JPWO2019136413A5 - - Google Patents
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- JPWO2019136413A5 JPWO2019136413A5 JP2020537593A JP2020537593A JPWO2019136413A5 JP WO2019136413 A5 JPWO2019136413 A5 JP WO2019136413A5 JP 2020537593 A JP2020537593 A JP 2020537593A JP 2020537593 A JP2020537593 A JP 2020537593A JP WO2019136413 A5 JPWO2019136413 A5 JP WO2019136413A5
- Authority
- JP
- Japan
- Prior art keywords
- nucleic acid
- target nucleic
- modified
- sequence
- dhu
- 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.)
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- 150000007523 nucleic acids Chemical class 0.000 claims description 138
- 108020004707 nucleic acids Proteins 0.000 claims description 136
- OIVLITBTBDPEFK-UHFFFAOYSA-N Dihydrouracil Chemical compound O=C1CCNC(=O)N1 OIVLITBTBDPEFK-UHFFFAOYSA-N 0.000 claims description 51
- RWQNBRDOKXIBIV-UHFFFAOYSA-N Thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 claims description 46
- 229940113082 Thymine Drugs 0.000 claims description 23
- 229940104302 Cytosine Drugs 0.000 claims description 18
- OPTASPLRGRRNAP-UHFFFAOYSA-N Cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 claims description 18
- 230000000903 blocking Effects 0.000 claims description 11
- 229910000085 borane Inorganic materials 0.000 claims description 8
- 229910000090 borane Inorganic materials 0.000 claims description 8
- DMJZZSLVPSMWCS-UHFFFAOYSA-N diborane Chemical compound B1[H]B[H]1 DMJZZSLVPSMWCS-UHFFFAOYSA-N 0.000 claims description 8
- 239000003638 reducing agent Substances 0.000 claims description 8
- UORVGPXVDQYIDP-UHFFFAOYSA-N trihydridoboron Substances B UORVGPXVDQYIDP-UHFFFAOYSA-N 0.000 claims description 8
- FHSISDGOVSHJRW-UHFFFAOYSA-N 5-formylcytosine Chemical compound NC1=NC(=O)NC=C1C=O FHSISDGOVSHJRW-UHFFFAOYSA-N 0.000 claims description 6
- 108090000790 Enzymes Proteins 0.000 claims description 5
- 102000004190 Enzymes Human genes 0.000 claims description 5
- BLQMCTXZEMGOJM-UHFFFAOYSA-N 5-carboxycytosine Chemical compound NC=1NC(=O)N=CC=1C(O)=O BLQMCTXZEMGOJM-UHFFFAOYSA-N 0.000 claims description 4
- 101700043716 TET1 Proteins 0.000 claims description 4
- 101700048164 TET2 Proteins 0.000 claims description 4
- 101700085225 TET3 Proteins 0.000 claims description 4
- QHXLIQMGIGEHJP-UHFFFAOYSA-N boron;2-methylpyridine Chemical group [B].CC1=CC=CC=N1 QHXLIQMGIGEHJP-UHFFFAOYSA-N 0.000 claims description 4
- 238000009585 enzyme analysis Methods 0.000 claims description 4
- 238000002493 microarray Methods 0.000 claims description 4
- 108091007521 restriction endonucleases Proteins 0.000 claims description 4
- AGGHKNBCHLWKHY-UHFFFAOYSA-N sodium;triacetyloxyboron(1-) Chemical compound [Na+].CC(=O)O[B-](OC(C)=O)OC(C)=O AGGHKNBCHLWKHY-UHFFFAOYSA-N 0.000 claims description 4
- RYVNIFSIEDRLSJ-UHFFFAOYSA-N 5-Hydroxymethylcytosine Chemical compound NC=1NC(=O)N=CC=1CO RYVNIFSIEDRLSJ-UHFFFAOYSA-N 0.000 claims description 3
- LRSASMSXMSNRBT-UHFFFAOYSA-N 5-Methylcytosine Chemical compound CC1=CNC(=O)N=C1N LRSASMSXMSNRBT-UHFFFAOYSA-N 0.000 claims description 3
- 241000283690 Bos taurus Species 0.000 claims description 2
- 241000224436 Naegleria Species 0.000 claims description 2
- 102100003997 TET1 Human genes 0.000 claims description 2
- 102100003998 TET2 Human genes 0.000 claims description 2
- 102100004000 TET3 Human genes 0.000 claims description 2
