Table 4 Definitions of hidden states in ADTEx zygosity detection HMM
From: Inferring copy number and genotype in tumour exome data
State | Copy | Copy number alteration status | Genotype | BAF | Zygosity |
|---|---|---|---|---|---|
1 | 0/1 | Deletion | A,B | 0,1 | LOH |
2 | 2 | Copy neutral with LOH | AA,BB | 0,1 | LOH |
3 | 2 | Normal | AB | 0.5 | HET |
4 | 3 | Three copies with LOH | AAA,BBB | 0,1 | LOH |
5 | 3 | Three copies with duplication of one allele | AAB, ABB | 0.33,0.67 | ASCNA |
6 | 4 | Four copies with LOH | AAAA,BBBB | 0,1 | LOH |
7 | 4 | Four copies with duplication of both alleles | AABB | 0.5 | HET |
8 | 4 | Four copies with duplication of one allele | AAAB,ABBB | 0.25,0.75 | ASCNA |
9 | 5 | Five copies with LOH | AAAAA,BBBBB | 0,1 | LOH |
10 | 5 | Five copies with duplication of one allele | AAAAB,ABBBB | 0.2,0.8 | ASCNA |
11 | 5 | Five copies with duplication of both alleles | AAABB,AABBB | 0.4,0.6 | ASCNA |
12 | 6 | Six copies with LOH | AAAAAA,BBBBBB | 0,1 | LOH |
13 | 6 | Six copies with duplication in one allele | AAAAAB,ABBBBB | 0.17,0.83 | ASCNA |
14 | 6 | Six copies with duplication in both alleles | AAABBB | 0.5 | HET |
15 | 6 | Six copies with duplication in both alleles | AAAABB,AABBBB | 0.33,0.67 | ASCNA |