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Table 1 OncoSNP tumor states

From: A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data

Tumor states
Tumor state Tumor copy number Allowable tumor-normal genotypes Description
1 0 (-, AA), (-, AB), (-, BB) Homozygous deletion
2 1 (A, AA), (A, AB), (B, AB), (B, BB) Hemizygous deletion
3 2 (AAAA, AA), (AAAB, AB), (ABBB, AB), (BBBB, BB) Normal
4 3 (AAA, AA), (AAB, AB), (ABB, AB), (BBB, BB) Single copy duplication
5 4 (AAAA, AA), (AAAB, AB), (ABBB, AB), (BBBB, BB) 4n monoallelic amplification
6 4 (AAAA, AA), (AABB, AB), (BBBB, BB) 4n balanced amplification
7 5 (AAAAA, AA), (AAAAB, AB), (ABBBB, AB), (BBBBB, BB) 5n monoallelic amplification
8 5 (AAAAA, AA), (AAABB, AB), (AABBB, AB), (BBBBB, BB) 5n unbalanced amplification
9 6 (AAAAAA, AA), (AAAAAB, AB), (ABBBBB, AB), (BBBBBB, BB) 6n unbalanced amplification
10 6 (AAAAAA, AA), (AAAABB, AB), (AABBBB, AB), (BBBBB, BB) 6n unbalanced amplification
11 6 (AAAAAA, AA), (AAABBB, AB), (BBBBB, BB) 6n unbalanced amplification
12 2 (AA, AA), (AA, AB), (BB, AB), (BB, BB) 2n somatic LOH
13 3 (AAA, AA), (AAA, AB), (BBB, AB), (BBB, BB) 3n somatic LOH
14 4 (AAAA, AA), (AAAA, AB), (BBBB, AB), (BBBB, BB) 4n somatic LOH
15 5 (AAAAA, AA), (AAAAA, AB), (BBBBB, AB), (BBBBB, BB) 5n somatic LOH
16 6 (AAAAAA, AA), (AAAAAA, AB), (BBBBBB, AB), (BBBBBB, BB) 6n somatic LOH
17 2 (AA, AA), (BB, BB) 2n germline LOH
18 2 (AAA, AA), (BBB, BB) 3n germline LOH
19 2 (AAAA, AA), (BBBB, BB) 4n germline LOH
20 2 (AAAAA, AA), (BBBBB, BB) 5n germline LOH
21 2 (AAAAAA, AA), (BBBBBB, BB) 6n germline LOH
  1. Description of the 21 tumor states showing corresponding copy numbers and genotypes. OncoSNP assigns a score of each SNP being in each of the twenty-one tumor states.