Table 2.
The mean, standard deviation, and range of five genomic features derived from whole-exome sequencing testing for their differences between tissue type and by MUTYH or NTHL1 case or non-hereditary status. Statistically significant p-values are highlighted in bold.
| Biallelic MUTYH cases | Biallelic NTHL1 cases | Proficient Controls | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Adenom a biallelic MUTYH (n=9, 10.7%) | CRC biallelic MUTYH (n=13, 15.5%)1 | t-test (p-value)2 | Effect Size (Cohen’s d) | Adenoma biallelic NTHL1 (n=7, 8.3%) | CRC biallelic NTHL1 (n=2, 2.4%) | t-test (p-value)2 | Effect Size (Cohen’s d) | Adenoma proficient control (n=27, 32.1%) | CRC proficient control (n=26, 31.0%) | t-test (p-value)2 | Effect Size (Cohen’s d) | Total (n=84, 100%) | |
| SBS18+SBS36 | 0.37 | −0.4 | 0.30 | 0.5 | 0.53 | 0.2 | |||||||
| Mean | 65.6% | 76.2% | 1.0% | 0.4% | 7.6% | 6.5% | 23.4% | ||||||
| SD | 29.6% | 20.5% | 1.4% | 0.0% | 7.0% | 5.5% | 32.0% | ||||||
| Range | 6.6% – 91.3% | 19.8% – 94.2% | 0% – 3.2% | 0.4% – 0.4% | 0% – 25.4% | 0% – 19.5% | 0% – 94.2% | ||||||
| SBS30 | 0.38 | 0.4 | 0.31 | −0.5 | 0.14 | −0.4 | |||||||
| Mean | 6.0% | 2.0% | 74.5% | 78.8% | 2.8% | 5.4% | 11.6% | ||||||
| SD | 12.3% | 6.0% | 9.4% | 2.4% | 3.6% | 8.0% | 23.4% | ||||||
| Range | 0% – 32.4% | 0% – 21.4% | 55% – 82.3% | 77.1% – 80.5% | 0% – 13.6% | 0% – 33.2% | 0% – 82.3% | ||||||
| TMB | 0.12 | −0.8 | 0.87 | −0.1 | 7.4×10 −5 | −1.2 | |||||||
| Mean | 4.8 | 7.5 | 7.1 | 7.5 | 1.5 | 2.8 | 3.8 | ||||||
| SD | 4.3 | 2.9 | 4.2 | 2.0 | 0.9 | 1.3 | 3.3 | ||||||
| Range | 0.3 – 12.7 | 3.5 – 13.3 | 2.5 – 14.8 | 6.1 – 8.8 | 0.3 – 4.1 | 1.4 – 5.9 | 0.3 – 14.8 | ||||||
| INDEL count | 0.02 | −1.1 | 0.95 | 0.0 | 2.3×10 −3 | −0.9 | |||||||
| Mean | 4.4 | 9.7 | 10.7 | 10.5 | 7.1 | 11.3 | 8.9 | ||||||
| SD | 4.9 | 4.6 | 9.3 | 0.7 | 4.2 | 5.4 | 5.6 | ||||||
| Range | 1 – 17 | 2 – 16 | 2 – 25 | 10 – 11 | 1 – 17 | 3 – 20 | 1 – 25 | ||||||
| SNV count | 0.13 | −0.7 | 0.87 | −0.1 | 9.8×10 −5 | −1.2 | |||||||
| Mean | 318.6 | 494.3 | 466.9 | 491.0 | 91.1 | 178.1 | 245.6 | ||||||
| SD | 285.4 | 197.5 | 274.5 | 132.9 | 56.8 | 86.9 | 217.9 | ||||||
| Range | 19 – 851 | 231 – 895 | 168 – 974 | 397 – 585 | 16 – 262 | 84 – 381 | 16 – 974 | ||||||
Abbreviations: CRC, colorectal cancer; SBS, single base substitution; SD, standard deviation; TMB, tumour mutation burden; INDEL, large insertion/deletion; SNV, single nucleotide variant.
1
MMR-proficient CRCs only from biallelic MUTYH cases were included.
2
two-tailed t-test.