Creating Allelic Transmission Scores

Abecasis, Cookson, and Cardon (2000) define a pair of orthogonal allelic transmission scores, and , the expected genotype and deviate, respectively, for each individual at each marker. To create these scores, the genotype in terms of allele must first be defined as for individual , where represents the number of alleles that the genotype comprises. For any founder , an individual whose parents are not observed, in the sample, these scores are defined as and . Otherwise, let and be the respective indices of the mother and father of individual . Then for any nonfounder, assuming scores for an individual’s ancestors are calculated before his or her own,

     

where , and then . These scores are calculated for all alleles at the markers specified in the VAR statement and are included in the OUTQ= data set.