PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations
PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations
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DOI：
10.1093/bioinformatics/btz469
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发表时间：
2019-11-15
期刊：
影响因子：
5.8
通讯作者：
Staley, James R.
中科院分区：
文献类型：
--
作者：
Kamat, Mihir A.;Blackshaw, James A.;Staley, James R.
摘要：PhenoScanner是一个精心策划的数据库，其中包括大规模人类遗传关联研究的公开结果。这个在线工具促进了“现象组扫描”，在这种扫描中，遗传变异被交叉引用，以与不同类型的许多表型相关联。在这里，我们介绍了PhenoScanner(“PhenoScanner V2”)的重大更新，包括超过1.5亿个遗传变异和超过650亿个关联(与PhenoScanner V1中的3.5亿个关联)与疾病和特征、基因表达、代谢物和蛋白质水平以及表观遗传标记。查询选项已扩展到包括按基因、基因组区域和表型以及遗传变异进行搜索。使用变量效应预测器对所有变量进行位置标注，并将表型映射到实验因素本体论术语。来自1000基因组计划的连锁不平衡统计数据可用于搜索与代理变种的表型关联。
A Summary: PhenoScanner is a curated database of publicly available results from large-scale genetic association studies in humans. This online tool facilitates 'phenome scans', where genetic variants are cross-referenced for association with many phenotypes of different types. Here we present a major update of PhenoScanner ('PhenoScanner V2'), including over 150 million genetic variants and more than 65 billion associations (compared to 350 million associations in PhenoScanner V1) with diseases and traits, gene expression, metabolite and protein levels, and epigenetic markers. The query options have been extended to include searches by genes, genomic regions and phenotypes, as well as for genetic variants. All variants are positionally annotated using the Variant Effect Predictor and the phenotypes are mapped to Experimental Factor Ontology terms. Linkage disequilibrium statistics from the 1000 Genomes project can be used to search for phenotype associations with proxy variants.