Genetic dissection of canine hip dysplasia phenotypes and osteoarthritis reveals three novel loci

BMC Genomics

Table 2 Top SNPs from the GWAS on OA

Trait	Chr	Locus	Alleles	N per SNP	SNP(s)	P-value from FASTA, corrected with the inflation factor lambda (λ = 1.007)
OA status (binary; osteoarthritis present or not)	1	45,382,633 46,279,297 46,268,586 45,405,601 45,161,186 45,381,667 48,007,784 48,065,207	C/A A/G C/A G/A G/C G/A A/G A/G	655 650 654 652 655 655 655 655	BICF2P468585 BICF2P357728 BICF2P1037296 BICF2S23120955 BICF2S23248027 BICF2P392839 BICF2S23216908 BICF2S2305568	2.86 × 10–7 8.93 × 10–7 2.39 × 10–6 4.48 × 10–6 5.62 × 10–6 7.05 × 10–6 7.81 × 10–6 7.81 × 10–6
	9	36,579,921	A/G	655	BICF2G630837240	4.69 × 10–6
	25	10,301,514	A/C	652	BICF2G630468961	6.22 × 10–6

SNPs with P-values < 1.0 × 10–5 are listed. The SNPs and their corresponding P-values are in bold font if the P-value passed the threshold for genome-wide significance (1.82 × 10–6) determined with the estimated number of independent tests from SimpleM (see methods). N refers to the number dogs in analysis after exclusion of dogs by FASTA because they lack either the phenotype or a covariate. Covariates for the OA status: age at radiographing, genetic cluster, genotyping batch and birth month. See also Additional file 1

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