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Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network.基于基因组学和流行病学的人群结构研究（PAGE）网络中的表型全基因组关联研究（PheWAS），用于检测多效性。
PLoS Genet. 2013;9(1):e1003087. doi: 10.1371/journal.pgen.1003087. Epub 2013 Jan 31.
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Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View.使用 PheWAS-View 直观整合和探索高通量表型全基因组关联研究（PheWAS）结果。
BioData Min. 2012 Jun 8;5(1):5. doi: 10.1186/1756-0381-5-5.
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Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies.FOXE1 附近的变体与甲状腺功能减退症和其他甲状腺疾病有关：利用电子病历进行全基因组和表型全基因组研究。
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R全表型组关联研究分析与绘图工具：用于R环境下全表型组关联研究的数据分析与绘图工具。

R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.

作者信息

Carroll Robert J, Bastarache Lisa, Denny Joshua C

机构信息

Department of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USA.

Department of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USADepartment of Biomedical Informatics and Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37212, USA.

出版信息

Bioinformatics. 2014 Aug 15;30(16):2375-6. doi: 10.1093/bioinformatics/btu197. Epub 2014 Apr 14.

DOI:10.1093/bioinformatics/btu197
PMID:24733291
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4133579/
Abstract

UNLABELLED

Phenome-wide association studies (PheWAS) have been used to replicate known genetic associations and discover new phenotype associations for genetic variants. This PheWAS implementation allows users to translate ICD-9 codes to PheWAS case and control groups, perform analyses using these and/or other phenotypes with covariate adjustments and plot the results. We demonstrate the methods by replicating a PheWAS on rs3135388 (near HLA-DRB, associated with multiple sclerosis) and performing a novel PheWAS using an individual's maximum white blood cell count (WBC) as a continuous measure. Our results for rs3135388 replicate known associations with more significant results than the original study on the same dataset. Our PheWAS of WBC found expected results, including associations with infections, myeloproliferative diseases and associated conditions, such as anemia. These results demonstrate the performance of the improved classification scheme and the flexibility of PheWAS encapsulated in this package.

AVAILABILITY AND IMPLEMENTATION

This R package is freely available under the Gnu Public License (GPL-3) from http://phewascatalog.org. It is implemented in native R and is platform independent.

摘要

未标注

全表型关联研究（PheWAS）已被用于复制已知的基因关联，并发现基因变异的新表型关联。这种PheWAS实现方式允许用户将ICD - 9编码转换为PheWAS病例组和对照组，使用这些和/或其他经协变量调整的表型进行分析，并绘制结果。我们通过在rs3135388（靠近HLA - DRB，与多发性硬化症相关）上复制PheWAS并使用个体的最大白细胞计数（WBC）作为连续测量进行一项新的PheWAS来演示这些方法。我们对rs3135388的结果复制了已知关联，且比在同一数据集上的原始研究结果更显著。我们对白细胞计数的PheWAS发现了预期结果，包括与感染、骨髓增殖性疾病及相关病症（如贫血）的关联。这些结果证明了改进分类方案的性能以及此软件包中封装的PheWAS的灵活性。

可用性与实现方式

此R软件包根据Gnu公共许可证（GPL - 3）可从http://phewascatalog.org免费获取。它以原生R实现，且与平台无关。