JP7546486B2 - 融合事象によって引き起こされるアライメントエラーを検出および抑制する方法 - Google Patents

融合事象によって引き起こされるアライメントエラーを検出および抑制する方法 Download PDF

Info

Publication number
JP7546486B2
JP7546486B2 JP2020555454A JP2020555454A JP7546486B2 JP 7546486 B2 JP7546486 B2 JP 7546486B2 JP 2020555454 A JP2020555454 A JP 2020555454A JP 2020555454 A JP2020555454 A JP 2020555454A JP 7546486 B2 JP7546486 B2 JP 7546486B2
Authority
JP
Japan
Prior art keywords
sequence
reads
sequence reads
nucleic acid
sample
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.)
Active
Application number
JP2020555454A
Other languages
English (en)
Japanese (ja)
Other versions
JP2021520810A5 (https=
JP2021520810A (ja
Inventor
カルロ アルティエリ，
マーシン シコラ，
Original Assignee
ガーダント ヘルス， インコーポレイテッド
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 ガーダント ヘルス， インコーポレイテッド filed Critical ガーダント ヘルス， インコーポレイテッド
Publication of JP2021520810A publication Critical patent/JP2021520810A/ja
Publication of JP2021520810A5 publication Critical patent/JP2021520810A5/ja
Application granted granted Critical
Publication of JP7546486B2 publication Critical patent/JP7546486B2/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Landscapes

  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Public Health (AREA)
  • Molecular Biology (AREA)
  • Epidemiology (AREA)
  • Genetics & Genomics (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Biomedical Technology (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Pathology (AREA)
  • Primary Health Care (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
JP2020555454A 2018-04-13 2019-04-12 融合事象によって引き起こされるアライメントエラーを検出および抑制する方法 Active JP7546486B2 (ja)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201862657200P 2018-04-13 2018-04-13
US62/657,200 2018-04-13
PCT/US2019/027337 WO2019200328A1 (en) 2018-04-13 2019-04-12 Methods for detecting and suppressing alignment errors caused by fusion events

Publications (3)

Publication Number Publication Date
JP2021520810A JP2021520810A (ja) 2021-08-26
JP2021520810A5 JP2021520810A5 (https=) 2022-04-19
JP7546486B2 true JP7546486B2 (ja) 2024-09-06

Family

ID=68163816

Family Applications (1)

Application Number Title Priority Date Filing Date
JP2020555454A Active JP7546486B2 (ja) 2018-04-13 2019-04-12 融合事象によって引き起こされるアライメントエラーを検出および抑制する方法

Country Status (6)

Country Link
US (1) US12322476B2 (https=)
EP (1) EP3785268A4 (https=)
JP (1) JP7546486B2 (https=)
CN (1) CN112334983A (https=)
AU (1) AU2019252947A1 (https=)
WO (1) WO2019200328A1 (https=)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112687341B (zh) * 2021-03-12 2021-06-04 上海思路迪医学检验所有限公司 一种以断点为中心的染色体结构变异鉴定方法
US20230207054A1 (en) * 2021-12-29 2023-06-29 Illumina, Inc. Deep learning network for evolutionary conservation

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2016518123A (ja) 2013-04-17 2016-06-23 ライフ テクノロジーズ コーポレーション 癌に関連付けられる遺伝子融合物及び遺伝子変異型

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6582908B2 (en) 1990-12-06 2003-06-24 Affymetrix, Inc. Oligonucleotides
WO2003046146A2 (en) 2001-11-28 2003-06-05 Applera Corporation Compositions and methods of selective nucleic acid isolation
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
US8945556B2 (en) * 2010-11-19 2015-02-03 The Regents Of The University Of Michigan RAF gene fusions
CN104781421B (zh) 2012-09-04 2020-06-05 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
CN114574581A (zh) * 2013-03-15 2022-06-03 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
ES2660989T3 (es) * 2013-12-28 2018-03-27 Guardant Health, Inc. Métodos y sistemas para detectar variantes genéticas
CN107075730A (zh) 2014-09-12 2017-08-18 利兰·斯坦福青年大学托管委员会 循环核酸的鉴定及用途
WO2017062970A1 (en) 2015-10-10 2017-04-13 Guardant Health, Inc. Methods and applications of gene fusion detection in cell-free dna analysis
EP3625713A1 (en) 2017-05-19 2020-03-25 Guardant Health, Inc. Methods and systems for detecting insertions and deletions

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2016518123A (ja) 2013-04-17 2016-06-23 ライフ テクノロジーズ コーポレーション 癌に関連付けられる遺伝子融合物及び遺伝子変異型

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
Genome Biology，2013年，Vol. 14, No. 4, R36，pp. 1-13

Also Published As

Publication number Publication date
AU2019252947A1 (en) 2020-10-29
US20200020416A1 (en) 2020-01-16
WO2019200328A1 (en) 2019-10-17
CN112334983A (zh) 2021-02-05
US12322476B2 (en) 2025-06-03
JP2021520810A (ja) 2021-08-26
EP3785268A1 (en) 2021-03-03
CA3096261A1 (en) 2019-10-17
EP3785268A4 (en) 2022-01-05

Similar Documents

Publication Publication Date Title
JP7699261B2 (ja) 無細胞ｄｎａにおけるマイクロサテライト不安定性の検出
JP7573536B2 (ja) 無細胞ｄｎａを単離するための組成物および方法
CN112752854B (zh) 用于通过肿瘤分数和覆盖率调整肿瘤突变负荷的方法和系统
JP2026012397A (ja) セルフリー核酸の細胞起源を決定するための方法およびシステム
JP2023540221A (ja) バリアントの起源を予測するための方法およびシステム
JP7577067B2 (ja) 対立遺伝子頻度に基づく機能喪失のコンピューターモデリング
US20220344004A1 (en) Detecting the presence of a tumor based on off-target polynucleotide sequencing data
US20220028494A1 (en) Methods and systems for determining the cellular origin of cell-free dna
US20260120797A1 (en) Cell-free dna blood-based test for cancer screening
JP2024056984A (ja) エピジェネティック区画アッセイを較正するための方法、組成物およびシステム
JP7546486B2 (ja) 融合事象によって引き起こされるアライメントエラーを検出および抑制する方法
JP2025028203A (ja) 脱アミノ化に誘導される配列エラーの補正
US20260128120A1 (en) Methods for detecting and suppressing alignment errors caused by fusion events
CA3096261C (en) Methods for detecting and suppressing alignment errors caused by fusion events
CN116981782A (zh) 基于脱靶多核苷酸测序数据检测肿瘤的存在
US20250034627A1 (en) Methods for amplification-free enrichment

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20220411

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20220411

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20230501

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20230725

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20230929

A02 Decision of refusal

Free format text: JAPANESE INTERMEDIATE CODE: A02

Effective date: 20231222

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20240422

A911 Transfer to examiner for re-examination before appeal (zenchi)

Free format text: JAPANESE INTERMEDIATE CODE: A911

Effective date: 20240501

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20240801

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20240827

R150 Certificate of patent or registration of utility model

Ref document number: 7546486

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150