- 101700066455 TRN2 Proteins 0.000 claims description 2
- OPCPRUQQEJNFIV-UHFFFAOYSA-N disodium;cyanoboron(1-) Chemical compound [Na+].[Na+].[B-]C#N.[B-]C#N OPCPRUQQEJNFIV-UHFFFAOYSA-N 0.000 claims description 2
- 229910000033 sodium borohydride Inorganic materials 0.000 claims description 2
- YOQDYZUWIQVZSF-UHFFFAOYSA-N sodium borohydride Substances [BH4-].[Na+] YOQDYZUWIQVZSF-UHFFFAOYSA-N 0.000 claims description 2
- ODGROJYWQXFQOZ-UHFFFAOYSA-N sodium;boron(1-) Chemical compound [B-].[Na+] ODGROJYWQXFQOZ-UHFFFAOYSA-N 0.000 claims description 2
- 229920001850 Nucleic acid sequence Polymers 0.000 claims 2
- 240000004997 Coprinus comatus Species 0.000 claims 1
- 235000004439 Coprinus comatus Nutrition 0.000 claims 1
- 238000000034 method Methods 0.000 claims 1
- 230000004048 modification Effects 0.000 claims 1
- 238000006011 modification reaction Methods 0.000 claims 1
- LMDZBCPBFSXMTL-UHFFFAOYSA-N 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide Chemical compound CCN=C=NCCCN(C)C LMDZBCPBFSXMTL-UHFFFAOYSA-N 0.000 description 4
- XCCTYIAWTASOJW-XVFCMESISA-N Uridine-5'-Diphosphate Chemical compound O[C@@H]1[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O[C@H]1N1C(=O)NC(=O)C=C1 XCCTYIAWTASOJW-XVFCMESISA-N 0.000 description 2
- 125000002791 glucosyl group Chemical group C1([C@H](O)[C@@H](O)[C@H](O)[C@H](O1)CO)* 0.000 description 2
- OAKJQQAXSVQMHS-UHFFFAOYSA-N hydrazine Chemical compound NN OAKJQQAXSVQMHS-UHFFFAOYSA-N 0.000 description 2
- 150000002443 hydroxylamines Chemical class 0.000 description 2
- 239000007800 oxidant agent Substances 0.000 description 2
- 238000003752 polymerase chain reaction Methods 0.000 description 2
- LPGWNCNRGQANGC-UHFFFAOYSA-N pyridin-1-ium-1-ylboranuide Chemical compound [BH3-][N+]1=CC=CC=C1 LPGWNCNRGQANGC-UHFFFAOYSA-N 0.000 description 2
- 101700034878 setA Proteins 0.000 description 2
- 241001515965 unidentified phage Species 0.000 description 2
- 229920000160 (ribonucleotides)n+m Polymers 0.000 description 1
- WQZGKKKJIJFFOK-GASJEMHNSA-N D-Glucose Natural products OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O WQZGKKKJIJFFOK-GASJEMHNSA-N 0.000 description 1
- QRXWMOHMRWLFEY-UHFFFAOYSA-N Isoniazid Chemical class NNC(=O)C1=CC=NC=C1 QRXWMOHMRWLFEY-UHFFFAOYSA-N 0.000 description 1
- AQFWNELGMODZGC-UHFFFAOYSA-N O-ethylhydroxylamine Chemical group CCON AQFWNELGMODZGC-UHFFFAOYSA-N 0.000 description 1
- 150000001412 amines Chemical class 0.000 description 1
- 150000001732 carboxylic acid derivatives Chemical class 0.000 description 1
- 239000003153 chemical reaction reagent Substances 0.000 description 1
- 150000001875 compounds Chemical class 0.000 description 1
- 229920003013 deoxyribonucleic acid Polymers 0.000 description 1
- QUSNBJAOOMFDIB-UHFFFAOYSA-N ethyl amine Chemical compound CCN QUSNBJAOOMFDIB-UHFFFAOYSA-N 0.000 description 1
- 239000008103 glucose Substances 0.000 description 1
- 150000002429 hydrazines Chemical class 0.000 description 1
- -1 hydroxylamine compound Chemical class 0.000 description 1
- 230000005012 migration Effects 0.000 description 1
- ZLMJMSJWJFRBEC-UHFFFAOYSA-N potassium Chemical group [K] ZLMJMSJWJFRBEC-UHFFFAOYSA-N 0.000 description 1
- 229910052700 potassium Inorganic materials 0.000 description 1
- 239000011591 potassium Substances 0.000 description 1
