Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093-0419, USA.
Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, 92093-0419, USA.
Nat Commun. 2020 Jun 10;11(1):2927. doi: 10.1038/s41467-020-16482-4.
Structural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.
结构变异（SVs）和短串联重复（STRs）是一组广泛的不同 DNA 变体，它们在基因组中的大小和分布上差异很大。在这里，我们确定了与基因表达和复杂性状相关的 SV 类和 STR 的基因组特征，包括它们相对于 eGenes 的位置、与多个 eGenes 相关的可能性、相关的 eGene 类型（例如，编码、非编码、进化约束程度）、效应大小、与用于 GWAS 的标记单核苷酸变体的连锁不平衡，以及与 GWAS 性状相关的可能性。我们通过染色质环鉴定了一组与三个或更多 eGenes 表达相关的高影响力 SVs/STRs，并表明它们与 GWAS 性状高度相关。我们的研究为与基因表达和人类性状相关的结构变异类和短串联重复的基因组特性提供了深入了解。
