JP2018518967A5 - - Google Patents
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- JP2018518967A5 JP2018518967A5 JP2017566374A JP2017566374A JP2018518967A5 JP 2018518967 A5 JP2018518967 A5 JP 2018518967A5 JP 2017566374 A JP2017566374 A JP 2017566374A JP 2017566374 A JP2017566374 A JP 2017566374A JP 2018518967 A5 JP2018518967 A5 JP 2018518967A5
- Authority
- JP
- Japan
- Prior art keywords
- nucleic acid
- target
- complementary
- probe
- methylated
- 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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Links
- 108020004707 nucleic acids Proteins 0.000 claims description 373
- 102000039446 nucleic acids Human genes 0.000 claims description 373
- 150000007523 nucleic acids Chemical class 0.000 claims description 372
- 239000000523 sample Substances 0.000 claims description 151
- 238000000034 method Methods 0.000 claims description 129
- 230000000295 complement effect Effects 0.000 claims description 101
- 108020005187 Oligonucleotide Probes Proteins 0.000 claims description 46
- 239000002751 oligonucleotide probe Substances 0.000 claims description 46
- LSNNMFCWUKXFEE-UHFFFAOYSA-M Bisulfite Chemical compound OS([O-])=O LSNNMFCWUKXFEE-UHFFFAOYSA-M 0.000 claims description 40
- 230000035772 mutation Effects 0.000 claims description 37
- 239000011541 reaction mixture Substances 0.000 claims description 36
- 230000003321 amplification Effects 0.000 claims description 28
- 238000004925 denaturation Methods 0.000 claims description 28
- 230000036425 denaturation Effects 0.000 claims description 28
- 238000003199 nucleic acid amplification method Methods 0.000 claims description 28
- DWAQJAXMDSEUJJ-UHFFFAOYSA-M Sodium bisulfite Chemical compound [Na+].OS([O-])=O DWAQJAXMDSEUJJ-UHFFFAOYSA-M 0.000 claims description 16
- 235000010267 sodium hydrogen sulphite Nutrition 0.000 claims description 16
- 101710163270 Nuclease Proteins 0.000 claims description 14
- 108060002716 Exonuclease Proteins 0.000 claims description 12
- 102000013165 exonuclease Human genes 0.000 claims description 12
- 238000009396 hybridization Methods 0.000 claims description 12
- 238000006243 chemical reaction Methods 0.000 claims description 11
- 108091034117 Oligonucleotide Proteins 0.000 claims description 10
- 230000000694 effects Effects 0.000 claims description 8
- 239000003960 organic solvent Substances 0.000 claims description 6
- 238000012163 sequencing technique Methods 0.000 claims description 6
- 238000012408 PCR amplification Methods 0.000 claims description 4
- 230000015572 biosynthetic process Effects 0.000 claims description 4
- 230000015556 catabolic process Effects 0.000 claims description 4
- 238000006731 degradation reaction Methods 0.000 claims description 4
- 238000002844 melting Methods 0.000 claims description 4
- 230000008018 melting Effects 0.000 claims description 4
- 239000012141 concentrate Substances 0.000 claims description 3
- 230000003247 decreasing effect Effects 0.000 claims description 3
- 230000000368 destabilizing effect Effects 0.000 claims description 3
- 101000829171 Hypocrea virens (strain Gv29-8 / FGSC 10586) Effector TSP1 Proteins 0.000 claims description 2
- 108091093037 Peptide nucleic acid Proteins 0.000 claims description 2
- 239000011324 bead Substances 0.000 claims description 2
- 210000001124 body fluid Anatomy 0.000 claims description 2
- 239000010839 body fluid Substances 0.000 claims description 2
- 238000003776 cleavage reaction Methods 0.000 claims description 2
- 230000029087 digestion Effects 0.000 claims description 2
