Quality control and quality assurance in genotypic data for genome-wide association studies.
paper
Primary
Public
- Authors
- Laurie, Cathy C; Doheny, Kimberly F; Mirel, Daniel B; Pugh, Elizabeth W; Bierut, Laura J; Bhangale, Tushar; Boehm, Frederick; Caporaso, Neil E; Cornelis, Marilyn C; Edenberg, Howard J; Gabriel, Stacy B; Harris, Emily L; Hu, Frank B; Jacobs, Kevin B; Kraft, Peter; Landi, Maria Teresa; Lumley, Thomas; Manolio, Teri A; McHugh, Caitlin; Painter, Ian; Paschall, Justin; Rice, John P; Rice, Kenneth M; Zheng, Xiuwen; Weir, Bruce S; GENEVA Investigators
- Year
- 2010
- Journal
- Genetic epidemiology
- PMID
- 20718045
- DOI
- 10.1002/gepi.20516
- PMCID
- PMC3061487
Genome-wide scans of nucleotide variation in human subjects are providing an increasing number of replicated associations with complex disease traits. Most of the variants detected have small effects and, collectively, they account for a small fraction of the total genetic variance. Very large sample sizes are required to identify and validate findings. In this situation, even small sources of systematic or random error can cause spurious results or obscure real effects. The need for careful attention to data quality has been appreciated for some time in this field, and a number of strategies for quality control and quality assurance (QC/QA) have been developed. Here we extend these methods and describe a system of QC/QA for genotypic data in genome-wide association studies (GWAS). This system includes some new approaches that (1) combine analysis of allelic probe intensities and called genotypes to distinguish gender misidentification from sex chromosome aberrations, (2) detect autosomal chromosome aberrations that may affect genotype calling accuracy, (3) infer DNA sample quality from relatedness and allelic intensities, (4) use duplicate concordance to infer SNP quality, (5) detect genotyping artifacts from dependence of Hardy-Weinberg equilibrium test P-values on allelic frequency, and (6) demonstrate sensitivity of principal components analysis to SNP selection. The methods are illustrated with examples from the "Gene Environment Association Studies" (GENEVA) program. The results suggest several recommendations for QC/QA in the design and execution of GWAS.
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| Genome-wide association study of generalized anxiety symptoms in the Hispanic Community Health Study/Study of Latinos. | Dunn EC et al. | β | 2017 | β |
| Genome-Wide Association Study of Male Sexual Orientation. | Sanders AR et al. | β | 2017 | β |
| Genome-Wide Association Study of Radiographic Knee Osteoarthritis in North American Caucasians. | Yau MS et al. | β | 2017 | β |
| Genome-wide meta-analysis identifies novel loci of plaque burden in carotid artery. | Pott J et al. | β | 2017 | β |
| Genome-wide minor histocompatibility matching as related to the risk of graft-versus-host disease. | Martin PJ et al. | β | 2017 | β |
| Germline variation in inflammation-related pathways and risk of Barrett's oesophagus and oesophageal adenocarcinoma. | Buas MF et al. | β | 2017 | β |
| GWAS Identifies New Loci for Painful Temporomandibular Disorder: Hispanic Community Health Study/Study of Latinos. | Sanders AE et al. | β | 2017 | β |
| Human Facial Shape and Size Heritability and Genetic Correlations. | Cole JB et al. | β | 2017 | β |
| Identifying and mitigating batch effects in whole genome sequencing data. | Tom JA et al. | β | 2017 | β |
| IL33 and IL1RL1 variants are associated with asthma and atopy in a Brazilian population. | Queiroz GA et al. | β | 2017 | β |
| Single nucleotide polymorphisms within MicroRNAs, MicroRNA targets, and MicroRNA biogenesis genes and their impact on colorectal cancer survival. | Mullany LE et al. | β | 2017 | β |
| Testing Departure from Hardy-Weinberg Proportions. | Wang J et al. | β | 2017 | β |
| The influence of genetic susceptibility and calcium plus vitamin D supplementation on fracture risk. | Wang Y et al. | β | 2017 | β |
| A Common Polymorphism in HIBCH Influences Methylmalonic Acid Concentrations in Blood Independently of Cobalamin. | Molloy AM et al. | β | 2016 | β |
| Admixture Mapping of African-American Women in the AMBER Consortium Identifies New Loci for Breast Cancer and Estrogen-Receptor Subtypes. | Ruiz-NarvΓ‘ez EA et al. | β | 2016 | β |
| A fast and powerful W-test for pairwise epistasis testing. | Wang MH et al. | β | 2016 | β |
| A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3. | Leslie EJ et al. | β | 2016 | β |
| Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. | Luo W et al. | β | 2016 | β |
| A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13. | Leslie EJ et al. | β | 2016 | β |
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| Associations between Polygenic Risk for Psychiatric Disorders and Substance Involvement. | Carey CE et al. | β | 2016 | β |
| A thrifty variant in CREBRF strongly influences body mass index in Samoans. | Minster RL et al. | β | 2016 | β |
| Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci. | Di Narzo AF et al. | β | 2016 | β |
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| Effects of Recent Stress and Variation in the Serotonin Transporter Polymorphism (5-HTTLPR) on Depressive Symptoms: A Repeated-Measures Study of Adults Age 50 and Older. | Arpawong TE et al. | β | 2016 | β |
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| Genetic variation near IRS1 is associated with adiposity and a favorable metabolic profile in U.S. Hispanics/Latinos. | Qi Q et al. | β | 2016 | β |
| Genetic variations in the Hippo signaling pathway and breast cancer risk in African American women in the AMBER Consortium. | Zhang J et al. | β | 2016 | β |
| Genetic variations in vitamin D-related pathways and breast cancer risk in African American women in the AMBER consortium. | Yao S et al. | β | 2016 | β |
| Genome-wide association of familial prostate cancer cases identifies evidence for a rare segregating haplotype at 8q24.21. | Teerlink CC et al. | β | 2016 | β |
| Genome-Wide Association Study in Immunocompetent Patients with Delayed Hypersensitivity to Sulfonamide Antimicrobials. | Reinhart JM et al. | β | 2016 | β |
| Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape. | Cole JB et al. | β | 2016 | β |
| Genome-Wide Association Study of Bladder Cancer in a Chinese Cohort Reveals a New Susceptibility Locus at 5q12.3. | Wang M et al. | β | 2016 | β |
| Genome-wide association study of dental caries in the Hispanic Communities Health Study/Study of Latinos (HCHS/SOL). | Morrison J et al. | β | 2016 | β |
| Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. | Schick UM et al. | β | 2016 | β |
| Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology. | Shaffer JR et al. | β | 2016 | β |
| Genome-wide autozygosity is associated with lower general cognitive ability. | Howrigan DP et al. | β | 2016 | β |
| Genome-wide estimate of the heritability of Multiple System Atrophy. | Federoff M et al. | β | 2016 | β |
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| Justification for setting the individual animal genotype call rate threshold at eighty-five percent. | Purfield DC et al. | β | 2016 | β |
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| The identification of novel genetic variants associated with antipsychotic treatment response outcomes in first-episode schizophrenia patients. | DrΓΆgemΓΆller BI et al. | β | 2016 | β |
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| Genome-wide association of polycystic ovary syndrome implicates alterations in gonadotropin secretion in European ancestry populations. | Hayes MG et al. | β | 2015 | β |
| Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. | Hong X et al. | β | 2015 | β |
| Genome-wide association study of selenium concentrations. | Cornelis MC et al. | β | 2015 | β |
| Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence. | Hancock DB et al. | β | 2015 | β |
| Genome-wide scan demonstrates significant linkage for male sexual orientation. | Sanders AR et al. | β | 2015 | β |
| Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension. | Jeong S et al. | β | 2015 | β |
| Identification of susceptibility genes for peritoneal, ovarian, and deep infiltrating endometriosis using a pooled sample-based genome-wide association study. | Borghese B et al. | β | 2015 | β |
| Impact of carotid atherosclerosis loci on cardiovascular events. | Hemerich D et al. | β | 2015 | β |
| Inbreeding among Caribbean Hispanics from the Dominican Republic and its effects on risk of Alzheimer disease. | Vardarajan BN et al. | β | 2015 | β |
| Influences of gestational obesity on associations between genotypes and gene expression levels in offspring following maternal gastrointestinal bypass surgery for obesity. | GuΓ©nard F et al. | β | 2015 | β |
| Joint Associations of Diet, Lifestyle, andΒ Genes with Age-Related MacularΒ Degeneration. | Meyers KJ et al. | β | 2015 | β |
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| MiRNA-Related SNPs and Risk of Esophageal Adenocarcinoma and Barrett's Esophagus: Post Genome-Wide Association Analysis in the BEACON Consortium. | Buas MF et al. | β | 2015 | β |
| Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis. | Carey CE et al. | β | 2015 | β |
| PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers. | Nato AQ et al. | β | 2015 | β |
| Polygenic risk, stressful life events and depressive symptoms in older adults: a polygenic score analysis. | Musliner KL et al. | β | 2015 | β |
| Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness. | Conomos MP et al. | β | 2015 | β |
| SNP Regulation of microRNA Expression and Subsequent Colon Cancer Risk. | Mullany LE et al. | β | 2015 | β |
| Using genetics to test the causal relationship of total adiposity and periodontitis: Mendelian randomization analyses in the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium. | Shungin D et al. | β | 2015 | β |
| Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. | Chang D et al. | β | 2014 | β |
