Biostatistical aspects of genome-wide association studies.
paper
Cited
Public
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- Authors
- Ziegler, Andreas; König, Inke R; Thompson, John R
- Year
- 2008
- Journal
- Biometrical journal. Biometrische Zeitschrift
- PMID
- 18217698
- DOI
- 10.1002/bimj.200710398
To search the entire human genome for association is a novel and promising approach to unravelling the genetic basis of complex genetic diseases. In these genome-wide association studies (GWAs), several hundreds of thousands of single nucleotide polymorphisms (SNPs) are analyzed at the same time, posing substantial biostatistical and computational challenges. In this paper, we discuss a number of biostatistical aspects of GWAs in detail. We specifically consider quality control issues and show that signal intensity plots are a sine qua condition non in today's GWAs. Approaches to detect and adjust for population stratification are briefly examined. We discuss different strategies aimed at tackling the problem of multiple testing, including adjustment of p -values, the false positive report probability and the false discovery rate. Another aspect of GWAs requiring special attention is the search for gene-gene and gene-environment interactions. We finally describe multistage approaches to GWAs.
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| The goldmine of GWAS summary statistics: a systematic review of methods and tools. | Kontou PI et al. | — | 2024 | → |
| Weighted kernels improve multi-environment genomic prediction. | Hu X et al. | — | 2023 | → |
| Combinational Drug Repurposing from Genetic Networks Applied to Alzheimer's Disease. | Nabirotchkin S et al. | — | 2022 | → |
| Genome-wide analysis of genetic predisposition to common polygenic cancers. | Nazarian A et al. | — | 2022 | → |
| Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies. | Wang J et al. | — | 2022 | → |
| New Distance-Based approach for Genome-Wide Association Studies. | Irigoien I et al. | — | 2022 | → |
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| Novel EDGE encoding method enhances ability to identify genetic interactions. | Hall MA et al. | — | 2021 | → |
| A genome-wide association study for mastitis resistance in phenotypically well-characterized Holstein dairy cattle using a selective genotyping approach. | Kurz JP et al. | — | 2019 | → |
| Genome-wide analysis of genetic predisposition to Alzheimer's disease and related sex disparities. | Nazarian A et al. | — | 2019 | → |
| Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis. | Braliou GG et al. | — | 2019 | → |
| Multivariate Methods for Meta-Analysis of Genetic Association Studies. | Dimou NL et al. | — | 2018 | → |
| Apolipoprotein E Polymorphism and Left Ventricular Failure in Beta-Thalassemia: A Multivariate Meta-Analysis. | Dimou NL et al. | — | 2017 | → |
| Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.). | Ademe MS et al. | — | 2017 | → |
| Estimated allele substitution effects underlying genomic evaluation models depend on the scaling of allele counts. | Bouwman AC et al. | — | 2017 | → |
| GWAR: robust analysis and meta-analysis of genome-wide association studies. | Dimou NL et al. | — | 2017 | → |
| Rethinking the Epigenetic Framework to Unravel the Molecular Pathology of Schizophrenia. | Cariaga-Martinez A et al. | — | 2017 | → |
| A genome-wide association study meta-analysis of clinical fracture in 10,012 African American women. | Taylor KC et al. | — | 2016 | → |
| GenoMatrix: A Software Package for Pedigree-Based and Genomic Prediction Analyses on Complex Traits. | Nazarian A et al. | — | 2016 | → |
| Identifying Prognostic SNPs in Clinical Cohorts: Complementing Univariate Analyses by Resampling and Multivariable Modeling. | Hieke S et al. | — | 2016 | → |
| A genome-wide pleiotropy scan for prostate cancer risk. | Panagiotou OA et al. | — | 2015 | → |
| Analysis of the Association between Catechol-O-Methyltransferase Val158Met and Male Sexual Orientation. | Yu W et al. | — | 2015 | → |
| Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis. | Grange L et al. | — | 2015 | → |
| [Methodological challenges for genome-based prediction of diseases]. | Foraita R et al. | — | 2015 | → |
