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Table 2 Results summary for 49 HapMap samples and 50 SNPs

From: Robust SNP genotyping by multiplex PCR and arrayed primer extension

Method Call rate Concordance with HapMap
Manual calling only 100% 99.92%1
MACGT (no cut-off) 100% 99.84%2
LDA (0 threshold) Total cases 100% (1,941 cases vs. 1,941) 99.89%3 (1,939 vs. 1,941)
LDA (0 threshold) Homozygous cases 100% (1,289 vs. 1,289) 100%4 (1,289 vs. 1,289)
LDA (0 threshold) Heterozygous cases 100% (652 vs. 652) 99.7%5 (650 vs. 652)
MACGT (0.001 cut-off) 94.04% 99.94%6
LDA (0.65 threshold) Total cases 99.18% (1,925 vs. 1,941) 99.90%3 (1,923 vs. 1,925)
LDA (0.65 threshold) Homozygous cases 98.91%7 (1,275 vs. 1,289) 100% (1,275 vs. 1,275)
LDA (0.65 threshold) Heterozygous cases 99.7% (650 vs. 652) 99.7% (648 vs. 650)
  1. 1 Two discrepancies amongst 2,450 genotype cases.
  2. 2 Three discrepancies amongst 1,926 genotype cases (524 cases used in training set).
  3. 3 Two discrepancies amongst 1,941 genotype cases (509 cases used in training set).
  4. 4 No discrepancy amongst 1289 cases (327 cases used in training set)
  5. 5 Two discrepancies amongst 652 cases (182 cases used in training set)
  6. 6 One discrepancy amongst 1,926 genotype cases (524 cases used in training set).
  7. 7 Eleven predictions (all TT and correct) with confidence score less than 0.65 for a single SNP (rs1891403).