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Evaluation of power of the Illumina HumanOmni5M-4v1 BeadChip to detect risk variants for human complex diseases.
- Source :
-
European journal of human genetics : EJHG [Eur J Hum Genet] 2016 Jul; Vol. 24 (7), pp. 1029-34. Date of Electronic Publication: 2015 Nov 18. - Publication Year :
- 2016
-
Abstract
- Although emerging sequencing technologies can characterize all genetic variants, the cost is still high. Illumina released the HumanOmni5M-4v1 (Omni5) genotype array with ~4.3M assayed SNPs, a much denser array compared with other available arrays. The Omni5 balances both cost and array density. In this article, we illustrate the power of Omni5 to detect genetic associations. The Omni5 includes variants with a wide range of minor allele frequencies down to <1%. The theoretical power calculation examples indicate the increased power of the Omni5 array compared with other arrays with lower density when evaluating associations with some known loci, although there are exceptions. We further evaluate the genetic associations between known loci and several quantitative traits in the Framingham Heart Study: femoral neck bone mineral density, lumbar spine bone mineral density and hippocampal volume. Finally, we search genome wide for novel associations using the Omni5 genotypes. We compare our association results from Affymetrix 500K+MIPS 50K arrays and two imputed data sets: (1) HapMap Phase II and (2) 1000 Genomes reference panel. We observed increased evidence for genotype-phenotype associations with smaller P-values for selected known loci using the Omni5 genotypes. With limited sample sizes, we identify novel variants with genome-wide significant P-values. Our observations support the notion that dense genotyping using the Omni5 can be powerful in detecting novel associated variants. Comparison with imputed data with higher density also suggests that imputation helps but cannot replace genotyping, especially when imputation quality is low.
- Subjects :
- Bone Density genetics
Genetic Testing standards
Genome-Wide Association Study standards
Genotyping Techniques methods
Hippocampus growth & development
Humans
Mutation
Oligonucleotide Array Sequence Analysis standards
Organ Size genetics
Sensitivity and Specificity
Genetic Testing methods
Genome-Wide Association Study methods
Genotyping Techniques standards
Oligonucleotide Array Sequence Analysis methods
Quantitative Trait Loci
Subjects
Details
- Language :
- English
- ISSN :
- 1476-5438
- Volume :
- 24
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- European journal of human genetics : EJHG
- Publication Type :
- Academic Journal
- Accession number :
- 26577045
- Full Text :
- https://doi.org/10.1038/ejhg.2015.244