| Statistical analysis for genome-wide association study. | Zeng P et al. | — | 2015 | → |
| Association mapping for epistasis and environmental interaction of yield traits in 323 cotton cultivars under 9 different environments. | Jia Y et al. | — | 2014 | → |
| Comparison of statistics in association tests of genetic markers for survival outcomes. | Mendolia F et al. | — | 2014 | → |
| Rejoinder. | Ziegler A | — | 2014 | → |
| SNPQC--an R pipeline for quality control of Illumina SNP genotyping array data. | Gondro C et al. | — | 2014 | → |
| Testing gene-gene interactions in genome wide association studies. | Hu JK et al. | — | 2014 | → |
| Toward a road map for global -omics: a primer on -omic technologies. | Coughlin SS | — | 2014 | → |
| An efficient and robust method for analyzing population pharmacokinetic data in genome-wide pharmacogenomic studies: a generalized estimating equation approach. | Nagashima K et al. | — | 2013 | → |
| Combining genetic association study designs: a GWAS case study. | Estus JL et al. | — | 2013 | → |
| Empirical hierarchical bayes approach to gene-environment interactions: development and application to genome-wide association studies of lung cancer in TRICL. | Sohns M et al. | — | 2013 | → |
| Milk metabolites and their genetic variability. | Wittenburg D et al. | — | 2013 | → |
| Parametric estimation of the local false discovery rate for identifying genetic associations. | Yang Y et al. | — | 2013 | → |
| Quality control for genome-wide association studies. | Gondro C et al. | — | 2013 | → |
| Using Bayesian networks to discover relations between genes, environment, and disease. | Su C et al. | — | 2013 | → |
| A knowledge-based method for association studies on complex diseases. | Nazarian A et al. | — | 2012 | → |
| Association of single nucleotide polymorphisms in the genes ATM, GSTP1, SOD2, TGFB1, XPD and XRCC1 with risk of severe erythema after breast conserving radiotherapy. | Raabe A et al. | — | 2012 | → |
| Cancer heterogeneity: origins and implications for genetic association studies. | Urbach D et al. | — | 2012 | → |
| Chapter 11: challenges in and principles for conducting systematic reviews of genetic tests used as predictive indicators. | Jonas DE et al. | — | 2012 | → |
| Correction for population stratification in random forest analysis. | Zhao Y et al. | — | 2012 | → |
| Genetic predictors of cue- and stress-induced cigarette craving: an exploratory study. | Erblich J et al. | — | 2012 | → |
| Genotype calling for the Affymetrix platform. | Schillert A et al. | — | 2012 | → |
| Lack of an association between E-selectin gene polymorphisms and risk of Kawasaki disease. | Shirakawa T et al. | — | 2012 | → |
| Unrecognized sequence homologies may confound genome-wide association studies. | Galichon P et al. | — | 2012 | → |
| Association of CD14 -260 (-159) C>T and asthma: a systematic review and meta-analysis. | Zhao L et al. | — | 2011 | → |
| Cardiovascular diseases and genome-wide association studies. | Ndiaye NC et al. | — | 2011 | → |
| Differential susceptibility to adolescent externalizing trajectories: examining the interplay between CHRM2 and peer group antisocial behavior. | Latendresse SJ et al. | — | 2011 | → |
| Evaluating the influence of quality control decisions and software algorithms on SNP calling for the affymetrix 6.0 SNP array platform. | de Andrade M et al. | — | 2011 | → |
| Genome-wide prediction of discrete traits using Bayesian regressions and machine learning. | González-Recio O et al. | — | 2011 | → |
| Genomic, transcriptomic, and epigenomic approaches to recovery after acquired brain injury. | Conley YP et al. | — | 2011 | → |
| Incorporating genetics into your studies: a guide for social scientists. | Dick DM et al. | — | 2011 | → |
| Investigating Hardy-Weinberg equilibrium in case-control or cohort studies or meta-analysis. | Ziegler A et al. | — | 2011 | → |
| Quantitative Models for Causal Analysis in the Era of Genome Wide Association Studies. | Coughlin SS | — | 2011 | → |
| The meta-analysis of genome-wide association studies. | Thompson JR et al. | — | 2011 | → |
| Validation in genetic association studies. | König IR | — | 2011 | → |
| A confidence-limit-based approach to the assessment of Hardy-Weinberg equilibrium. | Wellek S et al. | — | 2010 | → |
