Table 2.
Hidden states, associated copy numbers and biological interpretation
| Hidden state, z | Copy number, c(z) | Number of genotypes, K(z) | Description |
|---|---|---|---|
| 1 | 0 | 0 | Full deletion |
| 2 | 1 | 1 | Single copy deletion |
| 3 | 2 | 3 | Normal (heterozygote) |
| 4 | 2 | 2 | Normal (homozygote) |
| 5 | 3 | 4 | Single copy duplication |
| 6 | 4 | 5 | Double copy duplication |
We 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.