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
|
- 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).