Table 6

SNP genotypes from NTC samples

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 assay1


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 assay1


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


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).

Bergen et al. BMC Biotechnology 2005 5:24   doi:10.1186/1472-6750-5-24

Open Data