CA3153208A1 - Improved variant caller using single-cell analysis - Google Patents

Improved variant caller using single-cell analysis Download PDF

Info

Publication number
CA3153208A1
CA3153208A1 CA3153208A CA3153208A CA3153208A1 CA 3153208 A1 CA3153208 A1 CA 3153208A1 CA 3153208 A CA3153208 A CA 3153208A CA 3153208 A CA3153208 A CA 3153208A CA 3153208 A1 CA3153208 A1 CA 3153208A1
Authority
CA
Canada
Prior art keywords
base
sequence reads
interest
calls
cell
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
Application number
CA3153208A
Other languages
English (en)
French (fr)
Inventor
Manimozhi MANIVANNAN
Dongmyunghee KIM
Sombeet SAHU
Saurabh GULATI
Shu Wang
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Mission Bio Inc
Original Assignee
Mission Bio Inc
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 Mission Bio Inc filed Critical Mission Bio Inc
Publication of CA3153208A1 publication Critical patent/CA3153208A1/en
Pending legal-status Critical Current

Links

Classifications

    • 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
    • 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
    • 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
    • G16B40/20—Supervised data analysis

Landscapes

  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Data Mining & Analysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3153208A 2019-10-02 2020-10-02 Improved variant caller using single-cell analysis Pending CA3153208A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201962909670P 2019-10-02 2019-10-02
US62/909,670 2019-10-02
PCT/US2020/053971 WO2021067721A1 (en) 2019-10-02 2020-10-02 Improved variant caller using single-cell analysis

Publications (1)

Publication Number Publication Date
CA3153208A1 true CA3153208A1 (en) 2021-04-08

Family

ID=75336484

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3153208A Pending CA3153208A1 (en) 2019-10-02 2020-10-02 Improved variant caller using single-cell analysis

Country Status (7)

Country Link
US (1) US20220351804A1 (https=)
EP (1) EP4042429A4 (https=)
JP (1) JP2022550841A (https=)
CN (1) CN114766056A (https=)
AU (1) AU2020358083A1 (https=)
CA (1) CA3153208A1 (https=)
WO (1) WO2021067721A1 (https=)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023196928A2 (en) * 2022-04-06 2023-10-12 Mission Bio, Inc. True variant identification via multianalyte and multisample correlation
CN120813690A (zh) * 2022-10-25 2025-10-17 康奈尔大学 核酸误差抑制
CN117523559B (zh) * 2024-01-08 2024-03-29 深圳赛陆医疗科技有限公司 碱基识别方法及装置、基因测序仪及存储介质

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013040583A2 (en) * 2011-09-16 2013-03-21 Complete Genomics, Inc Determining variants in a genome of a heterogeneous sample
US20150073724A1 (en) * 2013-07-29 2015-03-12 Agilent Technologies, Inc Method for finding variants from targeted sequencing panels
US10354747B1 (en) * 2016-05-06 2019-07-16 Verily Life Sciences Llc Deep learning analysis pipeline for next generation sequencing
CA3049682C (en) * 2017-01-20 2023-06-27 Sequenom, Inc. Methods for non-invasive assessment of genetic alterations
WO2019013534A1 (ko) * 2017-07-11 2019-01-17 주식회사 엘지화학 이차전지의 불량 검사 장치 및 불량 검사 방법
JP2021503922A (ja) * 2017-11-28 2021-02-15 グレイル， インコーポレイテッドＧｒａｉｌ， Ｉｎｃ． ターゲットシーケンシングのためのモデル

Also Published As

Publication number Publication date
CN114766056A (zh) 2022-07-19
EP4042429A1 (en) 2022-08-17
WO2021067721A1 (en) 2021-04-08
US20220351804A1 (en) 2022-11-03
JP2022550841A (ja) 2022-12-05
EP4042429A4 (en) 2023-10-25
AU2020358083A1 (en) 2022-05-26

Similar Documents

Publication Publication Date Title
US20250061969A1 (en) Methods, systems, and computer readable media for making base calls in nucleic acid sequencing
US12596094B2 (en) Methods, systems, and computer readable media for making base calls in nucleic acid sequencing
US20240079092A1 (en) Systems and methods for deriving and optimizing classifiers from multiple datasets
EP3622524B1 (en) Variant classifier based on deep neural networks
US20240355472A1 (en) Deep Learning and Artificial Intelligence-Based Non-Sequence Altering Change Latent Space using Variational Autoencoders (VAEs)
US11710536B2 (en) Methods and systems for identifying target genes
CN110945594A (zh) 基于深度学习的剪接位点分类
US20220351804A1 (en) Improved Variant Caller Using Single-Cell Analysis
Azad et al. Use of artificial genomes in assessing methods for atypical gene detection
US12112833B2 (en) Systems and methods for index hopping filtering
Warnat-Herresthal et al. Artificial intelligence in blood transcriptomics
WO2024220594A1 (en) Cancer detection through integrated analysis of whole genome sequencing
WO2023196928A2 (en) True variant identification via multianalyte and multisample correlation
KR20240072970A (ko) 대치된 하플로타입을 사용한 그래프 참조 게놈 및 염기 결정 접근법
US20230340571A1 (en) Machine-learning models for selecting oligonucleotide probes for array technologies
WO2022109330A1 (en) Cellular clustering analysis in sequencing datasets
US20240379229A1 (en) Cancer diagnosis and cancer-type prediction method based on cell-free dna and image analysis technology
US20220068433A1 (en) Computational detection of copy number variation at a locus in the absence of direct measurement of the locus
EP4721063A2 (en) Linking human genes to clinical phenotypes using graph neural networks
HK40110801A (zh) 确定读段质量分数的方法、测序方法及装置
Kumari et al. Foundations of Computational 1 Techniques in Healthcare and Drug
de Lena et al. RNA Sequencing Platforms and Bioinformatics Tools
Baudeau Studying the properties of viral long reads mapping methods
WO2025254588A1 (en) Method for detection and identification of rna modifications
Barrese Data integration for the analysis of the oncogenic potential of gene fusions

Legal Events

Date Code Title Description
EEER Examination request

Effective date: 20220926

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 4TH ANNIV.) - STANDARD

Year of fee payment: 4

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20240927

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT DETERMINED COMPLIANT

Effective date: 20240927

Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20240927

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: A-2-2-W10-W00-W100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: LETTER SENT

Effective date: 20251114