frequencies given in the BeadStudio Manual), and Ns is the number of hidden states. Table 2.Hidden states, associated copy numbers and biological interpretationHidden state, zCopy number, c(z)Number of genotypes, K(z)Description100Full deletion211Single copy deletion323Normal (heterozygote)422Normal (homozygote)534Single copy duplication645Double copy duplicationWe associate each hidden state z with a given copy number c(z) and genotype number K(z). For each copy number there can be a number of genotypes, for example, for copy number 3 there can be one of four genotypes {AAA, AAB, ABB, BBB}. The genotype number gives the number of components in the mixture distribution of B allele frequencies for that state. We have split the diploid (copy number 2) into heterozygous and homozygous sub-states {3,4} to take into account naturally occurring regions of homozygosity without allelic loss.
