Myers Timothy A, Chanock Stephen J, Machiela Mitchell J
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States.
Front Genet. 2020 Feb 28;11:157. doi: 10.3389/fgene.2020.00157. eCollection 2020.
Genomic research involving human genetics and evolutionary biology relies heavily on linkage disequilibrium (LD) to investigate population-specific genetic structure, functionally map regions of disease susceptibility and uncover evolutionary history. Interactive and powerful tools are needed to calculate population-specific LD estimates for integrative genomics research. LDlink is an interactive suite of web-based tools developed to query germline variants in 1000 Genomes Project population groups of interest and generate interactive tables and plots of LD estimates. As an expansion to this resource, we have developed an R package, , designed to rapidly calculate statistics for large lists of variants and LD attributes that eliminates the time needed to perform repetitive requests from the web-based LDlink tool. accelerates genomic research by providing efficient and user-friendly functions to programmatically interrogate and download pairwise LD estimates from expansive lists of genetic variants. is a free and publicly available R package that can be installed from the Comprehensive R Archive Network (CRAN) or downloaded from https://github.com/CBIIT/LDlinkR.
涉及人类遗传学和进化生物学的基因组研究在很大程度上依赖连锁不平衡（LD）来研究特定人群的遗传结构、对疾病易感性区域进行功能定位以及揭示进化历史。整合基因组学研究需要交互式且强大的工具来计算特定人群的LD估计值。LDlink是一套交互式的基于网络的工具套件，旨在查询1000基因组计划中感兴趣人群组的种系变异，并生成LD估计值的交互式表格和图表。作为对该资源的扩展，我们开发了一个R包，旨在快速计算大量变异列表和LD属性的统计数据，从而消除了从基于网络的LDlink工具执行重复请求所需的时间。通过提供高效且用户友好的功能，以便以编程方式询问和下载来自大量遗传变异列表的成对LD估计值，加速了基因组研究。是一个免费的、可公开获取的R包，可以从综合R存档网络（CRAN）安装，或从https://github.com/CBIIT/LDlinkR下载。
