title: Ranking of genome-wide association scan signals by different measures.
abstract: BACKGROUND
  The P-value approach has been employed to prioritizing genome-wide association (GWA) scan signals, with a genome-wide significance defined by a prior P-value threshold, although this is not ideal. A rationale put forward is that the association signals rather should be expected to give less support for single nucleotide polymorphisms (SNPs) that are rare (with associated low-power tests) than for common SNPs with equivalent P-values, unless investigators believe, a priori, that rare causative variants contribute to the disease and have more pronounced effects.
  
  
  METHODS
  Using data from a GWA scan for type 2 diabetes (1924 cases, 2938 controls, 393 453 SNPs), we compared P-values with four alternative signal measures: likelihood ratio (LR), Bayes factor (BF; with a specified prior distribution for true effects), 'frequentist factor' (FF; reflecting the ratio between estimated--post-data-- 'power' and P-value) and probability of pronounced effect size (PrPES).
  
  
  RESULTS
  The 19 common SNPs [minor allele frequency (MAF) among the controls >29%] yielding strong P-value signals (P < 5 x 10(-7)) were also top ranked by the other approaches. There was a strong similarity between the P-values, LR and BF signals, in terms of ranking SNPs. In contrast, FF and PrPES signals down-weighted rare SNPs (control MAF <10%) with low P-values.
  
  
  CONCLUSIONS
  For prioritization of signals that do not achieve compelling levels of evidence for association, the main driving force behind observed differences between the various association signals appears to be SNP MAF. The statistical power afforded by follow-up samples for establishing replication should be taken into account when tailoring the signal selection strategy.
authors.affiliation: Department of Occupational and Environmental Medicine, Lund University Hospital, Lund, Sweden. ulf.stromberg@med.lu.se
authors.forename: Ulf
authors.initials: U
authors.lastname: Strömberg
authors.forename: Jonas
authors.initials: J
authors.lastname: Björk
authors.forename: Paolo
authors.initials: P
authors.lastname: Vineis
authors.forename: Karin
authors.initials: K
authors.lastname: Broberg
authors.forename: Eleftheria
authors.initials: E
authors.lastname: Zeggini
mesh_terms: D001499:Bayes Theorem; D003924:Diabetes Mellitus, Type 2 / Q000453:epidemiology / Q000235:genetics*; D020022:Genetic Predisposition to Disease / Q000453:epidemiology / Q000235:genetics*; D015894:Genome, Human; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide