Expected versus observed mutation frequencies in microsatellite unstable tumorsa
| Locus or gene . | SMT . | Obs. hom. wt. freq. . | Obs. het. mut. freq. . | Obs. biallelic mut. freq. . | Exp. het. mut. freq.b . | Exp. biallelic mut. freq.b . | Binomal sumc . |
|---|---|---|---|---|---|---|---|
| Examples | 10% | 46% | 44% | ||||
| 25% | 50% | 25% | |||||
| 50% | 42% | 8% | |||||
| 75% | 22% | 2% | |||||
| 90% | 10% | 0.2% | |||||
| Published data | |||||||
| SMT 14 | (G)8 | 54% | 38% | 8% | 39% | 7% | >0.1 |
| SMT 4 | (A)8 | 71% | 25% | 4% | 27% | 3% | >0.1 |
| SMT 28 | (G)8 | 71% | 25% | 4% | 27% | 3% | >0.1 |
| SMT 10 | (A)8 | 75% | 25% | 0% | 23% | 2% | >0.1 |
| SMT 1 | (G)8 | 75% | 25% | 0% | 23% | 2% | >0.1 |
| SMT 25 | (G)8 | 79% | 17% | 4% | 20% | 1% | >0.1 |
| SMT 19 | (A)8 | 79% | 21% | 0% | 20% | 1% | >0.1 |
| SMT 18 | (G)8 | 88% | 13% | 0% | 12% | 0.4% | >0.1 |
| SMT 26 | (A)8 | 88% | 13% | 0% | 12% | 0.4% | >0.1 |
| SMT 2 | (A)8 | 92% | 8% | 0% | 8% | 0.2% | >0.1 |
| SMT 3, 7, 17, 21, 22, 27 | (A)8 | 96% | 4% | 0% | 4% | 0.04% | N/A |
| SMT 24 | (A)8 | 96% | 0% | 4% | 4% | 0.04% | N/A |
| SMT 5, 8, 9, 11, 12, 13, 20, 23 | (A)8 | 100% | 0% | 0% | 0% | 0% | N/A |
| BAX | |||||||
| SMT mutations | (G)8 | 43% | 29% | 29% | 45% | 12% | 0.009 |
| Current study | |||||||
| TGFBR2 | |||||||
| All mutations | 0%d | 7%e | 93%e | 29% | 68% | 0.004 | |
| SMT mutations | (A)10 | 0%d | 21% | 79% | 29% | 68% | 0.24 |
| ACVR2 | |||||||
| All mutations | 7% | 4% | 89% | 39% | 54% | 0.00001 | |
| SMT mutations | (A)8 x 2 | 7% | 7% | 86% | 39% | 54% | 0.0001 |
| Locus or gene . | SMT . | Obs. hom. wt. freq. . | Obs. het. mut. freq. . | Obs. biallelic mut. freq. . | Exp. het. mut. freq.b . | Exp. biallelic mut. freq.b . | Binomal sumc . |
|---|---|---|---|---|---|---|---|
| Examples | 10% | 46% | 44% | ||||
| 25% | 50% | 25% | |||||
| 50% | 42% | 8% | |||||
| 75% | 22% | 2% | |||||
| 90% | 10% | 0.2% | |||||
| Published data | |||||||
| SMT 14 | (G)8 | 54% | 38% | 8% | 39% | 7% | >0.1 |
| SMT 4 | (A)8 | 71% | 25% | 4% | 27% | 3% | >0.1 |
| SMT 28 | (G)8 | 71% | 25% | 4% | 27% | 3% | >0.1 |
| SMT 10 | (A)8 | 75% | 25% | 0% | 23% | 2% | >0.1 |
| SMT 1 | (G)8 | 75% | 25% | 0% | 23% | 2% | >0.1 |
| SMT 25 | (G)8 | 79% | 17% | 4% | 20% | 1% | >0.1 |
| SMT 19 | (A)8 | 79% | 21% | 0% | 20% | 1% | >0.1 |
| SMT 18 | (G)8 | 88% | 13% | 0% | 12% | 0.4% | >0.1 |
| SMT 26 | (A)8 | 88% | 13% | 0% | 12% | 0.4% | >0.1 |
| SMT 2 | (A)8 | 92% | 8% | 0% | 8% | 0.2% | >0.1 |
| SMT 3, 7, 17, 21, 22, 27 | (A)8 | 96% | 4% | 0% | 4% | 0.04% | N/A |
| SMT 24 | (A)8 | 96% | 0% | 4% | 4% | 0.04% | N/A |
| SMT 5, 8, 9, 11, 12, 13, 20, 23 | (A)8 | 100% | 0% | 0% | 0% | 0% | N/A |
| BAX | |||||||
| SMT mutations | (G)8 | 43% | 29% | 29% | 45% | 12% | 0.009 |
| Current study | |||||||
| TGFBR2 | |||||||
| All mutations | 0%d | 7%e | 93%e | 29% | 68% | 0.004 | |
| SMT mutations | (A)10 | 0%d | 21% | 79% | 29% | 68% | 0.24 |
| ACVR2 | |||||||
| All mutations | 7% | 4% | 89% | 39% | 54% | 0.00001 | |
| SMT mutations | (A)8 x 2 | 7% | 7% | 86% | 39% | 54% | 0.0001 |
Obs., observed; hom., homozygous; wt., wild type; freq., frequency; mut., mutation; het., heterozygous; SMT, short mononucleotide tracts.
Expected values are derived from the mathematical model on the assumption of the given hypothetical or observed wild-type frequencies.
The binomial sum is not reported for expected biallelic mutation frequencies of 0.
3% was imputed for calculation of expected frequencies, as described in the text. The binomial sum will be lower with higher imputed values and vice versa.
Assumption of biallelic mutations in Co53 and KM12.