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摘要 : 5月8日的《Nature Communications》杂志上发布上海交通大学、哈佛大学公共卫生学院等处的研究人员采用表达数量性状基因座定位(eQTL mapping)方法鉴别出了多个组织中的插入和删除特异性的eQTLs的研究成果。

 5月8日的《Nature Communications》杂志上发布上海交通大学、哈佛大学公共卫生学院等处的研究人员采用表达数量性状基因座定位(eQTL mapping)方法鉴别出了多个组织中的插入和删除特异性的eQTLs的研究成果。

在这篇文章中研究人员报告称,将源于最近千人基因组计划(1,000 Genomes Project)调查的1,380,133个indels填补到3个多组织eQTL数据集中。填补进indels将power值提高了9.9%,鉴别出了325个基因的indel特异性eQTLs。他们发现一些内含子和UTRs附近更加富集indel eQTLs,以往发现的3.6%(单组织)—9.2%%(多组织)eSNPs是eindels的标签(taggers)。功能分析鉴别出了一些表观遗传标记、基因本体类别,和受到SNPs和indels eQTLs影响,显示组织异质性或组织特异性效应的一些疾病GWAS基因座。这项研究提供了有关多个组织基因表达潜在遗传结构的一些新见解,并为解读与结构变异相关的一些疾病和性状提供了新资源。


eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues


Genome-wide gene expression quantitative trait loci (eQTL) mapping have been focused on single-nucleotide polymorphisms and have helped interpret findings from diseases mapping studies. The functional effect of structure variants, especially short insertions and deletions (indel) has not been well investigated. Here we impute 1,380,133 indels based on the latest 1,000 Genomes Project panel into three eQTL data sets from multiple tissues. Imputation of indels increased 9.9% power and identifies indel-specific eQTLs for 325 genes. We find introns and vicinities of UTRs are more enriched of indel eQTLs and 3.6 (single-tissue)–9.2%(multi-tissue) of previous identified eSNPs were taggers of eindels. Functional analyses identifies epigenetics marks, gene ontology categories and disease GWAS loci affected by SNPs and indels eQTLs showing tissue-consistent or tissue-specific effects. This study provides new insights into the underlying genetic architecture of gene expression across tissues and new resource to interpret function of diseases and traits associated structure variants.

来源: Nature Communications 浏览次数:1


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