WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data.
Background: Identification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reporta...
| Publicado en: | Computers in Biology & Medicine Vol. 68; pp. 165 - 170 |
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| Autores principales: | , , , , , |
| Formato: | research Journal Article |
| Publicado: |
Elsevier B.V.
1/1/2016
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=113005915&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 113005915 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00104825 JC2 jtl: Computers in Biology & Medicine issn: 00104825 maglogo: N pubinfo: dt: 1/1/2016 vid: 68 pid: 82545 pub: Elsevier B.V. place: Philadelphia, Pennsylvania artinfo: ui: 113005915 113005915 NLM25890833 113005915 10.1016/j.compbiomed.2015.03.028 NLM25890833 PMC4598261 [Available on 01/01/17] 113005915 ppf: 165 ppct: 5 formats: tig: atl: WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data. aug: au: Ye, Zhan Kadolph, Christopher Strenn, Robert Wall, Daniel McPherson, Elizabeth Lin, Simon affil: Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA sug: subj: Genetics Sequence Analysis Methods Sequence Analysis User-Computer Interface Funding Source ab: Background: Identification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reportable incidental genetic findings. However, no informatics tools are currently available to support evaluation of incidental findings in next-generation sequencing data.Methods: The Wisconsin Hierarchical Analysis Tool for Incidental Findings (WHATIF), was developed as a stand-alone Windows-based desktop executable, to support the interactive analysis of incidental findings in the context of the ACMG recommendations. WHATIF integrates the European Bioinformatics Institute Variant Effect Predictor (VEP) tool for biological interpretation and the National Center for Biotechnology Information ClinVar tool for clinical interpretation.Results: An open-source desktop program was created to annotate incidental findings and present the results with a user-friendly interface. Further, a meaningful index (WHATIF Index) was devised for each gene to facilitate ranking of the relative importance of the variants and estimate the potential workload associated with further evaluation of the variants. Our WHATIF application is available at: http://tinyurl.com/WHATIF-SOFTWARE CONCLUSIONS: The WHATIF application offers a user-friendly interface and allows users to investigate the extracted variant information efficiently and intuitively while always accessing the up to date information on variants via application programming interfaces (API) connections. WHATIF׳s highly flexible design and straightforward implementation aids users in customizing the source code to meet their own special needs. pubtype: Academic Journal doctype: research Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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