VAReporter: variant reporter for cancer research of massive parallel sequencing |
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Authors: | Po-Jung Huang Chi-Ching Lee Ling-Ya Chiu Kuo-Yang Huang Yuan-Ming Yeh Chia-Yu Yang Cheng-Hsun Chiu Petrus Tang |
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Affiliation: | 1.Department of Biomedical Sciences,Chang Gung University,Taoyuan,Taiwan;2.Genomic Medicine Research Core Laboratory,Chang Gung Memorial Hospital,Linkou,Taiwan;3.Department and Graduate Institute of Computer Science and Information Engineering,Chang Gung University,Taoyuan,Taiwan;4.Molecular Medicine Research Center,Chang Gung University,Taoyuan,Taiwan;5.Graduate Institute of Pathology and Parasitology,National Defense Medical Center,Taipei,Taiwan;6.Graduate Institute of Biomedical Sciences,Chang Gung University,Taoyuan,Taiwan |
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Abstract: | BackgroundHigh 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.ResultsWe 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.ConclusionsIn 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. |
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