Table 4

SNP 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 assay4


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


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.

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

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