Assumption
CNV event is clonal — present in 100% of tumor cells.
Inputs
Tumor karyotype (A, AA, AAB, …) and observed minor allele fraction.
Output
Estimated tumor purity as a percentage, plus a MAF-vs-purity curve.
Normal background
Non-tumor cells are assumed diploid AB (MAF = 0.5).
Method
For a sample with tumor purity p, tumor karyotype with
a minor-allele copies out of t total copies,
and a diploid (AB) normal background, the observed MAF is:
MAF = (p·a + (1−p)·1) / (p·t + (1−p)·2)
Solving for p:
p = (1 − 2·MAF) / (MAF·(t − 2) + (1 − a))
| Karyotype | Minor copies (a) | Total copies (t) | Tumor MAF | Note |
|---|---|---|---|---|
| A | 0 | 1 | 0.000 | Hemizygous deletion |
| AA | 0 | 2 | 0.000 | Copy-neutral LOH |
| AB | 1 | 2 | 0.500 | Diploid — indeterminate |
| AAB | 1 | 3 | 0.333 | Copy Gain |
| AAA | 0 | 3 | 0.000 | Triploid, all major |
| AABB | 2 | 4 | 0.500 | Tetraploid balanced — indeterminate |
| AAAB | 1 | 4 | 0.250 | Tetraploid, 1 minor |
| AAAA | 0 | 4 | 0.000 | Tetraploid, all major |