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LDtrait：一个在线工具，用于识别连锁不平衡中已发表的表型关联。

LDtrait: An Online Tool for Identifying Published Phenotype Associations in Linkage Disequilibrium.

机构信息

Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland.

出版信息

Cancer Res. 2020 Aug 15;80(16):3443-3446. doi: 10.1158/0008-5472.CAN-20-0985. Epub 2020 Jun 30.

DOI:10.1158/0008-5472.CAN-20-0985
PMID:32606005
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7442674/
Abstract

Genome-wide association studies (GWAS) have identified thousands of germline susceptibility loci associated with risk for cancer as well as a wide range of other traits and diseases. An interest of many investigators is identifying traits or diseases that share common susceptibility loci. We developed LDtrait (https://ldlink.nci.nih.gov/?tab=ldtrait) as an open access web tool for finding germline variation associated with multiple traits. LDtrait searches the NHGRI-EBI GWAS Catalog to identify susceptibility loci in linkage disequilibrium (LD) with a user-provided list of query variants. Options allow for modifying LD thresholds, calculating LD from a diverse set of reference populations, and downloading annotated variant lists. Results from example query searches highlight the utility of LDtrait in uncovering cross-trait associations for cancer risk and other traits. LDtrait accelerates etiologic understanding of cancer genetics by rapidly identifying genetic similarities with other traits or diseases. SIGNIFICANCE: The new GWAS search tool LDtrait will expedite discovery of shared genetic components underlying seemingly unrelated diseases and may offer novel insights into cancer research.

摘要

全基因组关联研究（GWAS）已经确定了数千个与癌症风险以及广泛的其他特征和疾病相关的种系易感性基因座。许多研究人员感兴趣的是确定具有共同易感性基因座的特征或疾病。我们开发了 LDtrait（https://ldlink.nci.nih.gov/?tab=ldtrait），这是一种用于查找与多种特征相关的种系变异的开放获取网络工具。LDtrait 搜索 NHGRI-EBI GWAS 目录，以识别与用户提供的查询变体处于连锁不平衡（LD）状态的易感性基因座。该选项允许修改 LD 阈值，从多种参考人群中计算 LD，并下载带注释的变体列表。示例查询搜索的结果突出了 LDtrait 在揭示癌症风险和其他特征的跨特征关联方面的实用性。LDtrait 通过快速识别与其他特征或疾病的遗传相似性，加速了对癌症遗传学病因的理解。

意义

新的 GWAS 搜索工具 LDtrait 将加快发现看似无关疾病的共同遗传成分的速度，并可能为癌症研究提供新的见解。

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