Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples.
Pharmacogenomics J
; 10(4): 364-74, 2010 Aug.
Article
en En
| MEDLINE
| ID: mdl-20368714
ABSTRACT
The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Haplotipos
/
Estudio de Asociación del Genoma Completo
/
Genotipo
Tipo de estudio:
Risk_factors_studies
Límite:
Humans
Idioma:
En
Revista:
Pharmacogenomics J
Asunto de la revista:
BIOLOGIA MOLECULAR
/
FARMACOLOGIA
Año:
2010
Tipo del documento:
Article
País de afiliación:
Estados Unidos