Robust Genome-Wide Association Studies
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Corresponding Organization : German Cancer Research Center
Other organizations : University of Pisa, University of South Carolina, Hospital Universitario Virgen de las Nieves, Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Górnośląskie Centrum Medyczne, Odense University Hospital, University of California, San Francisco, UCSF Helen Diller Family Comprehensive Cancer Center, The University of Texas MD Anderson Cancer Center, Semmelweis University, Gdańsk Medical University, The Maria Sklodowska-Curie National Research Institute of Oncology, BC Cancer Agency, University of British Columbia, Aarhus University Hospital, National Cancer Institute, Rzeszów University, Hospital Universitario 12 De Octubre, Centro de Investigación Biomédica en Red de Cáncer, Copernicus Memorial Hospital, University of Melbourne, Monash Health, Monash University, Cancer Council Victoria, Wroclaw Medical University, Instytut Hematologii i Transfuzjologi, Wojskowy Instytut Medycyny Lotniczej, University of Minho, Hospital de Câncer de Barretos, Universidad de Salamanca, Instituto de Investigación Biomédica de Salamanca, Jagiellonian University, Copenhagen University Hospital, Rigshospitalet, Cracow University of Technology, Medical University of Lublin, Hospices Civils de Lyon, University of Bydgoszcz, University of Utah, Holy Cross University, University of Alabama at Birmingham, Mayo Clinic in Florida
Variable analysis
- Genotyping platforms (Affymetrix 6.0, Illumina 610 Quad, Illumina Human660W-quad Beadchip, Illumina Omni5, Illumina OmniExpress Beadchip, Illumina Oncoarray)
- Genotyped variants
- Information score > 0.6 for imputed variants
- Genotype rate > 95%
- Minor allele frequencies > 0.01
- Hardy-Weinberg equilibrium (HWE) > 1 x 10^-5 in controls
- Missingness
- Duplicates
- Sex mismatch
- Abnormal heterozygosity
- Cryptic relatedness
- Population outliers (principal components analyses: Eigenstrat)
- Genomic inflation (λ > 1.00)
- Haplotype Reference Consortium (HRC) as reference for imputation
- Not specified
Annotations
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