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Table 3 Correlations between predicted and observed body mass index for all genotype masking rates and family layouts

From: Effect of genotype imputation on genome-enabled prediction of complex traits: an empirical study with mice data

90% genotype masking rate
Model* Across families Within families
1809 1809ia 201 1809 1809ia 201
BL 0.227 0.193 0.191 0.199 0.164 −0.047
RKHS 0.238 0.195 0.199 0.208 0.132 −0.054
BRANN 0.112 0.092 0.147 0.163 0.041 0.054
75% genotype masking rate
Model* Across families Within families
1809 1809ib 453 1809 1809ib 453
BL 0.228 0.219 0.199 0.200 0.196 0.184
RKHS 0.238 0.226 0.211 0.208 0.204 0.200
BRANN 0.118 0.115 0.145 0.172 0.154 0.170
50% genotype masking rate
Model* Across families Within families
1809 1809ic 905 1809 1809ic 905
BL 0.227 0.231 0.225 0.199 0.197 0.189
RKHS 0.238 0.238 0.236 0.207 0.206 0.202
BRANN 0.118 0.131 0.149 0.172 0.168 0.149
  1. aImputed from 201 SNPs.
  2. bImputed from 453 SNPs.
  3. cImputed from 905 SNPs.
  4. *BL: Bayesian LASSO; RKHS: Reproducing Kernel Hilbert Spaces (RKHS) and; BRANN: Bayesian Regularized Neural Networks.