AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease.
Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not...
| Publicado en: | Journal of Biomedical Informatics Vol. 133 |
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| Autores principales: | , , , , , , , , , , , , , , , , , , , |
| Formato: | Journal Article |
| Publicado: |
Academic Press Inc.
Sep2022
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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=159012773&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 159012773 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 15320464 OMB jtl: Journal of Biomedical Informatics issn: 15320464 maglogo: N pubinfo: dt: Sep2022 vid: 133 pid: 735 pub: Academic Press Inc. place: Burlington, Massachusetts artinfo: ui: 159012773 159012773 NLM35998814 10.1016/j.jbi.2022.104174 NLM35998814 159012773 ppct: 1 formats: tig: atl: AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease. aug: au: Bouzinier, M.A. Etin, D. Trifonov, S.I. Evdokimova, V.N. Ulitin, V. Shen, J. Kokorev, A. Ghazani, A.A. Chekaluk, Y. Albertyn, Z. Giersch, A. Morton, C.C. Abraamyan, F. Bendapudi, P.K. Sunyaev, S. Undiagnosed Diseases Network Brigham Genomic Medicine SEQuencing a Baby for an Optimal Outcome Quantori Krier, J.B. affil: Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA sug: subj: Genomics Methods Software Reproducibility of Results Management Information Systems Bioinformatics Methods Resource Databases Systems Analysis Multidimensional Health Locus of Control Scales Scales ab: Despite genomic sequencing rapidly transforming from being a bench-side tool to a routine procedure in a hospital, there is a noticeable lack of genomic analysis software that supports both clinical and research workflows as well as crowdsourcing. Furthermore, most existing software packages are not forward-compatible in regards to supporting ever-changing diagnostic rules adopted by the genetics community. Regular updates of genomics databases pose challenges for reproducible and traceable automated genetic diagnostics tools. Lastly, most of the software tools score low on explainability amongst clinicians. We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers, and professional software developers. The design of AnFiSA addresses the aforementioned issues via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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