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. 2013 Dec 4;8(12):e80642. doi: 10.1371/journal.pone.0080642

Table 1. Summary of results for the genome-wide association study using a mixed linear model and a sex-stratified case-control analysis for canine congenital sensorineural deafness in Dalmatian dogs.

Trait Position Position SNP-ID Minor allele MAF MAFa MAFu VE OR CI-L CI-U -log10P Candidate gene Distance to the nearest candidate gene in Mb
CFA CanFam3.1 CanFam2.0
Deafness in brown eyed dogs
2 13,786,700 16,675,682 BICF2P176848 T 0.08 0.19 0.03 0.14 7.76 3.48 17.30 6.15 ARHGAP12 1.19 (-)
6 45,474,835 48,537,551 TIGRP2P83893_RS8732055 A 0.49 0.69 0.42 0.12 3.13 1.96 5.00 5.09 COL11A1 1.95 (−)
6 68,927,940 71,986,567 BICF2P590845 A 0.14 0.15 0.13 0.13 1.30 0.71 2.33 5.68 GIPC2 0.06 (+)
14 39,561,348 42,518,712 BICF2G630529431 T 0.17 0.13 0.18 0.13 1.41 0.77 2.56 5.85 DFNA5 1.29 (+)
HOXA1 0.71 (−)
27 9,400,352 12,412,335 BICF2S23410492 C 0.05 0.17 0.02 0.11 10.70 3.87 29.6 5.80 TWF1 0.88 (−)
29 23,903,462 26,901,967 BICF2G630625485 T 0.20 0.23 0.20 0.12 1.18 0.72 1.96 5.26 GDAP1 1.07 (+)
Deafness in blue eyed dogs
17 28,929,911 32,032,913 BICF2G630212376 A 0.11 0.17 0.08 0.17 2.20 0.78 6.25 5.41 CRIM1 intragenic
18 51,795,260 54,820,227 BICF2P28982 G 0.16 0.24 0.15 0.15 1.73 0.75 4.01 5.08 CDC42EP2 0.06 (−)
27 25,549,421 28,568,843 BICF2P507470 T 0.11 0.35 0.07 0.15 7.85 3.40 18.1 5.32 AEBP2 2.11 (−)
31 30,836,962 32,955,387 BICF2G630740465 G 0.20 0.44 0.16 0.26 4.18 1.94 8.98 8.13 CLDN14 0.84 (−)

The SNP-ID, the position on dog chromosome (CFA) in base pairs (bp) according to CanFam3.1 and CanFam2.0, minor allele, minor allele frequency (MAF) for all, affected (MAFa) and unaffected (MAFu) dogs (controls), variance explained by the respective SNP (VE) and -log10P-values (-log10P) from the mixed linear model analysis and positional candidate genes with their distance to the CCSD-associated SNP are given. SNPs downstream of the nearest candidate gene are marked with a plus sign (+) and SNPs upstream of the nearest candidate gene are marked with a minus sign (−). Odds ratios (OR) are from a case-control study stratified by sex with 95% confidence intervals (CI).