Table 1 Results summary for 287 HapMap samples and 41 SNPs
From: Robust SNP genotyping by multiplex PCR and arrayed primer extension
Method | Call rate | Concordance with HapMap |
|---|---|---|
MACGT (0.001 cut-off) + manual calls | 98.90% (9% manual calls) | 99.94% |
LDA (0.75 threshold) Total cases | 94.91% (10,523 cases vs. 11,087) | 99.91% (10,514 vs. 10,523) |
LDA (0.75 threshold) Homozygous cases | 95.41% (6,883 vs. 7,214) | 99.96% (6,880 vs. 6,883) |
LDA (0.75 threshold) Heterozygous cases | 93.98% (3,640 vs. 3,873) | 99.84% (3,634 vs. 3,640) |