Allele Specific Copy Number Example
The Somatic WGS CNV Caller can report the total tumor copy number by estimating tumor purity. The BAF estimations from matched normal SNVs or population SNPs allow for allele specific copy number calling.
The following table provides examples for a DUP in a reference diploid region.
|
Total Copy Number |
Minor Copy Number |
ASCN Scenario |
|---|---|---|
|
4 |
2 |
2+2 |
|
4 |
1 |
3+1 |
|
[LOH] 4* |
0 |
4+0 |
*The entry represents a Loss of Heterozygosity (LOH) case. The total copy number is still considered a DUP, so the entry is annotated as GAINLOH to distinguish the value from Copy Neutral LOH (CNLOH), which would be annotated as 2+0.
