Table 1. Top 25 ranked findings from analysis for presbycusis in Border Collies.a .
| SNP | A1/A2 | FreqCase | FreqControl | PEMMAX | PAllelic | PPerm | OR (95% CI) |
| Chr6.25819273 | C/A | 0.00 | 0.78 | 1.09E-13 | 6.42E-14 | 1.00E-06 | N/A |
| Chr6.26517587 | A/G | 0.83 | 0.14 | 1.64E-10 | 2.71E-11 | 1.00E-06 | 28.29 (9.35–85.57) |
| Chr6.24591869 | T/C | 0.10 | 0.77 | 4.46E-10 | 1.09E-10 | 2.00E-06 | 0.034 (0.01–0.11) |
| Chr6.24577002 | C/T | 0.89 | 0.20 | 5.68E-10 | 2.91E-11 | 1.00E-06 | 34.77 (10.18–118.7) |
| Chr6.25174415 | C/G | 0.10 | 0.78 | 1.07E-09 | 8.06E-11 | 2.00E-06 | 0.03 (0.01–0.11) |
| Chr6.28753894 | A/G | 0.78 | 0.13 | 1.78E-09 | 1.36E-10 | 3.00E-06 | 24.11 (8.15–71.38) |
| Chr6.25181733 | G/A | 0.89 | 0.21 | 2.03E-09 | 9.38E-11 | 2.00E-06 | 31.17 (9.23–105.20) |
| Chr6.22844453 | G/A | 0.80 | 0.19 | 5.21E-09 | 3.07E-09 | 2.60E-05 | 17.6 (6.25–49.56) |
| Chr6.29363433 | T/G | 0.78 | 0.15 | 9.45E-09 | 1.07E-09 | 6.00E-06 | 19.81 (6.89–56.92) |
| Chr6.24570819 | T/G | 0.10 | 0.75 | 1.07E-08 | 3.28E-10 | 4.00E-06 | 0.037 (0.01–0.12) |
| Chr6.21475826 | C/T | 0.80 | 0.23 | 1.83E-08 | 3.87E-08 | 4.20E-04 | 13.23 (4.90–35.7) |
| Chr8.62484232 | T/G | 0.00 | 0.37 | 3.75E-08 | 1.44E-05 | 1.70E-01 | N/A |
| Chr6.25913101 | C/T | 0.00 | 0.61 | 4.14E-08 | 8.67E-10 | 5.00E-06 | N/A |
| Chr6.29470484 | T/C | 0.76 | 0.15 | 5.20E-08 | 3.15E-09 | 2.60E-05 | 18.53 (6.42–53.46) |
| Chr6.35491820 | G/C | 0.50 | 0.04 | 1.00E-07 | 2.68E-07 | 2.82E-03 | 25.00 (5.34–117.00) |
| Chr6.23160353 | C/A | 0.53 | 0.05 | 1.95E-07 | 1.45E-07 | 1.57E-03 | 19.53 (5.23–72.98) |
| Chr6.23166082 | G/A | 0.53 | 0.05 | 1.95E-07 | 1.45E-07 | 1.57E-03 | 19.53 (5.23–72.98) |
| Chr6.25900591 | G/A | 0.00 | 0.54 | 2.21E-07 | 2.37E-08 | 2.21E-04 | N/A |
| Chr6.26959216 | C/A | 0.03 | 0.61 | 2.40E-07 | 5.15E-09 | 3.60E-05 | 0.02 (0.002–0.13) |
| Chr6.34915222 | G/A | 0.63 | 0.14 | 3.21E-07 | 9.41E-07 | 1.18E-02 | 10.00 (3.74–26.77) |
| Chr6.23177930 | C/T | 0.53 | 0.06 | 3.48E-07 | 2.46E-07 | 2.57E-03 | 18.79 (5.02–70.3) |
| Chr6.26917473 | C/A | 0.03 | 0.59 | 3.67E-07 | 1.20E-08 | 9.50E-05 | 0.02 (0.002–0.14) |
| Chr6.24104844 | A/G | 0.08 | 0.66 | 3.76E-07 | 9.54E-09 | 7.30E-05 | 0.04 (0.01–0.15) |
| Chr6.34819558 | A/T | 0.03 | 0.38 | 8.32E-07 | 5.76E-05 | 5.31E-01 | 0.04 (0.005–0.33) |
| Chr6.22861769 | T/A | 0.50 | 0.05 | 1.58E-06 | 4.37E-07 | 4.99E-03 | 17.67 (4.73–66) |
a
SNP: marker name (location information); A1: risk allele; A2: reference allele; FreqCase: allele frequency of A1 in cases; FreqControl: allele frequency of A1 in controls; PEMMAX: p-values from EMMAX primary GWAS; PAllelic: p-values from allelic association analysis; PPerm: genome-wide (EMP2) permuted p-values from PLINK; OR (95% CI): odds ratio with 95% confidence interval as calculated with logistic regression.
All top 25 hits from the EMMAX analysis reached statistical significance at the Bonferroni-corrected level, and all but one are on CFA6. All top 25 findings also reached genome-wide significance after empirical significance testing with permutation. Odds ratios calculated in PLINK demonstrate strong effects for all top hits.