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. 2012 Jul 31;44(1):25. doi: 10.1186/1297-9686-44-25

Table 4.

Accuracy and costs of imputation for different genotyping scenarios

Scenario
 Genotyping strategy1
 Cost: $
 Imputation accuracy: R-squared
Other
 Grandparents
 Parents
 Testing individuals
  
  
    MGS + PGS MGD + PGD Sire Dam        
CostA
 H
 H
 0
 H
 0
 L384
 −2
 .888
 
 H
 H
 L384
 H
 L384
 L384
 20.58
 .935
 
 H
 H
 L3k
 H
 L3k
 L384
 24.74
 .955
 
 H
 H
 L6k
 H
 L6k
 L384
 26.28
 .956
 
 H
 H
 H
 H
 H
 L384
 34.84
 .967
 
 H
 H
 0
 H
 0
 L3k
 −2
 .968
 
 H
 H
 L384
 H
 L384
 L3k
 −2
 .980
 
 H
 H
 L3k
 H
 L3k
 L3k
 35.58
 .985
 
 H
 H
 L6k
 H
 L6k
 L3k
 41.28
 .988
 
 H
 H
 H
 H
 H
 L3k
 49.84
 .990
 
 H
 H
 0
 H
 0
 L6k
 −2
 .981
 
 H
 H
 L384
 H
 L384
 L6k
 −2
 .987
 
 H
 H
 L3k
 H
 L3k
 L6k
 −2
 .991
 
 H
 H
 L6k
 H
 L6k
 L6k
 48.58
 .991
 
 H
 H
 H
 H
 H
 L6k
 62.84
 .996
  H H H H H H 120.00 1.000

1Animals were split into groups (ordered by generation) of testing individuals, their parents, and their grandparents; grandparents were further divided into two groups: MGS + PGS which included maternal grandsire and paternal grandsire, and MGD + PGD which included maternal granddam and paternal granddam; the remaining individuals were placed in the “Other” category; gGroups of animals were genotyped with high density (H), L384, L3k, L6k panels or not genotyped (0); 2Represents a scenario that would require the dam of the candidate to be re-genotyped at a lower-density than it would have been originally genotyped when it was itself a selection candidate and this would not occur in practice.