Figure 1

(a-c) Refining mechanism for homozygous major SNPs: when the first sibling is homozygous major (a), homozygous minor (b), or heterozygous (c) at a given SNP, this constrains the possible parental genotypes; in the first case, five of nine parental genotypic combinations can be eliminated (crossed boxes). Using HapMap CEPH SNP population frequencies, p and q, the probability frequencies are populated for the remaining squares, and normalized. The probability that subsequent sibs will be homozygous major, heterzygous, or homozygous minor can then be calculated using the probabilities that parents would contribute specific allelic values. (d) For each of 30 HapMap CEPH trios, the Sib₁ genotype and the SNP population frequencies are used (without the parent genotypes) to infer p('AA'), p('Aa'), and p('aa') for subsequent siblings. Those probabilities are then validated against those that would be expected given only the parental genotypes at each SNP.