VAReporter: variant reporter for cancer research of massive parallel sequencing

BMC Genomics

Chi-Ching Lee¹  Po-Jung Huang²  Cheng-Hsun Chiu³  Petrus Tang³  Kuo-Yang Huang⁴  Yuan-Ming Yeh⁵  Chia-Yu Yang⁵  Ling-Ya Chiu⁵ 

[1] Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University;Department of Biomedical Sciences, Chang Gung University;Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital;Graduate Institute of Pathology and Parasitology, National Defense Medical Center;Molecular Medicine Research Center, Chang Gung University;

关键词: NGS;    Exomes;    SNV annotation;    TCGA;    ICGC;   

DOI  :  10.1186/s12864-018-4468-5

来源: DOAJ

【 摘 要 】

Abstract Background High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and clinical outcomes. In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel biomarkers from panels of entire human coding exome or disease-associated genes. Results We introduce a workflow named VAReporter to facilitate the management of variant assessment in disease-targeted sequencing, the identification of pathogenic variants, the interpretation of biological effects and the prioritization of clinically actionable targets. State-of-art algorithms that account for mutation phenotypes are used to rank the importance of mutated genes through visual analytic strategies. We established an extensive annotation source by integrating a wide variety of biomedical databases and followed the American College of Medical Genetics and Genomics (ACMG) guidelines for interpretation and reporting of sequence variations. Conclusions In summary, VAReporter is the first web server designed to provide a “one-stop” resource for individual’s diagnosis and large-scale cohort studies, and is freely available at http://rnd.cgu.edu.tw/vareporter.

【 授权许可】

Unknown