Streamlining large-scale genomic data management: Insights from the UK Biobank whole-genome sequencing data.

IF 11.1 Q1 CELL BIOLOGY

Cell genomics Pub Date : 2025-09-18 DOI:10.1016/j.xgen.2025.101009

Xihao Li, Andrew R Wood, Yuxin Yuan, Manrui Zhang, Yushu Huang, Gareth Hawkes, Robin N Beaumont, Michael N Weedon, Wenyuan Li, Xiaoyu Li, Xihong Lin, Zilin Li

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引用次数: 0

Abstract

Biobank-scale whole-genome sequencing (WGS) studies are increasingly pivotal in unraveling the genetic bases of diverse health outcomes. However, managing and analyzing these datasets' sheer volume and complexity presents significant challenges. We highlight the annotated genomic data structure (aGDS) format, substantially reducing the WGS data file size while enabling seamless integration of genomic and functional information for comprehensive WGS analyses. The aGDS format yielded 23 chromosome-specific files for the UK Biobank 500k WGS dataset, occupying only 1.10 tebibytes of storage. We develop the vcf2agds toolkit that streamlines the conversion of WGS data from VCF to aGDS format. Additionally, the STAARpipeline equipped with the aGDS files enabled scalable, comprehensive, and functionally informed WGS analysis, facilitating the detection of common and rare coding and noncoding phenotype-genotype associations. Overall, the vcf2agds toolkit and STAARpipeline provide a streamlined solution that facilitates efficient data management and analysis of biobank-scale WGS data across hundreds of thousands of samples.

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精简大规模基因组数据管理：来自英国生物银行全基因组测序数据的见解。

生物库规模的全基因组测序（WGS）研究在揭示多种健康结果的遗传基础方面越来越重要。然而，管理和分析这些数据集的庞大数量和复杂性带来了重大挑战。我们强调了注释基因组数据结构（aGDS）格式，大大减少了WGS数据文件大小，同时实现了基因组和功能信息的无缝集成，以进行全面的WGS分析。aGDS格式为UK Biobank 500k WGS数据集产生了23个染色体特异性文件，仅占用1.10 tb的存储空间。我们开发了vcf2agds工具包，简化了WGS数据从VCF到aGDS格式的转换。此外，配备了aGDS文件的STAARpipeline实现了可扩展、全面和功能知情的WGS分析，促进了常见和罕见编码和非编码表型-基因型关联的检测。总体而言，vcf2agds工具包和STAARpipeline提供了一个简化的解决方案，可以促进对数十万个样本的生物库规模WGS数据的有效数据管理和分析。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Cell genomics

CiteScore

7.10

自引率

0.00%

发文量