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| JP2022139122A JP2022174153A (ja) | 2018-01-08 | 2022-09-01 | シトシン修飾の、亜硫酸水素塩非含有、塩基分解能特定 |
Applications Claiming Priority (7)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201862614798P | 2018-01-08 | 2018-01-08 | |
| US62/614,798 | 2018-01-08 | ||
| US201862660523P | 2018-04-20 | 2018-04-20 | |
| US62/660,523 | 2018-04-20 | ||
| US201862771409P | 2018-11-26 | 2018-11-26 | |
| US62/771,409 | 2018-11-26 | ||
| PCT/US2019/012627 WO2019136413A1 (fr) | 2018-01-08 | 2019-01-08 | Identification par résolution de base sans bisulfite de modifications de cytosine |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2022139122A Division JP2022174153A (ja) | 2018-01-08 | 2022-09-01 | シトシン修飾の、亜硫酸水素塩非含有、塩基分解能特定 |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2021509587A JP2021509587A (ja) | 2021-04-01 |
| JPWO2019136413A5 true JPWO2019136413A5 (fr) | 2022-04-08 |
| JP7136899B2 JP7136899B2 (ja) | 2022-09-13 |
Family
ID=67143801
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2020537593A Active JP7136899B2 (ja) | 2018-01-08 | 2019-01-08 | シトシン修飾の、亜硫酸水素塩非含有、塩基分解能特定 |
| JP2022139122A Pending JP2022174153A (ja) | 2018-01-08 | 2022-09-01 | シトシン修飾の、亜硫酸水素塩非含有、塩基分解能特定 |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2022139122A Pending JP2022174153A (ja) | 2018-01-08 | 2022-09-01 | シトシン修飾の、亜硫酸水素塩非含有、塩基分解能特定 |
Country Status (15)
| Country | Link |
|---|---|
| US (4) | US20200370114A1 (fr) |
| EP (1) | EP3737748A4 (fr) |
| JP (2) | JP7136899B2 (fr) |
| KR (2) | KR20230030037A (fr) |
| CN (2) | CN115181783A (fr) |
| AU (2) | AU2019205416B2 (fr) |
| BR (1) | BR112020013718A2 (fr) |
| CA (1) | CA3087915A1 (fr) |
| IL (2) | IL296932A (fr) |
| MA (1) | MA51633A (fr) |
| MX (2) | MX2020007259A (fr) |
| NZ (1) | NZ765943A (fr) |
| SG (1) | SG11202006511YA (fr) |
| WO (1) | WO2019136413A1 (fr) |
| ZA (1) | ZA202004769B (fr) |
Families Citing this family (30)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| AU2019205416B2 (en) | 2018-01-08 | 2022-07-14 | Ludwig Institute For Cancer Research Ltd | Bisulfite-free, base-resolution identification of cytosine modifications |
| CN112105626A (zh) * | 2018-02-14 | 2020-12-18 | 蓝星基因组股份有限公司 | 用于dna、特别是细胞游离dna的表观遗传学分析的方法 |
| WO2020160414A1 (fr) | 2019-01-31 | 2020-08-06 | Guardant Health, Inc. | Compositions et méthodes pour isoler de l'adn acellulaire |
| EP3830285A4 (fr) * | 2019-05-31 | 2022-04-27 | Freenome Holdings, Inc. | Méthodes et systèmes de séquençage à haute profondeur d'acide nucléique méthylé |
| JP2022540453A (ja) * | 2019-07-08 | 2022-09-15 | ルドウイグ インスティテュート フォー キャンサー リサーチ エルティーディー | バイサルファイトを使用しない全ゲノムメチル化解析 |
| CN110669824A (zh) * | 2019-10-11 | 2020-01-10 | 广州迈森致远基因科技有限公司 | 低起始量血浆游离dna甲基化建库试剂盒及方法 |
| CN110820050A (zh) * | 2019-11-22 | 2020-02-21 | 北京吉因加科技有限公司 | 全基因组甲基化非重亚硫酸氢盐测序文库及构建 |
| WO2021161192A1 (fr) | 2020-02-11 | 2021-08-19 | The Chancellor, Masters And Scholars Of The University Of Oxford | Séquençage d'acide nucléique à lecture longue cible pour la détermination de modifications de cytosine |
| CN113373207A (zh) * | 2020-02-25 | 2021-09-10 | 深圳华大基因科技服务有限公司 | 确定胞嘧啶修饰的方法 |
| CA3187549A1 (fr) | 2020-07-30 | 2022-02-03 | Cambridge Epigenetix Limited | Compositions et procedes d'analyse d'acides nucleiques |
| US11946044B2 (en) | 2020-07-30 | 2024-04-02 | Guardant Health, Inc. | Methods for isolating cell-free DNA |
