Empirical evaluations of analytical issues arising from predicting HLA alleles using multiple SNPs

BMC Genomic Data

Table 4 Kappa coefficients of observed or imputed SNP genotypes between genotyping platforms using the WTCCC cohort data

Platform Pair	O-O^*	O-I⁺	I-O	I-I	Overall^#
Affy 500K & Affy 6.0	0.9969	0.9901	0.9860	0.9978	0.9968
Illumina 550K & Illumina 1.2M	0.9996	0.9945	0.9943	0.9988	0.9977
Affy 6.0 & Illumina 1.2M	0.9970	0.9947	0.9913	0.9976	0.9955
Affy 500K & Illumina 550K	0.9976	0.9942	0.9847	0.9959	0.9942
Affy 500K & Illumina 1.2M	0.9962	0.9956	0.9876	0.9954	0.9931
Illumina 550K & Affy 6.0	0.9979	0.9897	0.9934	0.9978	0.9962

* O stands for observed genotypes of HapMap SNPs;
+ I stands for imputed genotypes using IMPUTE v2 with HapMap reference panel of Caucasian, African and Asian.
# Overall stands for observed/imputed genotypes of HapMap SNPs;

ISSN: 2730-6844