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在生物库规模数据上进行高度并行和可重复的GWAS分析

Sebastian Schönherr¹, Johanna F Schachtl-Riess¹, Silvia Di Maio¹

¹Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria. Institutional Address: Schoepfstrasse 41, A-6020 Innsbruck, Austria.

NAR genomics and bioinformatics

|February 8, 2024

概括

nf-gwas是一个新的Nextflow管道,旨在进行大规模的全基因组关联研究 (GWAS). 这个工具简化了复杂的遗传分析,使得更快地发现基因型-表型关系.

科学领域:

基因组学就是基因组学.
计算生物学计算生物学
生物信息学是一种生物信息学.

背景情况:

在过去的二十年中,全基因组关联研究 (GWAS) 在众多特征中确定了超过60,000个遗传关联.
在GWAS中增加的样本大小给研究人员带来了重大的计算挑战.
可复制,模块化和并行分析管道对于高效的GWAS数据处理至关重要.

研究的目的:

引入nf-gwas,一个用于生物库规模全基因组关联研究的Nextflow管道.
为复杂的GWAS分析提供强大且可扩展的解决方案.
为了促进新型基因型-表型关系的发现.

主要方法:

nf-gwas是一个Nextflow管道,自动化了GWAS的加工前和后步骤.
集成REGENIE用于回归建模,支持单变体,基因和相互作用测试.
具有与交互式曼哈顿地图的自动报告功能,并使用nf-test进行测试.

主要成果:

该管道自动化了GWAS广泛的前后处理.
支持多种测试方法,包括单变体,基因和相互作用分析.
为成千上万的表型提供交互式报告,并在HPC和云平台上验证性能.

结论:

nf-gwas为生物库规模的GWAS提供了一个高度并行,可扩展和可重复的解决方案.
该管道简化了复杂的遗传数据分析,允许研究人员专注于生物解释.
自动化测试和验证确保了临床和制药应用的可靠性.

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