文章基本信息

标题：A bioinformatics pipeline for rare genetic diseases in South African patients
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作者：Maryke Schoonen ; Albertus S. Seyffert ; Francois H. van der Westhuizen 等
期刊名称：South African Journal of Science
印刷版ISSN：0038-2353
电子版ISSN：1996-7489
出版年度：2019
卷号：115
期号：3-4
页码：99-101
DOI：10.17159/sajs.2019/4876
语种：English
出版社：The Foundation for Research Development
摘要：The research fields of bioinformatics and computational biology are growing rapidly in South Africa. Bioinformatics pipelines play an integral part in handling sequencing data, which are used to investigate the aetiology of common and rare diseases. Bioinformatics platforms for common disease aetiology are well supported and continuously being developed in South Africa. However, the same is not the case for rare diseases aetiology research. Investigations into the latter rely on international cloud-based tools for data analyses and ultimately confirmation of a genetic disease. However, these tools are not necessarily optimised for ethnically diverse population groups. We present an in-house developed bioinformatics pipeline to enable researchers to annotate and filter variants in either exome or amplicon next-generation sequencing data. This pipeline was developed using next-generation sequencing data of a predominantly African cohort of patients diagnosed with rare disease.Significance:• We demonstrate the feasibility of in-country development of ethnicity-sensitive, automated bioinformatics pipelines using free software in a South African context.• We provide a roadmap for development of similarly ethnicity-sensitive bioinformatics pipelines.
关键词：computational tools;African cohort;next-generation sequencing;rare disease