Table 1.

DNA variant discovery using resequencing arrays

NA11840NA12156NA12878NA18507NA1962538 cases
(i) Number of sample-specific variants214224228234180465
(ii) Variant calls in this study212220225224180453
Overlap of variant calls in i and ii210218221223176445
False negative rate (FNR), %
False discovery rate (FDR), %
Concordance to known variants, %97.998.497.797.796.494.7
  • We used multiarray clustering for base calling of each position with the R package mclust (26) and ranked the confidence of each base call using a position-specific quality score (cutoff 0.67) (16). This analysis focused on verified DNA variants with a minor allele frequency larger than 0.05 in five HapMap individuals (columns 2–5) and in a pool of 38 medical cases (column 6) that we confirmed through Sanger sequencing (16). The variant calls from this study (ii) were compared with all previously reported sample variants in each sample (i) to estimate this method's performance. Concordance is the percentage of all variant and reference base calls in each sample that agreed with previously known base calls.