믹트리 대장암 검출 방법
CN114667355A (zh) * 2019-11-07 2022-06-24 基因特力株式会社 检测结直肠癌的方法
US11898199B2 (en) 2019-11-11 2024-02-13 Universal Diagnostics, S.A. Detection of colorectal cancer and/or advanced adenomas
CN110699437A (zh) * 2019-11-11 2020-01-17 益善生物技术股份有限公司 人sdc2基因甲基化检测试剂盒
WO2021209161A1 (fr) * 2020-04-17 2021-10-21 Universal Diagnostics, S.L. Détection d'un adénome avancé et/ou d'un cancer colorectal de stade précoce
US12467096B2 (en) 2020-05-15 2025-11-11 Universal Diagnostics, S.A. Methods and systems for identifying methylation biomarkers
CN111560435A (zh) * 2020-05-20 2020-08-21 深圳市新合生物医疗科技有限公司 一种用于结直肠癌检测的dna甲基化试剂盒及使用方法、应用
WO2022002424A1 (fr) * 2020-06-30 2022-01-06 Universal Diagnostics, S.L. Systèmes et procédés de détection de plusieurs types de cancer
US11530453B2 (en) 2020-06-30 2022-12-20 Universal Diagnostics, S.L. Systems and methods for detection of multiple cancer types
NL2027228B1 (en) * 2020-12-24 2022-07-20 Stichting Vumc Detection of nucleic acid markers in urine using DNA methylation analysis
WO2022139581A1 (fr) * 2020-12-24 2022-06-30 Stichting Vumc Détection de marqueurs d'acide nucléique dans l'urine à l'aide d'une analyse de méthylation de l'adn
US11821045B2 (en) 2021-04-13 2023-11-21 Geninus Inc. Colorectal cancer-specific methylation biomarkers for diagnosing colorectal cancer
EP4328325A4 (fr) * 2021-04-23 2025-05-21 BGI Genomics Co., Limited Composition, kit et application pour la détection du cancer colorectal
WO2022222146A1 (fr) * 2021-04-23 2022-10-27 华大数极生物科技(深圳)有限公司 Composition, kit et application pour la détection du cancer colorectal
AU2021442220B2 (en) * 2021-04-23 2025-10-16 Bgi Genomics Co., Ltd. Composition, kit, and application for detection of colorectal cancer
CN113403393A (zh) * 2021-05-06 2021-09-17 江苏为真生物医药技术股份有限公司 一种癌症和/或癌前病变检测试剂盒
CN114807373A (zh) * 2022-05-31 2022-07-29 益善生物技术股份有限公司 人bmp3和ndrg4基因甲基化检测试剂盒
CN116121387A (zh) * 2023-01-19 2023-05-16 深圳市人民医院 一种用于结直肠癌检测的组合标志物及其应用
CN117551762B (zh) * 2023-10-19 2024-05-10 嘉兴允英医学检验有限公司 作为结直肠肿瘤标志物的dna甲基化位点组合及其应用
CN117551762A (zh) * 2023-10-19 2024-02-13 嘉兴允英医学检验有限公司 作为结直肠肿瘤标志物的dna甲基化位点组合及其应用

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