CA3107376A1 - Method of sequencing using variable replicate multiplex pcr - Google Patents
Method of sequencing using variable replicate multiplex pcr Download PDFInfo
- Publication number
- CA3107376A1 CA3107376A1 CA3107376A CA3107376A CA3107376A1 CA 3107376 A1 CA3107376 A1 CA 3107376A1 CA 3107376 A CA3107376 A CA 3107376A CA 3107376 A CA3107376 A CA 3107376A CA 3107376 A1 CA3107376 A1 CA 3107376A1
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- 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
- C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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- 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
- C12Q1/6869—Methods for sequencing
-
- G—PHYSICS
- G06—COMPUTING OR CALCULATING; COUNTING
- G06F—ELECTRIC DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/10—Complex mathematical operations
- G06F17/18—Complex mathematical operations for evaluating statistical data, e.g. average values, frequency distributions, probability functions, regression analysis
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
-
- 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
- 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
-
- 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
-
- 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/158—Expression markers
-
- 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/16—Primer sets for multiplex assays
Landscapes
- Life Sciences & Earth Sciences (AREA)
- Engineering & Computer Science (AREA)
- Physics & Mathematics (AREA)
- Chemical & Material Sciences (AREA)
- Health & Medical Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Organic Chemistry (AREA)
- Analytical Chemistry (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- General Health & Medical Sciences (AREA)
- Theoretical Computer Science (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Evolutionary Biology (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Molecular Biology (AREA)
- Genetics & Genomics (AREA)
- Medical Informatics (AREA)
- General Engineering & Computer Science (AREA)
- Data Mining & Analysis (AREA)
- General Physics & Mathematics (AREA)
- Microbiology (AREA)
- Biochemistry (AREA)
- Immunology (AREA)
- Mathematical Analysis (AREA)
- Computational Mathematics (AREA)
- Databases & Information Systems (AREA)
- Mathematical Optimization (AREA)
- Pure & Applied Mathematics (AREA)
- Mathematical Physics (AREA)
- Bioethics (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Operations Research (AREA)
- Probability & Statistics with Applications (AREA)
- Algebra (AREA)
- Software Systems (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201862716082P | 2018-08-08 | 2018-08-08 | |
| US62/716,082 | 2018-08-08 | ||
| PCT/IB2019/056625 WO2020031048A1 (en) | 2018-08-08 | 2019-08-02 | Method of sequencing using variable replicate multiplex pcr |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3107376A1 true CA3107376A1 (en) | 2020-02-13 |
Family
ID=67953830
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3107376A Pending CA3107376A1 (en) | 2018-08-08 | 2019-08-02 | Method of sequencing using variable replicate multiplex pcr |
Country Status (9)
| Country | Link |
|---|---|
| US (4) | US11566274B2 (enExample) |
| EP (1) | EP3833783B1 (enExample) |
| JP (1) | JP7407193B2 (enExample) |
| KR (1) | KR102910949B1 (enExample) |
| CN (1) | CN112601824A (enExample) |
| AU (1) | AU2019319711B2 (enExample) |
| BR (1) | BR112021002189A2 (enExample) |
| CA (1) | CA3107376A1 (enExample) |
| WO (1) | WO2020031048A1 (enExample) |
Families Citing this family (10)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105190656B (zh) | 2013-01-17 | 2018-01-16 | 佩索纳里斯公司 | 用于遗传分析的方法和系统 |
| US10125399B2 (en) | 2014-10-30 | 2018-11-13 | Personalis, Inc. | Methods for using mosaicism in nucleic acids sampled distal to their origin |
| US11299783B2 (en) | 2016-05-27 | 2022-04-12 | Personalis, Inc. | Methods and systems for genetic analysis |
| JP7407193B2 (ja) | 2018-08-08 | 2023-12-28 | イニヴァータ リミテッド | 可変の複製多重ｐｃｒを使用した配列決定方法 |
| JP7470787B2 (ja) | 2019-11-05 | 2024-04-18 | パーソナリス，インコーポレイティド | 単一試料からの腫瘍純度の推定 |
| WO2023012521A1 (en) * | 2021-08-05 | 2023-02-09 | Inivata Limited | Highly sensitive method for detecting cancer dna in a sample |
| JP2023536325A (ja) * | 2020-08-05 | 2023-08-24 | イニヴァータ リミテッド | 試料中のがんｄｎａを検出するための高感度の方法 |
| WO2023059654A1 (en) | 2021-10-05 | 2023-04-13 | Personalis, Inc. | Customized assays for personalized cancer monitoring |
| EP4652604A1 (en) | 2023-01-18 | 2025-11-26 | Inivata Ltd. | Cancer-associated genetic variant filtering using mutational signatures |
| WO2026006629A1 (en) | 2024-06-27 | 2026-01-02 | Personalis, Inc. | System and method for management of compressed sequencing files |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| US5948902A (en) | 1997-11-20 | 1999-09-07 | South Alabama Medical Science Foundation | Antisense oligonucleotides to human serine/threonine protein phosphatase genes |
| US7727720B2 (en) | 2002-05-08 | 2010-06-01 | Ravgen, Inc. | Methods for detection of genetic disorders |
| US20040086892A1 (en) | 2002-11-06 | 2004-05-06 | Crothers Donald M. | Universal tag assay |
| US20050233340A1 (en) | 2004-04-20 | 2005-10-20 | Barrett Michael T | Methods and compositions for assessing CpG methylation |
| US20060263789A1 (en) | 2005-05-19 | 2006-11-23 | Robert Kincaid | Unique identifiers for indicating properties associated with entities to which they are attached, and methods for using |
| 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 |
| US20070068573A1 (en) | 2005-08-22 | 2007-03-29 | Applera Corporation | Device and method for microfluidic control of a first fluid in contact with a second fluid, wherein the first and second fluids are immiscible |
| WO2007133710A2 (en) | 2006-05-11 | 2007-11-22 | Raindance Technologies, Inc. | Microfluidic devices and methods of use thereof |
| AU2008255569A1 (en) | 2007-06-01 | 2008-12-04 | Monoquant Pty Ltd | A method for DNA breakpoint analysis |
| US20110230372A1 (en) * | 2008-11-14 | 2011-09-22 | Stc Unm | Gene expression classifiers for relapse free survival and minimal residual disease improve risk classification and outcome prediction in pediatric b-precursor acute lymphoblastic leukemia |
| US9524369B2 (en) | 2009-06-15 | 2016-12-20 | Complete Genomics, Inc. | Processing and analysis of complex nucleic acid sequence data |
| WO2011140187A2 (en) | 2010-05-04 | 2011-11-10 | University Of Rochester | Detecting chromosomal rearrangement |
| US9677118B2 (en) | 2014-04-21 | 2017-06-13 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US10316362B2 (en) | 2010-05-18 | 2019-06-11 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| EP3225697A3 (en) * | 2010-12-30 | 2017-11-22 | Foundation Medicine, Inc. | Optimization of multigene analysis of tumor samples |
| HK1199745A1 (en) | 2011-09-09 | 2015-07-17 | The Board Of Trustees Of The Leland Stanford Junior University | Methods for obtaining a sequence |
| AU2012385961B9 (en) | 2012-07-24 | 2017-05-18 | Natera, Inc. | Highly multiplex PCR methods and compositions |
| GB201301857D0 (en) | 2013-02-01 | 2013-03-20 | Selvi Ozan | Method |
| CN105102635B (zh) | 2013-03-15 | 2020-09-25 | 生命技术公司 | 肺癌的分类和可行性指数 |
| US20160032396A1 (en) | 2013-03-15 | 2016-02-04 | The Board Of Trustees Of The Leland Stanford Junior University | Identification and Use of Circulating Nucleic Acid Tumor Markers |
| US10262755B2 (en) | 2014-04-21 | 2019-04-16 | Natera, Inc. | Detecting cancer mutations and aneuploidy in chromosomal segments |
| EP3071706B1 (en) | 2013-11-21 | 2018-04-25 | Assistance Publique-Hôpitaux de Paris | Method for detecting chromosomal rearrangements |
| CN111534580B (zh) | 2013-12-28 | 2024-06-04 | 夸登特健康公司 | 用于检测遗传变异的方法和系统 |
| GB201412834D0 (en) | 2014-07-18 | 2014-09-03 | Cancer Rec Tech Ltd | A method for detecting a genetic variant |
| CN107002123A (zh) * | 2014-08-14 | 2017-08-01 | 生命技术公司 | 多重转录组分析 |
| US20170283854A1 (en) | 2014-09-05 | 2017-10-05 | University Of Florida Research Foundation, Inc. | Multiplexed pcr assay for high throughput genotyping |
| US11149305B2 (en) * | 2015-01-23 | 2021-10-19 | Washington University | Detection of rare sequence variants, methods and compositions therefor |
| US20160275240A1 (en) | 2015-02-18 | 2016-09-22 | Nugen Technologies, Inc. | Methods and compositions for pooling amplification primers |
