Table 2 Summary of genotype imputation accuracy
SNP PanelOffspring Genotyping StrategyGenotypes Masked to Mimic LD SNP Panels in Offspring
High density (78 K)100% LD0.850.76
75% LD and 25% HD0.900.85
Medium density (25 K)100% LD0.760.62
75% LD and 25% MD0.850.75
  • The correlation between true genotypes and imputed genotypes is presented based on genotype data from the HD SNP platform (78 K) and the MD SNP platform (25 K), with either 90 or 99% of genotypes were masked in the offspring to mimic LD SNP platforms (Table 1). The proportion of offspring genotyped for the LD SNP platforms was either 100 or 75%.