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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).
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BMC Medical Genomics

ISSN: 1755-8794

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