Table 2

Concordance with genotypes for NA07022 generated by the HapMap Project (release 24) and the highest quality Infinium assay subset of those genotypes, as well as genotyping on Illumina Infinium 1M assay. Discordances with reported HapMap Infinium genotypes were verified by Sanger sequencing (SOM).

Published concordance*Infinium 1MHapMap phase I and II SNPsHapMap Infinium subsetHapMap Infinium SNPs tested for accuracy by Sanger sequencing
NA07022Number reported1 M3.9 M143 KThese data correctThese data incorrectAffirmed (%)
Called (%)95.98%94.39%96.00%
Locus concordance (%)99.89%99.15%99.88%
HapMap genotype callsHomozygous reference99.96%99.34%99.96%18290%
Homozygous alternate99.81%98.14%99.84%281270%†

*Published concordance between Sanger sequencing and genotyping (34).

†Average false negative rate is <0.19.