| A quality control algorithm for filtering SNPs in genome-wide association studies. | Pongpanich M et al. | — | 2010 | → |
| Bayesian mixture modeling of gene-environment and gene-gene interactions. | Wakefield J et al. | — | 2010 | → |
| Beta2-adrenergic receptor gene polymorphisms as systemic determinants of healthy aging in an evolutionary context. | Kulminski AM et al. | — | 2010 | → |
| Bioinformatics challenges for genome-wide association studies. | Moore JH et al. | — | 2010 | → |
| Effectiveness of strategies to increase the validity of findings from association studies: size vs. replication. | Weitkunat R et al. | — | 2010 | → |
| Efficiency robust statistics for genetic linkage and association studies under genetic model uncertainty. | Joo J et al. | — | 2010 | → |
| Genome-wide association study of childhood acute lymphoblastic leukemia in Korea. | Han S et al. | — | 2010 | → |
| Immunological and genetic aspects of asthma and allergy. | Madore AM et al. | — | 2010 | → |
| Methods: genetic epidemiology. | Benke KS et al. | — | 2010 | → |
| Novel asthma-associated genes from genome-wide association studies: what is their significance? | Kabesch M | — | 2010 | → |
| Principal-component analysis for assessment of population stratification in mitochondrial medical genetics. | Biffi A et al. | — | 2010 | → |
| Quality control and quality assurance in genotypic data for genome-wide association studies. | Laurie CC et al. | — | 2010 | → |
| Quality control for genome-wide association studies. | Weale ME | — | 2010 | → |
| Spoiling the whole bunch: quality control aimed at preserving the integrity of high-throughput genotyping. | Pluzhnikov A et al. | — | 2010 | → |
| The identification of colon cancer susceptibility genes by using genome-wide scans. | Daley D | — | 2010 | → |
| ACPA: automated cluster plot analysis of genotype data. | Schillert A et al. | — | 2009 | → |
| A critique of the false-positive report probability. | Lucke JF | — | 2009 | → |
| Adapting the logical basis of tests for Hardy-Weinberg Equilibrium to the real needs of association studies in human and medical genetics. | Goddard KA et al. | — | 2009 | → |
| A genome-wide association study primer for clinicians. | Wang TH et al. | — | 2009 | → |
| Analysis of the host pharmacogenetic background for prediction of outcome and toxicity in diffuse large B-cell lymphoma treated with R-CHOP21. | Rossi D et al. | — | 2009 | → |
| Classification tree for detection of single-nucleotide polymorphism (SNP)-by-SNP interactions related to heart disease: Framingham Heart Study. | Yao L et al. | — | 2009 | → |
| Evaluation of single-nucleotide polymorphism imputation using random forests. | Schwarz DF et al. | — | 2009 | → |
| Family-based genome-wide association studies. | Benyamin B et al. | — | 2009 | → |
| Genetic studies of amyotrophic lateral sclerosis: controversies and perspectives. | Beleza-Meireles A et al. | — | 2009 | → |
| Genetic variations as cancer prognostic markers: review and update. | Savas S et al. | — | 2009 | → |
| Genome-wide association studies of bladder cancer risk: a field synopsis of progress and potential applications. | Wu X et al. | — | 2009 | → |
| Genome-wide association studies: quality control and population-based measures. | Ziegler A | — | 2009 | → |
| Genome-wide strategies for discovering genetic influences on cognition and cognitive disorders: methodological considerations. | Potkin SG et al. | — | 2009 | → |
| Host genetic susceptibility to pneumococcal and meningococcal disease: a systematic review and meta-analysis. | Brouwer MC et al. | — | 2009 | → |
| Order-restricted scores test for the evaluation of population-based case-control studies when the genetic model is unknown. | Hothorn LA et al. | — | 2009 | → |
| Pharmacogenetics of antihypertensive treatment: detailing disciplinary dissonance. | Arnett DK et al. | — | 2009 | → |
| Risk assessment and pharmacogenetics in molecular and genomic epidemiology. | Park SK et al. | — | 2009 | → |
| Studying genetic variations in cancer prognosis (and risk): a primer for clinicians. | Savas S et al. | — | 2009 | → |
| Classification with high-dimensional genetic data: assigning patients and genetic features to known classes. | Schwender H et al. | — | 2008 | → |