JPWO2020072829A5 - - Google Patents
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- Publication number
- JPWO2020072829A5 JPWO2020072829A5 JP2021518090A JP2021518090A JPWO2020072829A5 JP WO2020072829 A5 JPWO2020072829 A5 JP WO2020072829A5 JP 2021518090 A JP2021518090 A JP 2021518090A JP 2021518090 A JP2021518090 A JP 2021518090A JP WO2020072829 A5 JPWO2020072829 A5 JP WO2020072829A5
- Authority
- JP
- Japan
- Prior art keywords
- dna
- sample
- nucleic acid
- 5hmc
- barcode
- 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.)
- Pending
Links
- 108020004414 DNA Proteins 0.000 claims description 212
- 238000000034 method Methods 0.000 claims description 167
- 239000000523 sample Substances 0.000 claims description 164
- 150000007523 nucleic acids Chemical class 0.000 claims description 91
- 239000002299 complementary DNA Substances 0.000 claims description 90
- 108010033040 Histones Proteins 0.000 claims description 83
- 102000039446 nucleic acids Human genes 0.000 claims description 74
- 108020004707 nucleic acids Proteins 0.000 claims description 74
- 108090000623 proteins and genes Proteins 0.000 claims description 64
- 102000004169 proteins and genes Human genes 0.000 claims description 64
- 102000053602 DNA Human genes 0.000 claims description 61
- 230000004048 modification Effects 0.000 claims description 55
- 238000012986 modification Methods 0.000 claims description 55
- 238000012163 sequencing technique Methods 0.000 claims description 47
- 239000000203 mixture Substances 0.000 claims description 25
- 108091032973 (ribonucleotides)n+m Proteins 0.000 claims description 23
- 230000000295 complement effect Effects 0.000 claims description 19
- 239000008280 blood Substances 0.000 claims description 17
- 210000004369 blood Anatomy 0.000 claims description 17
- 108091028043 Nucleic acid sequence Proteins 0.000 claims description 15
- 108091007494 Nucleic acid- binding domains Proteins 0.000 claims description 15
- 102000004506 Blood Proteins Human genes 0.000 claims description 12
- 108010017384 Blood Proteins Proteins 0.000 claims description 12
- PJKKQFAEFWCNAQ-UHFFFAOYSA-N N(4)-methylcytosine Chemical group CNC=1C=CNC(=O)N=1 PJKKQFAEFWCNAQ-UHFFFAOYSA-N 0.000 claims description 12
- 239000012634 fragment Substances 0.000 claims description 12
- 230000002194 synthesizing effect Effects 0.000 claims description 12
- 108010047956 Nucleosomes Proteins 0.000 claims description 10
- 108091092259 cell-free RNA Proteins 0.000 claims description 10
- 210000001623 nucleosome Anatomy 0.000 claims description 10
- 238000004458 analytical method Methods 0.000 claims description 6
- 238000001712 DNA sequencing Methods 0.000 claims description 4
- 230000003321 amplification Effects 0.000 claims description 4
- 238000003199 nucleic acid amplification method Methods 0.000 claims description 4
- 102000003960 Ligases Human genes 0.000 claims description 3
- 108090000364 Ligases Proteins 0.000 claims description 3
- 238000009396 hybridization Methods 0.000 claims description 3
- 238000007031 hydroxymethylation reaction Methods 0.000 claims description 3
- 230000008685 targeting Effects 0.000 claims description 3
- 230000001413 cellular effect Effects 0.000 claims description 2
- RYVNIFSIEDRLSJ-UHFFFAOYSA-N 5-(hydroxymethyl)cytosine Chemical compound NC=1NC(=O)N=CC=1CO RYVNIFSIEDRLSJ-UHFFFAOYSA-N 0.000 claims 4
- 239000012472 biological sample Substances 0.000 description 18
- 238000003556 assay Methods 0.000 description 17
