Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks,American Journal of Human Genetics

当前位置： X-MOL 学术 › Am. J. Hum. Genet. › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks
American Journal of Human Genetics ( IF 8.1 ) Pub Date : 2020-09-28 , DOI: 10.1016/j.ajhg.2020.08.025
Lars G Fritsche ₁ , Snehal Patil ₂ , Lauren J Beesley ₃ , Peter VandeHaar ₂ , Maxwell Salvatore ₃ , Ying Ma ₂ , Robert B Peng ₄ , Daniel Taliun ₂ , Xiang Zhou ₅ , Bhramar Mukherjee ₆

Affiliation

Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Statistics, Northwestern University, Evanston, IL 60208, USA.
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.

To facilitate scientific collaboration on polygenic risk scores (PRSs) research, we created an extensive PRS online repository for 35 common cancer traits integrating freely available genome-wide association studies (GWASs) summary statistics from three sources: published GWASs, the NHGRI-EBI GWAS Catalog, and UK Biobank-based GWASs. Our framework condenses these summary statistics into PRSs using various approaches such as linkage disequilibrium pruning/p value thresholding (fixed or data-adaptively optimized thresholds) and penalized, genome-wide effect size weighting. We evaluated the PRSs in two biobanks: the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort at Michigan Medicine, and the population-based UK Biobank (UKB). For each PRS construct, we provide measures on predictive performance and discrimination. Besides PRS evaluation, the Cancer-PRSweb platform features construct downloads and phenome-wide PRS association study results (PRS-PheWAS) for predictive PRSs. We expect this integrated platform to accelerate PRS-related cancer research.

中文翻译：

Cancer PRSweb：一个在线存储库，包含主要癌症特征的多基因风险评分及其在两个独立生物库中的评估

为了促进多基因风险评分 (PRS) 研究的科学合作，我们为 35 种常见癌症特征创建了一个广泛的 PRS 在线存储库，整合了来自三个来源的免费全基因组关联研究 (GWAS) 摘要统计数据：已发布的 GWAS、NHGRI-EBI GWAS目录和基于英国生物库的 GWAS。我们的框架使用各种方法将这些汇总统计数据压缩为 PRS，例如连锁不平衡修剪/p 值阈值（固定或数据自适应优化阈值）和惩罚性全基因组效应大小加权。我们评估了两个生物库中的 PRS：密歇根基因组计划 (MGI)、密歇根医学的纵向生物样本库工作以及基于人群的英国生物库 (UKB)。对于每个 PRS 结构，我们提供了预测表现和歧视的衡量标准。除了 PRS 评估之外，Cancer-PRSweb 平台还提供用于预测 PRS 的构建体下载和全表组 PRS 关联研究结果 (PRS-PheWAS)。我们期望这个综合平台能够加速 PRS 相关的癌症研究。

更新日期：2020-11-06

点击分享查看原文

点击收藏

公开下载

阅读更多本刊最新论文本刊介绍/投稿指南11