Table 1

Mean error rates by imputation method and scenario

IMPUTE

MACH

PLINK

fastPHASE


Scenario 1: Imputation of untyped SNPs


Overall

0.112

0.114

0.142

0.135


By regiona

null1

0.251

0.251

0.284

0.271

null2

0.066

0.066

0.090

0.085

PADI4-1

0.083

0.092

0.131

0.111

PADI4-2

0.106

0.109

0.144

0.162

PTPN22-1

0.099

0.098

0.122

0.107

PTPN22-2

0.061

0.059

0.069

0.058


By max pairwise

r2 < 0.5

0.208

0.212

0.245

0.248

LD

r2 ≥ 0.5

0.030

0.030

0.053

0.038


Scenario 2: Imputation to combine two datasets

Overall

0.116

0.112

0.173

0.127

By regiona

null1

0.206

0.201

0.250

0.218

null2

0.123

0.122

0.175

0.139

PADI4

0.079

0.069

0.145

0.097

PTPN22

0.055

0.053

0.121

0.053

By max pairwise

r2 < 0.5

0.200

0.197

0.256

0.211

LD

r2 ≥ 0.5

0.046

0.041

0.105

0.059


aIn Scenario 1, for regions PADI4-1 and PTPN22-1, the most strongly associated SNP was removed and imputed, while for regions PADI4-2 and PTPN22-2, the two SNPs flanking the most strongly associated SNP were imputed, in addition to other SNPs as described in the methods.

Biernacka et al. BMC Proceedings 2009 3(Suppl 7):S5  

Open Data