- 238000007847 digital PCR Methods 0.000 claims description 2
- 230000003301 hydrolyzing effect Effects 0.000 claims description 2
- 230000000977 initiatory effect Effects 0.000 claims description 2
- 238000011901 isothermal amplification Methods 0.000 claims description 2
- 238000007854 ligation-mediated PCR Methods 0.000 claims description 2
- 238000007403 mPCR Methods 0.000 claims description 2
- 238000001840 matrix-assisted laser desorption--ionisation time-of-flight mass spectrometry Methods 0.000 claims description 2
- 230000011987 methylation Effects 0.000 claims description 2
- 238000007069 methylation reaction Methods 0.000 claims description 2
- 238000012175 pyrosequencing Methods 0.000 claims description 2
- 238000003753 real-time PCR Methods 0.000 claims description 2
- 238000007894 restriction fragment length polymorphism technique Methods 0.000 claims description 2
- 230000007017 scission Effects 0.000 claims description 2
- 210000002700 urine Anatomy 0.000 claims description 2
- LSNNMFCWUKXFEE-UHFFFAOYSA-N Sulfurous acid Chemical class OS(O)=O LSNNMFCWUKXFEE-UHFFFAOYSA-N 0.000 claims 3
- 239000002773 nucleotide Substances 0.000 claims 2
- 125000003729 nucleotide group Chemical group 0.000 claims 2
- 229910052739 hydrogen Inorganic materials 0.000 claims 1
- 239000001257 hydrogen Substances 0.000 claims 1
- 125000004435 hydrogen atom Chemical class [H]* 0.000 claims 1
- -1 nucleic acids bisulfite Chemical class 0.000 claims 1
- 230000004048 modification Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 238000001216 nucleic acid method Methods 0.000 description 1
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201562183854P | 2015-06-24 | 2015-06-24 | |
| US62/183,854 | 2015-06-24 | ||
| PCT/US2016/039167 WO2016210224A1 (en) | 2015-06-24 | 2016-06-24 | Selective degradation of wild-type dna and enrichment of mutant alleles using nuclease |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2018518967A JP2018518967A (ja) | 2018-07-19 |
| JP2018518967A5 true JP2018518967A5 (enExample) | 2019-07-25 |
| JP6941568B2 JP6941568B2 (ja) | 2021-09-29 |
Family
ID=57585693
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2017566374A Active JP6941568B2 (ja) | 2015-06-24 | 2016-06-24 | ヌクレアーゼを使用する野生型ｄｎａの選択的分解および突然変異体対立遺伝子の濃縮 |
Country Status (7)
| Country | Link |
|---|---|
| US (2) | US11725230B2 (enExample) |
| EP (1) | EP3313992B1 (enExample) |
| JP (1) | JP6941568B2 (enExample) |
| AU (1) | AU2016281718B2 (enExample) |
| CA (1) | CA2990846C (enExample) |
| ES (1) | ES2917175T3 (enExample) |
| WO (1) | WO2016210224A1 (enExample) |
Families Citing this family (22)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US11725230B2 (en) | 2015-06-24 | 2023-08-15 | Dana-Farber Cancer Institute, Inc. | Selective degradation of wild-type DNA and enrichment of mutant alleles using nuclease |
| US11371090B2 (en) | 2016-12-12 | 2022-06-28 | Dana-Farber Cancer Institute, Inc. | Compositions and methods for molecular barcoding of DNA molecules prior to mutation enrichment and/or mutation detection |
| US11174511B2 (en) | 2017-07-24 | 2021-11-16 | Dana-Farber Cancer Institute, Inc. | Methods and compositions for selecting and amplifying DNA targets in a single reaction mixture |
| CN107893109B (zh) * | 2017-11-08 | 2021-07-06 | 重庆邮电大学 | 一种基于移除野生型序列的低丰度基因突变富集方法 |
| KR102086689B1 (ko) * | 2018-02-06 | 2020-03-09 | 주식회사 진씨커 | 돌연변이 세포 유리 유전자 분리 키트 및 이를 이용한 돌연변이 세포 유리 유전자 분리 방법 |
| EP3775198A4 (en) | 2018-04-02 | 2022-01-05 | Grail, Inc. | METHYLATION MARKERS AND TARGETED METHYLATION PROBE PANELS |
