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Table 4 Accuracy and costs of imputation for different genotyping scenarios

From: Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost

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

  1. 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.
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Genetics Selection Evolution

ISSN: 1297-9686