Table 2

Accuracy of allele frequency estimation for DNA pools.

Correction methoda

Allele frequency difference

(Pools - Individual samples)

Absolute valuesb

% of SNPs with over-estimated allele frequencyc



Sample group

Mean difference

SD

Mean difference

SD


1

Case

0.0726

0.0414

0.0728

0.0411

99.1

2

Case

0.0725

0.0419

0.0725

0.0418

99.1

3

Case

0.0477

0.0435

0.0487

0.0423

94.3

4

Case

0.0690

0.0511

0.0740

0.0435

92.6

1

Control

0.0627

0.0467

0.0630

0.0463

99.1

2

Control

0.0625

0.0465

0.0626

0.0463

99.1

3

Control

0.0352

0.0512

0.0389

0.0484

85.7

4

Control

0.0591

0.0500

0.0637

0.0438

93.5

1

Case - Control

0.0099

0.0276

0.0246

0.0158

70.4

2

Case - Control

0.0100

0.0275

0.0247

0.0157

69.4

3

Case - Control

0.0125

0.0328

0.0298

0.0184

68.6

4

Case - Control

0.0099

0.0293

0.0253

0.0176

69.4


a Correction methods used include those based on (1) Hoogendoorn et al [6], (2) Meaburn et al [7], (3) Craig et al [8] plus Meaburn et al [7], and (4) no adjustment.

b Mean of the absolute values for the differences in allele frequencies between DNA pools and individual samples.

c In total, 108 SNPs were compared for allele frequency differences as estimated for DNA pools and individual DNA samples. However, only 105 SNPs were compared for the correction method (3) (Craig et al [8] plus Meaburn et al [7]) because 3 SNPs were filtered out.

Ho et al. BMC Genetics 2012 13:1   doi:10.1186/1471-2156-13-1

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