一种用于甲基化 QTL 作图的多重检验替代方法可减少假阳性 CpG 的比例。

An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs.

机构信息

Department of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2333 ZC Leiden and Biostatistics, Department for Health Evidence, Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands Department of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2333 ZC Leiden and Biostatistics, Department for Health Evidence, Radboud University Nijmegen Medical Center, 6500 HB Nijmegen, The Netherlands.

出版信息

Bioinformatics. 2015 Feb 1;31(3):340-5. doi: 10.1093/bioinformatics/btu654. Epub 2014 Oct 4.

DOI:10.1093/bioinformatics/btu654

PMID:25282645

Abstract

INTRODUCTION

An increasing number of studies investigates the influence of local genetic variation on DNA methylation levels, so-called in cis methylation quantitative trait loci (meQTLs). A common multiple testing approach in genome-wide cis meQTL studies limits the false discovery rate (FDR) among all CpG-SNP pairs to 0.05 and reports on CpGs from the significant CpG-SNP pairs. However, a statistical test for each CpG is not performed, potentially increasing the proportion of CpGs falsely reported on. Here, we presented an alternative approach that properly control for multiple testing at the CpG level.

RESULTS

We performed cis meQTL mapping for varying window sizes using publicly available single-nucleotide polymorphism (SNP) and 450 kb data, extracting the CpGs from the significant CpG-SNP pairs ([Formula: see text]). Using a new bait-and-switch simulation approach, we show that up to 50% of the CpGs found in the simulated data may be false-positive results. We present an alternative two-step multiple testing approach using the Simes and Benjamini-Hochberg procedures that does control the FDR among the CpGs, as confirmed by the bait-and-switch simulation. This approach indicates the use of window sizes in cis meQTL mapping studies that are significantly smaller than commonly adopted.

DISCUSSION

Our approach to cis meQTL mapping properly controls the FDR at the CpG level, is computationally fast and can also be applied to cis eQTL studies.

AVAILABILITY AND IMPLEMENTATION

An examplary R script for performing the Simes procedure is available as supplementary material.

CONTACT

e.w.van_zwet@lumc.nl or b.t.heijmans@lumc.nl

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

简介

越来越多的研究探讨了局部遗传变异对 DNA 甲基化水平的影响，即所谓的顺式甲基化数量性状基因座（meQTLs）。全基因组顺式 meQTL 研究中的一种常见多重检验方法将所有 CpG-SNP 对的错误发现率（FDR）限制在 0.05，并报告显著的 CpG-SNP 对中的 CpG。然而，并没有对每个 CpG 进行统计检验，这可能会增加假阳性报告的 CpG 比例。在这里，我们提出了一种替代方法，可以在 CpG 水平上正确控制多重检验。

结果

我们使用公开的单核苷酸多态性（SNP）和 450 kb 数据，针对不同的窗口大小进行顺式 meQTL 作图，从显著的 CpG-SNP 对中提取 CpG([公式：见正文])。我们使用一种新的诱饵和转换模拟方法，表明在模拟数据中发现的 CpG 中，高达 50%可能是假阳性结果。我们提出了一种替代的两步多重检验方法，使用 Simes 和 Benjamini-Hochberg 程序来控制 CpG 中的 FDR，这一点通过诱饵和转换模拟得到了证实。这种方法表明，在顺式 meQTL 作图研究中使用的窗口大小明显小于通常采用的大小。