- 239000012491 analyte Substances 0.000 description 14
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical compound N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 12
- 230000004481 post-translational protein modification Effects 0.000 description 7
- 229960002685 biotin Drugs 0.000 description 6
- 235000020958 biotin Nutrition 0.000 description 6
- 239000011616 biotin Substances 0.000 description 6
- 230000005730 ADP ribosylation Effects 0.000 description 2
- 108091093088 Amplicon Proteins 0.000 description 2
- 230000007067 DNA methylation Effects 0.000 description 2
- 230000006271 O-GlcNAcylation Effects 0.000 description 2
- 239000000090 biomarker Substances 0.000 description 2
- 238000006243 chemical reaction Methods 0.000 description 2
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical group NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 2
- 201000010099 disease Diseases 0.000 description 2
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 description 2
- 230000014509 gene expression Effects 0.000 description 2
- 238000005070 sampling Methods 0.000 description 2
- GUAHPAJOXVYFON-ZETCQYMHSA-N (8S)-8-amino-7-oxononanoic acid zwitterion Chemical compound C[C@H](N)C(=O)CCCCCC(O)=O GUAHPAJOXVYFON-ZETCQYMHSA-N 0.000 description 1
- 108090001008 Avidin Proteins 0.000 description 1
- 108091034117 Oligonucleotide Proteins 0.000 description 1
- 108010090804 Streptavidin Proteins 0.000 description 1
- 230000021736 acetylation Effects 0.000 description 1
- 238000006640 acetylation reaction Methods 0.000 description 1
- 239000000427 antigen Substances 0.000 description 1
- 102000036639 antigens Human genes 0.000 description 1
- 108091007433 antigens Proteins 0.000 description 1
- 230000006242 butyrylation Effects 0.000 description 1
- 238000010514 butyrylation reaction Methods 0.000 description 1
- 230000006329 citrullination Effects 0.000 description 1
- 238000010614 crotonylation reaction Methods 0.000 description 1
- 230000001973 epigenetic effect Effects 0.000 description 1
- 230000004049 epigenetic modification Effects 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 230000022244 formylation Effects 0.000 description 1
- 238000006170 formylation reaction Methods 0.000 description 1
- 125000002887 hydroxy group Chemical group [H]O* 0.000 description 1
- 230000017538 malonylation Effects 0.000 description 1
- 230000011987 methylation Effects 0.000 description 1
- 238000007069 methylation reaction Methods 0.000 description 1
- 230000026731 phosphorylation Effects 0.000 description 1
- 238000006366 phosphorylation reaction Methods 0.000 description 1
- 230000006289 propionylation Effects 0.000 description 1
- 238000010515 propionylation reaction Methods 0.000 description 1
- 238000009877 rendering Methods 0.000 description 1
- 239000007787 solid Substances 0.000 description 1
- 230000035322 succinylation Effects 0.000 description 1
- 238000010613 succinylation reaction Methods 0.000 description 1
- 230000010741 sumoylation Effects 0.000 description 1
- 238000010798 ubiquitination Methods 0.000 description 1
- 230000034512 ubiquitination Effects 0.000 description 1
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201862741473P | 2018-10-04 | 2018-10-04 | |
| US62/741,473 | 2018-10-04 | ||
| PCT/US2019/054582 WO2020072829A2 (en) | 2018-10-04 | 2019-10-03 | Simultaneous, sequencing-based analysis of proteins, nucleosomes, and cell-free nucleic acids from a single biological sample |
Publications (3)
| Publication Number | Publication Date |
|---|---|
| JP2022504078A JP2022504078A (ja) | 2022-01-13 |
| JPWO2020072829A5 true JPWO2020072829A5 (https=) | 2022-10-04 |
| JP2022504078A5 JP2022504078A5 (https=) | 2022-10-04 |
Family
ID=68296828
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| JP2021518090A Pending JP2022504078A (ja) | 2018-10-04 | 2019-10-03 | 単一の生物学的サンプル由来のタンパク質、ヌクレオソームおよび無細胞核酸のシーケンシングベースの同時分析 |
Country Status (9)
| Country | Link |
|---|---|
| US (1) | US12540319B2 (https=) |
| EP (1) | EP3861132A2 (https=) |
| JP (1) | JP2022504078A (https=) |
| CN (1) | CN113166796A (https=) |
| AU (1) | AU2019354789A1 (https=) |
| CA (1) | CA3114606A1 (https=) |
| MX (1) | MX2021003847A (https=) |
| SG (1) | SG11202102954QA (https=) |
| WO (1) | WO2020072829A2 (https=) |
Families Citing this family (11)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN113517026B (zh) * | 2021-06-16 | 2022-08-19 | 苏州拉索生物芯片科技有限公司 | 应用于生物制品的标签序列的生成方法、系统、智能终端及计算机可读存储介质 |
| EP4370711A4 (en) * | 2021-07-12 | 2025-07-02 | Univ Pennsylvania | MODIFIED ADAPTERS FOR ENZYMATIC DEAMINATION OF DNA AND METHODS OF USE THEREOF FOR EPIGENETIC SEQUENCING OF FREE AND IMMOBILIZED DNA |
| US20240301466A1 (en) * | 2021-07-15 | 2024-09-12 | University Of Washington | Efficient duplex sequencing using high fidelity next generation sequencing reads |
| US20230086611A1 (en) * | 2021-09-23 | 2023-03-23 | Genomic Testing Cooperative, LCA | Compositions and Methods for Targeted NGS Sequencing of cfRNA and cfTNA |
| CN118139987A (zh) * | 2021-09-23 | 2024-06-04 | 基因组检测合作社公司 | 用于cfrna和cftna靶向ngs测序的组合物和方法 |
| WO2023097295A1 (en) * | 2021-11-24 | 2023-06-01 | Alida Biosciences, Inc. | Rna and dna analysis using engineered surfaces |
| CN114934110A (zh) * | 2022-06-15 | 2022-08-23 | 江西烈冰生物科技有限公司 | 用于获取基因表达的原始位置的生物芯片、试剂盒及方法 |
| AU2023384167A1 (en) * | 2022-11-23 | 2025-04-24 | Alida Biosciences, Inc. | Chromatin profiling compositions and methods |
| WO2024112816A1 (en) | 2022-11-23 | 2024-05-30 | University Of Iowa Research Foundation | Therapeutic compounds and methods |
| CN116403645B (zh) * | 2023-03-03 | 2024-01-09 | 阿里巴巴（中国）有限公司 | 转录因子结合位点的预测方法及装置 |
| WO2026024692A1 (en) * | 2024-07-24 | 2026-01-29 | Guardant Health, Inc. | Direct methylation single-base resolution sequencing of enriched unmethylated dna |
Family Cites Families (27)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US5712126A (en) | 1995-08-01 | 1998-01-27 | Yale University | Analysis of gene expression by display of 3-end restriction fragments of CDNA |
| US6287825B1 (en) | 1998-09-18 | 2001-09-11 | Molecular Staging Inc. | Methods for reducing the complexity of DNA sequences |
| US20070020640A1 (en) | 2005-07-21 | 2007-01-25 | Mccloskey Megan L | Molecular encoding of nucleic acid templates for PCR and other forms of sequence analysis |
| ATE551349T1 (de) | 2005-11-30 | 2012-04-15 | Epict Technologies Corp | Methode unter verwendung von reversibel blockierten markierungsoligonukleotiden |
| EP2164985A4 (en) | 2007-06-01 | 2014-05-14 | 454 Life Sciences Corp | SYSTEM AND METHOD FOR IDENTIFYING INDIVIDUAL SAMPLES FROM A MULTIPLEX MIXTURE |
| US20090093378A1 (en) | 2007-08-29 | 2009-04-09 | Helen Bignell | Method for sequencing a polynucleotide template |
| US8268564B2 (en) | 2007-09-26 | 2012-09-18 | President And Fellows Of Harvard College | Methods and applications for stitched DNA barcodes |
| WO2010037001A2 (en) | 2008-09-26 | 2010-04-01 | Immune Disease Institute, Inc. | Selective oxidation of 5-methylcytosine by tet-family proteins |
| US20100323348A1 (en) | 2009-01-31 | 2010-12-23 | The Regents Of The University Of Colorado, A Body Corporate | Methods and Compositions for Using Error-Detecting and/or Error-Correcting Barcodes in Nucleic Acid Amplification Process |
| EP2816111B1 (en) | 2009-08-14 | 2016-04-13 | Epicentre Technologies Corporation | Methods, compositions, and kits for generating rRNA-depleted samples or isolating rRNA from samples |
| WO2011127136A1 (en) | 2010-04-06 | 2011-10-13 | University Of Chicago | Composition and methods related to modification of 5-hydroxymethylcytosine (5-hmc) |
| GB201107863D0 (en) * | 2011-05-11 | 2011-06-22 | Olink Ab | Method and product |
| ES2609845T3 (es) * | 2011-07-29 | 2017-04-24 | Cambridge Epigenetix Limited | Métodos para la detección de modificación de nucleótidos |
| WO2013113012A2 (en) | 2012-01-27 | 2013-08-01 | The Board Of Trustees Of The Leland Stanford Junior University | Methods for profiling and quantitating cell-free rna |
| GB201303575D0 (en) | 2013-02-28 | 2013-04-10 | Singapore Volition Pte Ltd | Method for detecting histone modifications in nucleosomes |
| CN105745334B (zh) | 2013-09-30 | 2019-12-10 | 吴迪 | 通过使用邻近条形编码分析分子复合物的概况的方法 |
| EP4389888A3 (en) | 2013-10-17 | 2024-09-04 | Takara Bio USA, Inc. | Methods for adding adapters to nucleic acids and compositions for practicing the same |
| US10760120B2 (en) | 2015-01-23 | 2020-09-01 | Qiagen Sciences, Llc | High multiplex PCR with molecular barcoding |
| US10844428B2 (en) * | 2015-04-28 | 2020-11-24 | Illumina, Inc. | Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS) |
| US11092607B2 (en) * | 2015-10-28 | 2021-08-17 | The Board Institute, Inc. | Multiplex analysis of single cell constituents |
| MX391039B (es) | 2016-04-07 | 2025-03-21 | Univ Leland Stanford Junior | Diagnostico no invasivo por medio de la secuenciacion del adn libre de celulas 5-hidroxi-metilado. |
| US20170298422A1 (en) | 2016-04-18 | 2017-10-19 | The Board Of Trustees Of The Leland Stanford Junior University | Simultaneous single-molecule epigenetic imaging of dna methylation and hydroxymethylation |
| US10093986B2 (en) | 2016-07-06 | 2018-10-09 | Youhealth Biotech, Limited | Leukemia methylation markers and uses thereof |
| WO2018031897A1 (en) * | 2016-08-12 | 2018-02-15 | Cdi Laboratories, Inc. | Compositions and methods for analyzing nucleic acids associated with an analyte |
| CN106367485B (zh) | 2016-08-29 | 2019-04-26 | 厦门艾德生物医药科技股份有限公司 | 一种用于检测基因突变的多定位双标签接头组及其制备方法和应用 |
| US20180080021A1 (en) | 2016-09-17 | 2018-03-22 | The Board Of Trustees Of The Leland Stanford Junior University | Simultaneous sequencing of rna and dna from the same sample |
| WO2019160994A1 (en) * | 2018-02-14 | 2019-08-22 | Bluestar Genomics, Inc. | Methods for the epigenetic analysis of dna, particularly cell-free dna |
-
2019
- 2019-10-03 US US17/282,694 patent/US12540319B2/en active Active
- 2019-10-03 JP JP2021518090A patent/JP2022504078A/ja active Pending
- 2019-10-03 CA CA3114606A patent/CA3114606A1/en active Pending
- 2019-10-03 SG SG11202102954QA patent/SG11202102954QA/en unknown
- 2019-10-03 CN CN201980077845.1A patent/CN113166796A/zh active Pending
- 2019-10-03 AU AU2019354789A patent/AU2019354789A1/en active Pending
- 2019-10-03 MX MX2021003847A patent/MX2021003847A/es unknown
- 2019-10-03 EP EP19791106.8A patent/EP3861132A2/en active Pending
- 2019-10-03 WO PCT/US2019/054582 patent/WO2020072829A2/en not_active Ceased
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