An open-source, integrated pedigree data management and visualization tool for genetic epidemiology

• Published in: International journal of epidemiology Vol. 47; no. 4; pp. 1034 - 1039
• Main Authors: Ranaweera, Thilina, Makalic, Enes, Hopper, John L, Bickerstaffe, Adrian
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.08.2018
• Subjects: Algorithms; Australia; Data Visualization; Demography; Humans; Internet; Medical Informatics - methods; Molecular Epidemiology - methods; Pedigree; Software; Australia; pedigree; Database; medical informatics; software; demography
• ISSN: 0300-5771; 1464-3685; 1464-3685
• DOI: 10.1093/ije/dyy049

Abstract With advances in genetic epidemiology, increasingly large amounts of pedigree-related information are being collected by family studies, including twin studies. To date, biomedical data management systems that cater for family data have usually done so as part of their standard (non-family-centric) data model. Consequently, data managers with computing expertise are needed to extract family datasets and perform family-centric operations. We present a robust approach to handling large family datasets. Our approach is implemented as a new module which extends the capabilities of The Ark, an open-source web-based biomedical data management tool. Using an algorithm designed by the authors, the pedigree module dynamically infers family relationships for any selected subject (not necessarily the proband). A web interface allows researchers to create, update, delete and navigate parental and twin relationships between subjects, and bulk import/export pedigrees. Consanguineous relationships can be captured, and configurable pedigree visualizations generated. A web services interface provides interoperability.