| CN108531603A (zh) * | 2018-05-31 | 2018-09-14 | 青岛普泽麦迪生物技术有限公司 | 一种用于braf基因v600e突变检测的引物对、试剂盒及其检测方法 |
| CN113286881A (zh) | 2018-09-27 | 2021-08-20 | 格里尔公司 | 甲基化标记和标靶甲基化探针板 |
| CN113260451A (zh) * | 2018-10-16 | 2021-08-13 | 辛辛那提大学 | 单分子表观遗传定位 |
| CN109880891B (zh) * | 2019-04-22 | 2021-07-30 | 上海交通大学 | 基于核酸酶偶联pcr原理富集低丰度dna突变的检测技术体系及应用 |
| WO2021034999A1 (en) * | 2019-08-21 | 2021-02-25 | Dana-Farber Cancer Institute, Inc. | Multi-site enrichment of deletions in dna microsatellites |
| EP4121557A4 (en) | 2020-08-06 | 2024-05-01 | Singular Genomics Systems, Inc. | Spatial sequencing |
| EP4121561A4 (en) | 2020-08-06 | 2024-04-17 | Singular Genomics Systems, Inc. | Methods for in situ transcriptomics and proteomics |
| GB2603203A (en) * | 2021-02-02 | 2022-08-03 | Univ Heriot Watt | Method for enriching nucelic acids |
| EP4337782A4 (en) * | 2021-05-14 | 2025-04-02 | Carmel-Haifa University Economic Corporation Ltd. | A method of identifying ultra-rare genetic variants |
| US11993792B2 (en) | 2021-05-27 | 2024-05-28 | New England Biolabs, Inc. | DNase I variants, compositions, methods, and kits |
| GB202111195D0 (en) * | 2021-08-03 | 2021-09-15 | Cergentis B V | Method for targeted sequencing |
| CN114280128B (zh) * | 2021-12-24 | 2022-11-18 | 清华大学 | 双标记gFET的制备及其在miRNA检测中的应用 |
| CN120400099A (zh) * | 2022-07-01 | 2025-08-01 | 中国科学院基础医学与肿瘤研究所(筹) | 一种基于可编程核酸酶的超灵敏目标核酸富集检测方法 |
| JP2025536281A (ja) * | 2022-10-19 | 2025-11-05 | バイオフィデリティ・リミテッド | 核酸の濃縮および検出 |
| WO2024249961A1 (en) | 2023-06-01 | 2024-12-05 | Singular Genomics Systems, Inc. | Methods and probes for detecting polynucleotide sequences in cells and tissues |
| WO2025029475A1 (en) * | 2023-07-28 | 2025-02-06 | Guardant Health, Inc. | Methods to enrich nucleotide variants by negative selection |
Family Cites Families (31)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| ES2101867T3 (es) | 1990-05-07 | 1997-07-16 | Daikin Ind Ltd | Aplicaciones diagnosticas de la formacion de lazos d dobles. |
| WO1994002500A1 (en) * | 1992-07-17 | 1994-02-03 | Aprogenex, Inc. | Oligonucleotide probes and primers for detecting chromosomal translocation |
| US5629178A (en) | 1994-10-28 | 1997-05-13 | Genetics & Ivf Institute | Method for enhancing amplification in the polymerase chain reaction employing peptide nucleic acid (PNA) |
| US6949340B2 (en) * | 2001-03-28 | 2005-09-27 | Creative Mines Llc | Optical phase modulator |
| DE10158516A1 (de) | 2001-11-29 | 2003-06-12 | Focusgenomics Gmbh | Verfahren zum Nachweis von Hybridisierungsereignissen in Nukleinsäuren |
| WO2003048378A2 (en) * | 2001-12-04 | 2003-06-12 | Euregen Llc | Methods and compositions for selectively cleaving dna containing duplex acids in a complex nucleic acid mixture |
| US8440404B2 (en) * | 2004-03-08 | 2013-05-14 | Rubicon Genomics | Methods and compositions for generating and amplifying DNA libraries for sensitive detection and analysis of DNA methylation |
| EP1854882A4 (en) | 2005-03-01 | 2010-09-22 | Wako Pure Chem Ind Ltd | METHOD OF OBTAINING A SUBTRACTIVE POLYNUCLEOTIDE |
| MX2008006663A (es) * | 2005-11-24 | 2008-09-22 | Basf Se | Proteinas efectoras de union a queratina quimericas. |
| US7544473B2 (en) | 2006-01-23 | 2009-06-09 | Population Genetics Technologies Ltd. | Nucleic acid analysis using sequence tokens |
| WO2008096146A1 (en) | 2007-02-07 | 2008-08-14 | Solexa Limited | Preparation of templates for methylation analysis |
| US20080254453A1 (en) | 2007-04-12 | 2008-10-16 | Affymetrix, Inc | Analysis of methylation using selective adaptor ligation |
