New York Genome Center, New York, NY, USA.
Department of Systems Biology, Columbia University, New York, NY, USA.
Genome Biol. 2020 Sep 11;21(1):234. doi: 10.1186/s13059-020-02122-z.
Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level. In addition, we develop an extension of our tool phASER that allows effect sizes of cis-regulatory variants to be estimated using haplotype-level AE data. This AE resource is the largest to date, and we are able to make haplotype-level data publicly available. We anticipate that the availability of this resource will enable future studies of regulatory variation across human tissues.
等位基因表达 (AE) 分析能够稳健地衡量顺式调控效应。在这里,我们展示并演示了从 GTEx v8 版本生成的庞大 AE 资源的实用性,该资源包含 15253 个样本,涵盖 54 个人体组织,总计进行了 4.31 亿次 SNP 水平的 AE 测量和 1.53 亿次单倍型水平的 AE 测量。此外,我们开发了 phASER 工具的扩展版本,该版本允许使用单倍型水平的 AE 数据来估计顺式调控变异的效应大小。这个 AE 资源是迄今为止最大的,我们能够公开提供单倍型水平的数据。我们预计,该资源的可用性将使未来能够在人类组织中研究调控变异。