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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.