| US7749708B2 (en) | 2007-09-12 | 2010-07-06 | Transgenomic, Inc. | Method for identifying the sequence of one or more variant nucleotides in a nucleic acid molecule |
| US20100216648A1 (en) * | 2009-02-20 | 2010-08-26 | Febit Holding Gmbh | Synthesis of sequence-verified nucleic acids |
| US10636413B2 (en) | 2009-06-13 | 2020-04-28 | Rolr, Inc. | System for communication skills training using juxtaposition of recorded takes |
| EP2272976A1 (en) * | 2009-07-06 | 2011-01-12 | Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. | Method for differentiation of polynucleotide strands |
| US20130059734A1 (en) | 2009-11-13 | 2013-03-07 | Commonwealth Scientific And Industrial Research Organisation | Epigenetic analysis |
| EP2545189B1 (en) | 2010-03-08 | 2018-01-10 | Dana-Farber Cancer Institute, Inc. | Full cold-pcr enrichment with reference blocking sequence |
| WO2012129363A2 (en) | 2011-03-24 | 2012-09-27 | President And Fellows Of Harvard College | Single cell nucleic acid detection and analysis |
| WO2012135053A2 (en) * | 2011-03-25 | 2012-10-04 | Integrated Dna Technologies, Inc. | Rnase h-based assays utilizing modified rna monomers |
| EP2691541B1 (en) | 2011-03-31 | 2017-10-18 | Dana-Farber Cancer Institute, Inc. | Method for enriching in single-stranded mutant sequences from mixture of wild-type and mutant sequences |
| CA2835942C (en) | 2011-05-19 | 2019-01-22 | Sequenom, Inc. | Products and processes for multiplex nucleic acid identification |
| US9238836B2 (en) * | 2012-03-30 | 2016-01-19 | Pacific Biosciences Of California, Inc. | Methods and compositions for sequencing modified nucleic acids |
| JP6009649B2 (ja) | 2013-03-14 | 2016-10-19 | タカラバイオ株式会社 | 耐熱性のミスマッチエンドヌクレアーゼの利用方法 |
| MX382588B (es) | 2013-04-17 | 2025-03-13 | Pioneer Hi Bred Int | Métodos para caracterizar la composición de secuencias de adn en un genoma. |
| WO2015013166A1 (en) | 2013-07-24 | 2015-01-29 | Dana-Farber Cancer Institute, Inc. | Methods and compositions to enable enrichment of minor dna alleles by limiting denaturation time in pcr or simply enable enrichment of minor dna alleles by limiting denaturation time in pcr |
| US9873908B2 (en) | 2013-11-27 | 2018-01-23 | Roche Molecular Systems, Inc. | Methods for the enrichment of mutated nucleic acid from a mixture |
| SG10201804519RA (en) | 2013-12-28 | 2018-07-30 | Guardant Health Inc | Methods and systems for detecting genetic variants |
| US11725230B2 (en) | 2015-06-24 | 2023-08-15 | Dana-Farber Cancer Institute, Inc. | Selective degradation of wild-type DNA and enrichment of mutant alleles using nuclease |
| US11371090B2 (en) | 2016-12-12 | 2022-06-28 | Dana-Farber Cancer Institute, Inc. | Compositions and methods for molecular barcoding of DNA molecules prior to mutation enrichment and/or mutation detection |
| WO2021034999A1 (en) | 2019-08-21 | 2021-02-25 | Dana-Farber Cancer Institute, Inc. | Multi-site enrichment of deletions in dna microsatellites |
-
2016
- 2016-06-24 US US15/739,301 patent/US11725230B2/en active Active
- 2016-06-24 EP EP16815352.6A patent/EP3313992B1/en active Active
- 2016-06-24 WO PCT/US2016/039167 patent/WO2016210224A1/en not_active Ceased
- 2016-06-24 ES ES16815352T patent/ES2917175T3/es active Active
- 2016-06-24 CA CA2990846A patent/CA2990846C/en active Active
- 2016-06-24 AU AU2016281718A patent/AU2016281718B2/en active Active
- 2016-06-24 JP JP2017566374A patent/JP6941568B2/ja active Active
-
2023
- 2023-08-13 US US18/448,941 patent/US20230392191A1/en active Pending
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