AnFiSA: An open-source computational platform for the analysis of sequencing data for rare genetic disease.

Autor: Bouzinier MA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Electronic address: michael_bouzinier@harvard.edu., Etin D; Forome Association, Boston, MA, USA; Oracle Corporation, USA. Electronic address: dmitry.etin@forome.org., Trifonov SI; Forome Association, Boston, MA, USA., Evdokimova VN; Forome Association, Boston, MA, USA; SBCS Scientific Biomedical Consulting Services, London, UK., Ulitin V; Forome Association, Boston, MA, USA., Shen J; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Kokorev A; ITMO University, St. Petersburg, Russian Federation., Ghazani AA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Brigham Genomic Medicine, Brigham and Women's Hospital, Boston, MA, USA., Chekaluk Y; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Albertyn Z; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Giersch A; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Morton CC; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Manchester Centre for Audiology and Deafness (ManCAD), School of Health Sciences, University of Manchester, UK., Abraamyan F; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Bendapudi PK; Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Boston, MA, USA; Division of Hematology and Blood Transfusion Service, Massachusetts General Hospital, Boston, MA, USA., Sunyaev S; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA., Undiagnosed Diseases Network; Undiagnosed Diseases Network, NIH, USA., Brigham Genomic Medicine; Brigham Genomic Medicine, Brigham and Women's Hospital, Boston, MA, USA., SEQuencing A Baby For An Optimal Outcome; SEQuencing a Baby for an Optimal Outcome, Brigham and Women's Hospital, Boston, MA, USA., Quantori; Quantori, Cambridge, MA, USA., Krier JB; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Electronic address: jkrier@bwh.harvard.edu.
Jazyk: angličtina
Zdroj: Journal of biomedical informatics [J Biomed Inform] 2022 Sep; Vol. 133, pp. 104174. Date of Electronic Publication: 2022 Aug 23.
DOI: 10.1016/j.jbi.2022.104174
Abstrakt: 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.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2022 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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