title: An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs.
abstract: BACKGROUND
  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.
  
  
  CONCLUSIONS
  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.
  
  
  METHODS
  An examplary R script for performing the Simes procedure is available as supplementary material.
  
  
  BACKGROUND
  e.w.van_zwet@lumc.nl or b.t.heijmans@lumc.nl
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: 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.
authors.forename: René
authors.initials: R
authors.lastname: Luijk
authors.affiliation: 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.
authors.forename: Jelle J
authors.initials: JJ
authors.lastname: Goeman
authors.affiliation: 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.
authors.forename: Eline P
authors.initials: EP
authors.lastname: Slagboom
authors.affiliation: 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.
authors.forename: Bastiaan T
authors.initials: BT
authors.lastname: Heijmans
authors.affiliation: 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.
authors.forename: Erik W
authors.initials: EW
authors.lastname: van Zwet
mesh_terms: D018899:CpG Islands; D019175:DNA Methylation; D005189:False Positive Reactions; D015894:Genome, Human; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci