Allele Specific Copy Number Example
By estimating tumor purity, the total tumor copy number can be reported. The BAF estimates, whether from matched normal SNVs or population SNPs, allows 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 |
|
4 |
0 |
4+0 |
The last entry is a loss of heterozygosity (LOH) case. The total copy number is still considered a DUP, so this is annotated as GAINLOH to distinguish it from copy neutral LOH CNLOH, which would be 2+0.