Variant Call Format-Diagnostic Annotation and Reporting Tool A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data

Benton Miles C.; Smith Robert A.; Haupt Larisa M.; Sutherland Heidi G.; Dunn Paul J.; Albury Cassie L.; Maksemous Neven; Lea Rodney; Griffiths Lyn

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Variant Call Format-Diagnostic Annotation and Reporting Tool A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data

机译：变体呼叫格式 - 诊断注释和报告工具可定制的分析管道，用于识别下一代测序数据中的临床相关的遗传变量

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In this article, we introduce the variant call format-diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them on the basis of standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators. The tool uses publicly available databases to identify a range of data to assist with variant classification and curation processes and includes robust logging of parameters and database versions to allow comparison of analyses performed at different times. VCF-DART-an online analysis pipeline for next-generation sequencing data-is a platform agnostic tool that leverages the use of publicly available databases to improve a laboratory's calling ability and reduce analysis times long-term. It also runs highly efficiently and scales from desk and laptop machines to servers. Overall, VCF-DART provides a simple, customizable, and entirely open-source method to identify genetic variants that may be of clinical importance in a variety of genetically important conditions.

机译：在本文中，我们介绍了变体呼叫格式 - 诊断注释和报告工具（VCF-DART），这是一种定制的分析管道工具，用于从外壳或基因组测序的快速注释的变体和遗传诊断的报告的产生。 VCF-DART使用自定义基因列表将变体分类为特定的分析层，并在标准参数的基础上将它们分类为便于人类运营商的潜在致病变种的快速询问。该工具使用公开的数据库来识别一系列数据，以帮助有变体分类和策策过程，并包括参数和数据库版本的强大日志记录，以允许在不同时间执行的分析比较。 VCF-DART-用于下一代测序数据的在线分析管道 - 是一种平台可靠性工具，利用使用公开的数据库来改善实验室的呼叫能力，并长期降低分析时间。它还高效地运行，并从桌面和笔记本电脑机器秤到服务器。总体而言，VCF-DART提供了一种简单，可定制和完全开源的方法来识别可能在各种根本重要条件下临床重要性的遗传变异。

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《The Journal of molecular diagnostics: JMD》 |2019年第6期|共10页
作者
Benton Miles C.; Smith Robert A.; Haupt Larisa M.; Sutherland Heidi G.; Dunn Paul J.; Albury Cassie L.; Maksemous Neven; Lea Rodney; Griffiths Lyn;
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作者单位

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

Queensland Univ Technol Sch Biomed Sci Inst Hlth &

Biomed Innovat Genom Res Ctr 60 Musk Ave;

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正文语种 eng
中图分类临床医学;
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1. Variant Call Format-Diagnostic Annotation and Reporting Tool A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data [J] . Benton Miles C., Smith Robert A., Haupt Larisa M., The Journal of molecular diagnostics: JMD . 2019,第6期

机译：变体呼叫格式 - 诊断注释和报告工具可定制的分析管道，用于识别下一代测序数据中的临床相关的遗传变量
2. Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools [J] . Bo Peng Bioinformatics . 2012,第3期

机译：使用变异工具对来自下一代测序研究的遗传变异进行集成注释和分析
3. The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification [J] . Nishio Shin-ya, Usami Shin-ichi Human mutation . 2017,第3期

机译：临床下一代测序数据库：用于统一管理的临床信息和遗传变异的工具，以加速变异致病性分类
4. AN INTEGRATED FRAMEWORK FOR REPORTING CLINICALLY RELEVANT BIOMARKERS FROM PAIRED TUMOR/NORMAL GENOMIC AND TRANSCRIPTOMIC SEQUENCING DATA IN SUPPORT OF CLINICAL TRIALS IN PERSONALIZED MEDICINE [C] . SARA NASSER, AHMET A. KURDOLGU, TYLER IZATT, Pacific Symposium on Biocomputing . 2015

机译：一种综合框架，用于报告来自配对肿瘤/正常基因组和转录组序列测序数据的临床相关的生物标志物，以支持个性化医学中的临床试验
5. Statistical methods for genome variant calling and population genetic inference from next-generation sequencing data. [D] . Ma, Xin. 2011

机译：从下一代测序数据进行基因组变异调用和群体遗传推断的统计方法。
6. Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools [O] . F. Anthony San Lucas, Gao Wang, Paul Scheet, -1

机译：使用变异工具对来自下一代测序研究的遗传变异进行集成注释和分析
7. CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting [O] . 2015

机译：CSN和CAVA：用于临床环境中快速，可靠的下一代测序分析的变体注释工具

Variant Call Format-Diagnostic Annotation and Reporting Tool A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data

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