PhenoScanner V2：一个扩展的搜索人类基因型-表型关联的工具。
PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations.
机构信息
MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK.
MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK.
出版信息
Bioinformatics. 2019 Nov 1;35(22):4851-4853. doi: 10.1093/bioinformatics/btz469.
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.
AVAILABILITY AND IMPLEMENTATION
PhenoScanner V2 is available at www.phenoscanner.medschl.cam.ac.uk.
摘要
PhenoScanner 是一个经过精心整理的数据库，其中包含了大量人类大规模遗传关联研究的公开结果。这个在线工具可以方便地进行“表型扫描”，即将遗传变异与多种不同类型的表型进行交叉参考，以寻找关联。在这里，我们展示了 PhenoScanner（“PhenoScanner V2”）的重大更新，其中包括超过 1.5 亿个遗传变异和超过 650 亿个与疾病和特征、基因表达、代谢物和蛋白质水平以及表观遗传标记的关联（相比之下，PhenoScanner V1 中只有 3.5 亿个关联）。查询选项已扩展到包括按基因、基因组区域和表型进行搜索，以及按遗传变异进行搜索。所有变异都使用 Variant Effect Predictor 进行位置注释，并将表型映射到 Experimental Factor Ontology 术语。可以使用 1000 Genomes 项目的连锁不平衡统计信息来搜索与代理变异相关的表型关联。
可用性和实现
PhenoScanner V2 可在 www.phenoscanner.medschl.cam.ac.uk 上获得。
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