On combining data from genome-wide association studies to discover disease-associated SNPs

DOI10.1214/09-STS286MaRDI QIDQ908136zbMATH OpenOpenAlexFDO

Authors Ruth M. Pfeiffer, Mitchell H. Gail, David Pee

Publication date 3 February 2016

Published in Statistical Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1010.5046, https://projecteuclid.org/euclid.ss/1271770348

zbMATH Keywords

hypothesis testingrandom effectsWald testmultiple comparisonwhole genome scans

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Paired and multiple comparisons; multiple testing (62J15)

Abstract: Combining data from several case-control genome-wide association (GWA) studies can yield greater efficiency for detecting associations of disease with single nucleotide polymorphisms (SNPs) than separate analyses of the component studies. We compared several procedures to combine GWA study data both in terms of the power to detect a disease-associated SNP while controlling the genome-wide significance level, and in terms of the detection probability ($mathitDP$). The $mathitDP$ is the probability that a particular disease-associated SNP will be among the $T$ most promising SNPs selected on the basis of low $p$-values. We studied both fixed effects and random effects models in which associations varied across studies. In settings of practical relevance, meta-analytic approaches that focus on a single degree of freedom had higher power and $mathitDP$ than global tests such as summing chi-square test-statistics across studies, Fisher's combination of $p$-values, and forming a combined list of the best SNPs from within each study.

Recommendations

• Association tests through combining \(p\)-values for case control genome-wide association studies
• Dealing with heterogeneity between cohorts in genomewide SNP association studies
• Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies
• Biostatistical aspects of genome-wide association studies
• A novel powerful joint analysis with data fusion in two-stage case-control genome-wide association studies

Cites work

• A systematic comparison of methods for combining \(p\)-values from independent tests
• From Genotypes to Genes: Doubling the Sample Size
• Genomic Control for Association Studies
• Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies
• Valid Inference in Random Effects Meta‐Analysis

Cited in

(14)

• Generating SNP barcode to evaluate SNP-SNP interaction of disease by particle swarm opti\-mi\-zation
• Collapsing SNP genotypes in case-control genome-wide association studies increases the type I error rate and power
• SHARE: an adaptive algorithm to select the most informative set of SNPs for candidate genetic association
• A novel random effect model for GWAS meta-analysis and its application to trans-ethnic meta-analysis
• Methodological issues in multistage genome-wide association studies
• Meta-analysis and Combining Information in Genetics and Genomics
• Robust tests in genome-wide scans under incomplete linkage disequilibrium
• On combining family based and population based case-control data in association studies
• Modeling the Association Between Clusters of SNPs and Disease Responses
• Association tests through combining \(p\)-values for case control genome-wide association studies
• Replicability analysis for genome-wide association studies
• Probability of detecting disease-associated single nucleotide polymorphisms in case-control genome-wide association studies
• Dealing with heterogeneity between cohorts in genomewide SNP association studies
• Joint analysis of SNP and gene expression data in genetic association studies of complex diseases

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