| WO2016201142A1 (en) | 2015-06-09 | 2016-12-15 | Life Technologies Corporation | Methods, systems, compositions, kits, apparatus and computer-readable media for molecular tagging |
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| CN106282356B (zh) * | 2016-08-30 | 2019-11-26 | 天津诺禾医学检验所有限公司 | 一种基于扩增子二代测序点突变检测的方法及装置 |
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| WO2019043059A1 (en) | 2017-08-30 | 2019-03-07 | Symphogen A/S | COMPOSITIONS AND METHODS FOR THE TREATMENT OF CANCER BY ANTI-EGFR ANTIBODIES |
| EP3682035B1 (en) * | 2017-09-15 | 2025-02-05 | The Regents of the University of California | Detecting somatic single nucleotide variants from cell-free nucleic acid with application to minimal residual disease monitoring |
| EP3704268B1 (en) | 2017-11-03 | 2025-01-22 | Guardant Health, Inc. | Normalizing tumor mutation burden |
| WO2019099750A1 (en) | 2017-11-17 | 2019-05-23 | Research Cancer Institute Of America | Compositions, methods, systems and/or kits for preventing and/or treating neoplasms |
| GB201804641D0 (en) | 2018-03-22 | 2018-05-09 | Inivata Ltd | Methods of sequencing nucleic acids and error correction of sequence reads |
| GB201804642D0 (en) | 2018-03-22 | 2018-05-09 | Inivata Ltd | Methods of labelling nucleic acids |
| EP3784805A1 (en) | 2018-04-23 | 2021-03-03 | Inivata Limited | Method for predicting and monitoring response to an immune checkpoint inhibitor |
| US20210040564A1 (en) | 2018-04-23 | 2021-02-11 | Inivata Ltd. | Method for predicting and monitoring response to an immune checkpoint inhibitor |
| US10329627B1 (en) | 2018-04-23 | 2019-06-25 | Inivata Ltd. | Method for predicting and monitoring response to an immune checkpoint inhibitor |
| JP7407193B2 (ja) | 2018-08-08 | 2023-12-28 | イニヴァータ リミテッド | 可変の複製多重ｐｃｒを使用した配列決定方法 |
| US11377698B2 (en) | 2018-09-05 | 2022-07-05 | Inivata Ltd. | Method of treating a cancer patient without the need for a tissue biopsy |
| EP4219763A3 (en) | 2018-12-12 | 2023-08-16 | Inivata Ltd. | Method for quantifying gene fusion dna |
| US10533214B2 (en) | 2018-12-21 | 2020-01-14 | Inivata Ltd. | Method for measuring mutational load |
| WO2020174406A1 (en) | 2019-02-28 | 2020-09-03 | Inivata Ltd. | Method for quantifying the amount of a target sequence in a nucleic acid sample |
| WO2021028768A1 (en) | 2019-08-13 | 2021-02-18 | Inivata Ltd. | METHOD FOR ALTERING THERAPY OF ADVANCED NON-SMALL CELL LUNG CANCER PATIENTS BASED ON ANALYSIS OF ctDNA |
| JP2023536325A (ja) | 2020-08-05 | 2023-08-24 | イニヴァータ リミテッド | 試料中のがんｄｎａを検出するための高感度の方法 |
-
2019
- 2019-08-02 JP JP2021531204A patent/JP7407193B2/ja active Active
- 2019-08-02 CA CA3107376A patent/CA3107376A1/en active Pending
- 2019-08-02 AU AU2019319711A patent/AU2019319711B2/en active Active
- 2019-08-02 KR KR1020217006940A patent/KR102910949B1/ko active Active
- 2019-08-02 CN CN201980055463.9A patent/CN112601824A/zh active Pending
- 2019-08-02 WO PCT/IB2019/056625 patent/WO2020031048A1/en not_active Ceased
- 2019-08-02 EP EP19768911.0A patent/EP3833783B1/en active Active
- 2019-08-02 BR BR112021002189-2A patent/BR112021002189A2/pt not_active Application Discontinuation
-
2020
- 2020-01-22 US US16/749,858 patent/US11566274B2/en active Active
-
2023
- 2023-03-17 US US18/123,235 patent/US11788116B2/en active Active
- 2023-09-13 US US18/367,944 patent/US12378595B2/en active Active
-
2025
- 2025-07-10 US US19/266,034 patent/US20250340926A1/en active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| KR102910949B1 (ko) | 2026-01-09 |
| US20230227890A1 (en) | 2023-07-20 |
| JP2022513173A (ja) | 2022-02-07 |
| EP3833783B1 (en) | 2024-10-02 |
| EP3833783A1 (en) | 2021-06-16 |
| US11566274B2 (en) | 2023-01-31 |
| WO2020031048A1 (en) | 2020-02-13 |
| US12378595B2 (en) | 2025-08-05 |
| US20200157604A1 (en) | 2020-05-21 |
| US20240110224A1 (en) | 2024-04-04 |
| JP7407193B2 (ja) | 2023-12-28 |
| KR20210044249A (ko) | 2021-04-22 |
| AU2019319711A1 (en) | 2021-02-11 |
| US20250340926A1 (en) | 2025-11-06 |
| US11788116B2 (en) | 2023-10-17 |
| BR112021002189A2 (pt) | 2021-05-04 |
| AU2019319711B2 (en) | 2025-08-28 |
| CN112601824A (zh) | 2021-04-02 |
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