| US20230357852A1 (en) | 2020-08-19 | 2023-11-09 | Mayo Foundation For Medical Education And Research | Detecting non-hodgkin lymphoma |
| WO2022053872A1 (fr) | 2020-09-14 | 2022-03-17 | The Chancellor, Masters And Scholars Of The University Of Oxford | Analyse de modifications de cytosine |
| US20220154286A1 (en) * | 2020-10-23 | 2022-05-19 | Guardant Health, Inc. | Compositions and methods for analyzing dna using partitioning and base conversion |
| GB202017653D0 (en) | 2020-11-09 | 2020-12-23 | Cambridge Entpr Ltd | Methods for detection of nucleotide modification |
| JP2024506854A (ja) | 2021-01-29 | 2024-02-15 | マヨ ファウンデーション フォア メディカル エデュケーション アンド リサーチ | 複数の種類のがんの有無の検出 |
| JP2024506899A (ja) | 2021-02-09 | 2024-02-15 | エフ． ホフマン－ラ ロシュ アーゲー | 核酸中のメチル化の塩基レベル検出のための方法 |
| GB202109469D0 (en) | 2021-06-30 | 2021-08-11 | Cambridge Entpr Ltd | Methods for detecting modified nucleotides |
| KR20240046525A (ko) * | 2021-07-27 | 2024-04-09 | 더 챈슬러 마스터즈 앤드 스칼라스 오브 더 유니버시티 오브 옥스포드 | 세포-유리 dna에 대한 tet-보조 피리딘 보란 시퀀싱과 관련된 조성물 및 방법 |
| CN113846160A (zh) * | 2021-09-14 | 2021-12-28 | 翌圣生物科技(上海)股份有限公司 | 正向筛选的胞嘧啶甲基化快速检测方法及过氧钨酸盐在将5hmC氧化为thT中的应用 |
| CN114085894A (zh) * | 2021-11-03 | 2022-02-25 | 翌圣生物科技(上海)股份有限公司 | 核酸甲基化胞嘧啶转化方法 |
| WO2023082240A1 (fr) * | 2021-11-15 | 2023-05-19 | 深圳华大智造科技股份有限公司 | Procédé de détection de modification de méthylation d'adn à l'échelle du génome |
| WO2023129965A2 (fr) * | 2021-12-29 | 2023-07-06 | Foundation Medicine, Inc. | Détection d'informations génétiques et épigénétiques dans un flux de travail unique |
| CN114045345B (zh) * | 2022-01-07 | 2022-04-29 | 臻和(北京)生物科技有限公司 | 基于游离dna的基因组癌变信息检测系统和检测方法 |
| AU2023234670A1 (en) * | 2022-03-15 | 2024-01-18 | Illumina, Inc. | Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection |
| WO2023183841A2 (fr) * | 2022-03-23 | 2023-09-28 | Exact Sciences Corporation | Compositions et méthodes d'oxydation assistée par tet de bases nucléotidiques méthylées |
| WO2023187012A1 (fr) | 2022-03-31 | 2023-10-05 | Illumina Cambridge Limited | Compositions comprenant des complexes amine-borane aqueux et des polynucléotides, et leurs procédés d'utilisation pour détecter la méthylcytosine ou l'hydroxyméthylcytosine |
| WO2024042217A1 (fr) | 2022-08-25 | 2024-02-29 | Illumina, Inc. | Procédés de modification de méthylcytosine ou d'un dérivé de celle-ci à l'aide d'une molécule nucléophile, et leurs procédés d'utilisation pour détecter la méthylcytosine ou un dérivé de celle-ci dans un polynucléotide |
| WO2024073043A1 (fr) | 2022-09-30 | 2024-04-04 | Illumina, Inc. | Procédés d'utilisation de protéines de liaison cpg dans la cartographie de nucléotides cytosine modifiés |
| CN116287166A (zh) * | 2023-04-19 | 2023-06-23 | 纳昂达(南京)生物科技有限公司 | 甲基化测序接头及其应用 |
Family Cites Families (14)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US7582420B2 (en) | 2001-07-12 | 2009-09-01 | Illumina, Inc. | Multiplex nucleic acid reactions |
| US9115386B2 (en) * | 2008-09-26 | 2015-08-25 | Children's Medical Center Corporation | Selective oxidation of 5-methylcytosine by TET-family proteins |
| WO2011127136A1 (fr) | 2010-04-06 | 2011-10-13 | University Of Chicago | Compositions et procédés liés à la modification de 5-hydroxyméthylcytosine (5-hmc) |
| EP2694686B2 (fr) | 2011-04-06 | 2023-07-19 | The University of Chicago | Composition et procédés se rapportant à la modification de la 5-méthylcytosine (5-mc) |
