Table 2.
The potential effects of CYP2D6 tumor LOH on Hardy Weinberg equilibrium
| Clinical subtype | HWE test: CYP2D6 *4 | HWE test: CYP2D6 *41 | |
|---|---|---|---|
| NGS-based calls | ER+ | 0.005 | 0.19 |
| NGS-based calls | ER- | 0.95 | 0.75 |
| NGS-based calls | All | 0.02 | 0.11 |
| *Germline allele <10% | ER+ | 7.2 x 10-4 | 0.16 |
| *Germline allele <10% | ER- | 0.78 | 0.75 |
| *Germline allele <10% | All | 3.2 x 10-4 | 0.09 |
| *Germline allele <20% | ER+ | 1.2 x 10-6 | 0.04 |
| *Germline allele <20% | ER- | 0.018 | 0.75 |
| *Germline allele <20% | All | 8.3 x 10-8 | 0.02 |
* Hardy Weinberg equilibrium calculation assuming a low-sensitivity genotyping assay would misclassify the low frequency allele as homozygous. CYPD6 = cytochrome P450 2D6; ER = estrogen receptor; HWE = Hardy Weinberg equilibrium; LOH = loss of heterozygosity; NGS = next generation sequencing.