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Table 4 SNP genotyping performance

From: Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance

gDNA Input (ng) Completed Genotypes1 % Completion Undeter. Genotypes % Undeter. No Amp. % No Amp. Concordant Genotypes % Concordance Discordant Genotypes % Discordance
1 ng gDNA or wgaDNA input into TaqMan® SNP genotype assay2,3
gDNA 2636 99.62 10 0.38 0 0 2636 100.00 0 0.00
1 25524 96.45 945 3.55 0 0 2546 99.76 68 0.24
10 2627 99.28 19 0.72 0 0 2627 100.00 0 0.00
25 2636 99.62 10 0.38 0 0 2635 99.96 1 0.04
50 2614 98.79 316 1.17 1 0.04 2614 100.00 0 0.00
100 2620 99.02 256 0.94 1 0.04 2620 100.00 0 0.00
200 2623 98.07 21 0.79 2 0.08 2622 99.96 1 0.04
4 ng gDNA or wgaDNA into TaqMan ® SNP genotype assay 4
gDNA 2634 99.55 12 0.45 0 0.00 2634 100.00 0 0.00
1 25894 97.85 555 2.08 2 0.08 2586 99.88 3 0.12
10 2628 99.32 17 0.64 1 0.04 2627 99.96 1 0.04
25 2629 99.36 14 0.53 3 0.11 2629 100.00 0 0.00
50 2621 99.06 235 0.87 2 0.08 2619 99.92 2 0.08
100 2619 98.98 205 0.76 77 0.26 2617 99.92 2 0.08
200 2635 99.4 10 0.38 1 0.04 2632 99.89 3 0.11
20 ng gDNA or wgaDNA into TaqMan ® SNP genotype assay
gDNA 2637 99.66 9 0.34 0 0 2637 100.00 0 0.00
1 25694 97.09 775 2.91 0 0 2566 99.88 3 0.12
10 2633 99.51 13 0.49 0 0 2633 100.00 0 0.00
25 2639 99.74 7 0.26 0 0 2638 99.96 1 0.04
50 2633 99.51 13 0.49 0 0 2632 99.96 1 0.04
100 2630 99.40 16 0.60 0 0 2629 99.96 1 0.04
200 2635 99.55 11 0.42 0 0 2632 99.89 3 0.11
  1. 1There were N = 27 samples gentoyped in duplicate at N = 49 SNPs for N = 2,646 attempted genotypes/sample. 21 versus 4 ng gDNA or wgaDNA input, SNP genotyping rates: completion, p = 0.0178; undetermined, p = 0.0022; no amplification, p = 0.0139; concordance, p = n.s. 31 versus 20 ng gDNA or wgaDNA input, SNP genotyping rates: completion, p = 0.0004; undetermined, p = 0.0008; no amplification, p = n.s.; concordance, p = n.s. 44 versus 20 ng gDNA or wgaDNA input, SNP genotyping rates: completion, p = n.s.; undetermined, p = n.s.; no amplification, p = 0.0002; concordance, p = n.s. 5gDNA versus wgaDNA produced from 1 ng gDNA input, SNP genotype completion rates, p < 0.0001. 6gDNA versus wgaDNA produced from 50 and 100 ng gDNA input, p ≤ 0.05. 7gDNA versus wgaDNA produced from 100 ng gDNA input, p = 0.02. 8wgaDNA produced from 1 ng versus gDNA and wgaDNA produced from 10, 50 and 100 ng of gDNA input, p ≤ 0.014.