GWAShug: a comprehensive platform for decoding the shared genetic basis between complex traits based on summary statistics

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nucleic Acids Research Pub Date : 2024-10-09 DOI:10.1093/nar/gkae873

Chen Cao, Min Tian, Zhenghui Li, Wenyan Zhu, Peng Huang, Sheng Yang

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Abstract

The shared genetic basis offers very valuable insights into the etiology, diagnosis and therapy of complex traits. However, a comprehensive resource providing shared genetic basis using the accessible summary statistics is currently lacking. It is challenging to analyze the shared genetic basis due to the difficulty in selecting parameters and the complexity of pipeline implementation. To address these issues, we introduce GWAShug, a platform featuring a standardized best-practice pipeline with four trait level methods and three molecular level methods. Based on stringent quality control, the GWAShug resource module includes 539 high-quality GWAS summary statistics for European and East Asian populations, covering 54 945 pairs between a measurement-based and a disease-based trait and 43 902 pairs between two disease-based traits. Users can easily search for shared genetic basis information by trait name, MeSH term and category, and access detailed gene information across different trait pairs. The platform facilitates interactive visualization and analysis of shared genetic basic results, allowing users to explore data dynamically. Results can be conveniently downloaded via FTP links. Additionally, we offer an online analysis module that allows users to analyze their own summary statistics, providing comprehensive tables, figures and interactive visualization and analysis. GWAShug is freely accessible at http://www.gwashug.com.

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GWAShug：基于汇总统计解码复杂性状之间共享遗传基础的综合平台

共有遗传基础为复杂性状的病因学、诊断和治疗提供了非常有价值的见解。然而，目前还缺乏利用可访问的汇总统计提供共有遗传基础的综合资源。由于参数选择困难和管道实施复杂，分析共有遗传基础具有挑战性。为了解决这些问题，我们引入了 GWAShug，这是一个具有标准化最佳实践管道的平台，包含四种性状水平方法和三种分子水平方法。基于严格的质量控制，GWAShug 资源模块包括欧洲和东亚人群的 539 个高质量 GWAS 统计摘要，涵盖 54 945 对基于测量的性状和基于疾病的性状，以及 43 902 对两个基于疾病的性状。用户可以通过性状名称、MeSH 术语和类别轻松搜索共享遗传基础信息，并访问不同性状对之间的详细基因信息。该平台有利于共享遗传基础结果的交互式可视化和分析，使用户能够动态地探索数据。用户可通过 FTP 链接方便地下载结果。此外，我们还提供了一个在线分析模块，允许用户分析自己的汇总统计数据，提供全面的表格、图表和交互式可视化分析。GWAShug 可在 http://www.gwashug.com 免费访问。

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

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.