Table III.
Analysis results for testing rare variant effects on ALT and AST using univariate SKAT, TATES and MAASS for rare variants with different filtering options.
| GPT | PCDHGB1 | ZNF620 | ||||
|---|---|---|---|---|---|---|
| MAF ≤1% | MAC ≥2 | Discovery for 13,317 genes (cut off : 3.75E-06) | # of SNPs | 3 | 3 | 4 |
| ALT | 5.51E-03 | 3.17E-02 | 3.52E-01 | |||
| AST | 4.70E-01 | 8.32E-05 | 3.98E-06 | |||
| TATES | 8.88E-03 | 1.34E-04 | 6.42E-06 | |||
| Homo-M | 7.59E-01 | 1.77E-04 | 8.02E-05 | |||
| Hetero-M | 2.84E-06 | 4.90E-04 | 9.80E-08 | |||
| replication | # of SNPs | 2 | 14 | - | ||
| Homo-M | 1.00E+00 | 9.47E-01 | - | |||
| Hetero-M | 9.96E-01 | 7.97E-01 | - | |||
| MAC ≥3 | Discovery for 11,348 genes (cut off : 4.41E-06) | # of SNPs | - | 2 | 4 | |
| ALT | - | 3.30E-02 | 3.52E-01 | |||
| AST | - | 8.45E-05 | 3.98E-06 | |||
| TATES | - | 1.36E-04 | 6.42E-06 | |||
| Homo-M | - | 2.55E-04 | 8.02E-05 | |||
| Hetero-M | - | 5.99E-04 | 9.80E-08 | |||
| replication | # of SNPs | - | 14 | - | ||
| Homo-M | - | 9.47E-01 | - | |||
| Hetero-M | - | 7.97E-01 | - | |||
| MAC ≥4 | Discovery for 9,818 genes (cut off : 5.09E-06) | # of SNPs | - | 2 | - | |
| ALT | - | 3.30E-02 | - | |||
| AST | - | 8.45E-05 | - | |||
| TATES | - | 1.36E-04 | - | |||
| Homo-M | - | 2.55E-04 | - | |||
| Hetero-M | - | 5.99E-04 | - | |||
| replication | # of SNPs | - | 14 | - | ||
| Homo-M | - | 9.47E-01 | - | |||
| Hetero-M | - | 7.97E-01 | - | |||
| MAF ≤5% | MAC ≥2 | Discovery for 13,731 genes (cut off : 3.64E-06) | # of SNPs | 3 | 6 | 4 |
| ALT | 5.51E-03 | 1.44E-03 | 3.52E-01 | |||
| AST | 4.70E-01 | 3.62E-06 | 3.98E-06 | |||
| TATES | 8.88E-03 | 5.83E-06 | 6.42E-06 | |||
| Homo-M | 7.59E-01 | 4.00E-06 | 8.02E-05 | |||
| Hetero-M | 2.84E-06 | 2.06E-05 | 9.80E-08 | |||
| replication | # of SNPs | 2 | 25 | - | ||
| Homo-M | 1.00E+00 | 4.12E-01 | - | |||
| Hetero-M | 9.96E-01 | 9.50E-02 | - | |||
| MAC ≥3 | Discovery for 12,139 genes (cut off : 4.12E-06) | # of SNPs | - | 5 | 4 | |
| ALT | - | 1.48E-03 | 3.52E-01 | |||
| AST | - | 4.01E-06 | 3.98E-06 | |||
| TATES | - | 6.46E-06 | 6.42E-06 | |||
| Homo-M | - | 4.26E-06 | 8.02E-05 | |||
| Hetero-M | - | 1.77E-05 | 9.80E-08 | |||
| replication | # of SNPs | - | 25 | - | ||
| Homo-M | - | 4.12E-01 | - | |||
| Hetero-M | - | 9.50E-02 | - | |||
| MAC ≥4 | Discovery for 10,954 genes (cut off : 4.56E-06) | # of SNPs | - | 5 | - | |
| ALT | - | 1.48E-03 | - | |||
| AST | - | 4.01E-06 | - | |||
| TATES | - | 6.46E-06 | - | |||
| Homo-M | - | 4.26E-06 | - | |||
| Hetero-M | - | 1.77E-05 | - | |||
| replication | # of SNPs | - | 25 | - | ||
| Homo-M | - | 4.12E-01 | - | |||
| Hetero-M | - | 9.50E-02 | - | |||
Five genes had at least one significant result using the four methods at the Bonferroni significance level. The significant results are shown in bold for each Bonferroni cutoff.