| CN103827321B (zh) * | 2011-07-29 | 2017-08-25 | 剑桥表现遗传学有限公司 | 用于检测核苷酸修饰的方法 |
| US9040239B2 (en) * | 2012-03-15 | 2015-05-26 | New England Biolabs, Inc. | Composition and methods of oxygenation of nucleic acids containing 5-methylpyrimidine |
| US9121061B2 (en) * | 2012-03-15 | 2015-09-01 | New England Biolabs, Inc. | Methods and compositions for discrimination between cytosine and modifications thereof and for methylome analysis |
| WO2014165770A1 (fr) * | 2013-04-05 | 2014-10-09 | The University Of Chicago | Séquençage avec une résolution de l'ordre de la base de la 5-formylcytosine (5fc) et de la 5-carboxylcytosine (5cac) |
| US20160194696A1 (en) | 2013-08-09 | 2016-07-07 | New England Biolabs, Inc. | Detecting, Sequencing and/or Mapping 5-Hydroxymethylcytosine and 5-Formylcytosine at Single-Base Resolution |
| US20180251815A1 (en) | 2015-09-04 | 2018-09-06 | The University Of Tokyo | Oxidizing agent for 5-hydroxymethylcytosine and method for analyzing 5-hydroxymethylcytosine |
| US11162139B2 (en) | 2016-03-02 | 2021-11-02 | Shanghai Epican Genetech Co. Ltd. | Method for genomic profiling of DNA 5-methylcytosine and 5-hydroxymethylcytosine |
| WO2017176630A1 (fr) | 2016-04-07 | 2017-10-12 | The Board Of Trustees Of The Leland Stanford Junior University | Diagnostics non invasifs par séquençage d'adn acellulaire 5-hydroxyméthylé |
| AU2019205416B2 (en) * | 2018-01-08 | 2022-07-14 | Ludwig Institute For Cancer Research Ltd | Bisulfite-free, base-resolution identification of cytosine modifications |
| CN112105626A (zh) * | 2018-02-14 | 2020-12-18 | 蓝星基因组股份有限公司 | 用于dna、特别是细胞游离dna的表观遗传学分析的方法 |
-
2019
- 2019-01-08 AU AU2019205416A patent/AU2019205416B2/en active Active
- 2019-01-08 IL IL296932A patent/IL296932A/en unknown
- 2019-01-08 IL IL275850A patent/IL275850B2/en unknown
- 2019-01-08 BR BR112020013718-9A patent/BR112020013718A2/pt unknown
- 2019-01-08 EP EP19736010.0A patent/EP3737748A4/fr active Pending
- 2019-01-08 MA MA051633A patent/MA51633A/fr unknown
- 2019-01-08 MX MX2020007259A patent/MX2020007259A/es unknown
- 2019-01-08 WO PCT/US2019/012627 patent/WO2019136413A1/fr unknown
- 2019-01-08 CA CA3087915A patent/CA3087915A1/fr active Pending
- 2019-01-08 CN CN202210527768.9A patent/CN115181783A/zh active Pending
- 2019-01-08 KR KR1020237005878A patent/KR20230030037A/ko not_active Application Discontinuation
- 2019-01-08 NZ NZ765943A patent/NZ765943A/en unknown
- 2019-01-08 JP JP2020537593A patent/JP7136899B2/ja active Active
- 2019-01-08 CN CN201980011272.2A patent/CN111971386A/zh active Pending
- 2019-01-08 KR KR1020207022948A patent/KR102503884B1/ko active IP Right Grant
- 2019-01-08 US US16/960,510 patent/US20200370114A1/en active Pending
- 2019-01-08 SG SG11202006511YA patent/SG11202006511YA/en unknown
-
2020
- 2020-07-13 MX MX2022010611A patent/MX2022010611A/es unknown
- 2020-07-31 ZA ZA2020/04769A patent/ZA202004769B/en unknown
-
2021
- 2021-03-15 US US17/201,825 patent/US11306355B2/en active Active
-
2022
- 2022-03-07 US US17/688,427 patent/US11987843B2/en active Active
- 2022-03-07 US US17/688,424 patent/US11959136B2/en active Active
- 2022-09-01 JP JP2022139122A patent/JP2022174153A/ja active Pending
- 2022-09-22 AU AU2022235598A patent/AU2022235598A1/en active Pending
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