| Acquired chromosomal anomalies in chronic lymphocytic leukemia patients compared with more than 50,000 quasi-normal participants. | Laurie CC et al. | β | 2014 | β |
| Association between AVPR1A, DRD2, and ASPM and endophenotypes of communication disorders. | Stein CM et al. | β | 2014 | β |
| Beyond cigarettes per day. A genome-wide association study of the biomarker carbon monoxide. | Bloom AJ et al. | β | 2014 | β |
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| DSM-5 cannabis use disorder: a phenotypic and genomic perspective. | Agrawal A et al. | β | 2014 | β |
| Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate. | Wu T et al. | β | 2014 | β |
| Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial. | Keene KL et al. | β | 2014 | β |
| Genetic evidence for role of carotenoids in age-related macular degeneration in the Carotenoids in Age-Related Eye Disease Study (CAREDS). | Meyers KJ et al. | β | 2014 | β |
| Genetic risk score for prediction of newborn adiposity and large-for-gestational-age birth. | Chawla R et al. | β | 2014 | β |
| Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. | Brown CC et al. | β | 2014 | β |
| Genome-wide association study of periodontal health measured by probing depth in adults ages 18-49 years. | Shaffer JR et al. | β | 2014 | β |
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| Investigating the Role of Gene-Gene Interactions in TB Susceptibility. | Daya M et al. | β | 2014 | β |
| Joint testing of genotypic and gene-environment interaction identified novel association for BMP4 with non-syndromic CL/P in an Asian population using data from an International Cleft Consortium. | Chen Q et al. | β | 2014 | β |
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| Value of Mendelian laws of segregation in families: data quality control, imputation, and beyond. | Blue EM et al. | β | 2014 | β |
| Variants near CHRNB3-CHRNA6 are associated with DSM-5 cocaine use disorder: evidence for pleiotropy. | Sadler B et al. | β | 2014 | β |
| A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus. | Levine DM et al. | β | 2013 | β |
| A Genome-Wide Association Study Suggests Novel Loci Associated with a Schizophrenia-Related Brain-Based Phenotype. | Hass J et al. | β | 2013 | β |
| A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis. | Reese SE et al. | β | 2013 | β |
| Automatic diagnosis of pathological myopia from heterogeneous biomedical data. | Zhang Z et al. | β | 2013 | β |
| Characterization and correction of error in genome-wide IBD estimation for samples with population structure. | Morrison J | β | 2013 | β |
| Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study. | Beaty TH et al. | β | 2013 | β |
| Genetic influences on craving for alcohol. | Agrawal A et al. | β | 2013 | β |
| Genome-wide and candidate gene association studies of placental abruption. | Workalemahu T et al. | β | 2013 | β |
| Genome-wide association studies of pit-and-fissure- and smooth-surface caries in permanent dentition. | Zeng Z et al. | β | 2013 | β |
| Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies. | Hayes MG et al. | β | 2013 | β |
| Interpreting Whole-Genome Marker Data. | Weir BS | β | 2013 | β |
| Meta-analysis of genome-wide association studies in five cohorts reveals common variants in RBFOX1, a regulator of tissue-specific splicing, associated with refractive error. | Stambolian D et al. | β | 2013 | β |
| Pleiotropy in complex traits: challenges and strategies. | Solovieff N et al. | β | 2013 | β |
| pyGenClean: efficient tool for genetic data clean up before association testing. | Lemieux Perreault LP et al. | β | 2013 | β |
| Secondary analysis of publicly available data reveals superoxide and oxygen radical pathways are enriched for associations between type 2 diabetes and low-frequency variants. | Yazdanpanah M et al. | β | 2013 | β |
| Stroke Genetics Network (SiGN) study: design and rationale for a genome-wide association study of ischemic stroke subtypes. | Meschia JF et al. | β | 2013 | β |
| Susceptibility loci associated with specific and shared subtypes of lymphoid malignancies. | Vijai J et al. | β | 2013 | β |
| The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study. | Urbanek M et al. | β | 2013 | β |
| A genome-wide association study of variations in maternal cardiometabolic genes and risk of placental abruption. | Moore A et al. | β | 2012 | β |
| A high-performance computing toolset for relatedness and principal component analysis of SNP data. | Zheng X et al. | β | 2012 | β |
| arrayMap: a reference resource for genomic copy number imbalances in human malignancies. | Cai H et al. | β | 2012 | β |
| CHRNB3 is more strongly associated with FagerstrΓΆm test for cigarette dependence-based nicotine dependence than cigarettes per day: phenotype definition changes genome-wide association studies results. | Rice JP et al. | β | 2012 | β |
| Comprehensive literature review and statistical considerations for GWAS meta-analysis. | Begum F et al. | β | 2012 | β |
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