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;

Zhang et al. BMC Genetics 2011 12:39   doi:10.1186/1471-2156-12-39

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