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Table 6 SNP genotypes from NTC samples

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

gDNA Input (ng) Allele 1 Allele 2 Both No Amp. Undeter. Total
1 ng gDNA or wgaDNA input into TaqMan® SNP genotype assay1
gDNA 0 2 0 385 5 392
13 27 29 2 315 19 392
10 6 12 1 362 11 392
25 6 10 0 364 12 392
503 38 49 5 266 34 392
1003 26 48 2 289 27 392
200 18 20 0 351 3 392
Total 121 1702 10 2332 111 2744
4 ng gDNA or wgaDNA input into TaqMan ® SNP genotype assay 1
gDNA 1 2 0 381 8 392
13 39 36 2 292 23 392
10 7 7 0 360 18 392
25 6 18 1 349 18 392
503 50 43 0 275 24 392
1003 26 43 2 274 47 392
200 26 38 3 316 9 392
Total 155 1872 8 2247 147 2744
20 ng gDNA or wgaDNA input into TaqMan ® SNP genotype assay 1
gDNA 0 1 0 383 8 392
13 29 37 2 297 27 392
10 11 15 1 346 19 392
25 8 9 0 364 11 392
503 37 54 4 263 34 392
1003 25 55 2 277 33 392
200 38 42 10 284 18 392
Total 148 2132 19 2214 150 2744
  1. 1A significant increase in the number of false positive and undetermined SNP genotypes is observed with increasing amounts of wgaDNA template: 11.0%, 12.8% and 13.8% for 1, 4 and 20 ng wgaDNA input, respectively, p = 0.045, 1 versus 4 ng wgaDNA input, and p = 0.0014, 1 versus 20 ng wgaDNA input, p = 0.0046 test for trend, 1 vs. 4 vs 20 ng wgaDNA input, for false positive genotypes; 4.0%, 5.34% and 5.47%, respectively, p = 0.026, 1 versus 4 ng, and p = 0.0159, 1 versus 20 ng, p = 0.0153 for trend, for undetermined genotypes. 2Significantly more allele 2 NTC TaqMan® SNP assay alleles were observed than allele 1 NTC TaqMan® assay alleles (p = 0.006, 0.091 and 0.001 for 1, 4 and 20 ng gDNA and wgaDNA input into the TaqMan® SNP assays, respectively), where the fluorescent label was 6-Fam for allele 1, and Vic for allele 2, in all the TaqMan® SNP assays in this study. 3The gDNA input strata of 1, 50 and 100 ng exhibited significantly greater numbers of false positive and undetermined SNP genotypes than did the gDNA input strata of 10, 25 and 200 ng (p < 0.0001).