Genome-Wide Analyses for Osteosarcoma in Leonberger Dogs Reveal the CDKN2A/B Gene Locus as a Major Risk Locus

Abstract

Dogs represent a unique spontaneous cancer model. Osteosarcoma (OSA) is the most common primary bone tumor in dogs (OMIA 001441-9615), and strongly resembles human forms of OSA. Several large- to giant-sized dog breeds, including the Leonberger, have a greatly increased risk of developing OSA. We performed genome-wide association analysis with high-density imputed SNP genotype data from 273 Leonberger cases with a median age of 8.1 [3.1-13.5] years and 365 controls older than eight years. This analysis revealed significant associations at the CDKN2A/B gene locus on canine chromosome 11, mirroring previous findings in other dog breeds, such as the greyhound, that also show an elevated risk for OSA. Heritability (h²_SNP) was determined to be 20.6% (SE = 0.08; p-value = 5.7 × 10^-4) based on a breed prevalence of 20%. The 2563 SNPs across the genome accounted for nearly all the h²_SNP of OSA, with 2183 SNPs of small effect, 316 SNPs of moderate effect, and 64 SNPs of large effect. As with many other cancers it is likely that regulatory, non-coding variants underlie the increased risk for cancer development. Our findings confirm a complex genetic basis of OSA, moderate heritability, and the crucial role of the CDKN2A/B locus leading to strong cancer predisposition in dogs. It will ultimately be interesting to study and compare the known genetic loci associated with canine OSA in human OSA.

Keywords: CDKN2A/B; Leonberger; animal model; bone cancer; canis familiaris; osteosarcoma.

Figure 1

Distribution of age at death in 220 OSA-affected cases and 251 OSA-unaffected controls in Leonbergers.

Figure 2

(a) Manhattan plot of the GWAS results using 273 OSA-cases and 365 controls shows an OSA-associated locus in Leonbergers on dog chromosome (CFA) 11. The −log p-values for each SNP are plotted on the y-axis and the position on each chromosome on the x-axis. The red line represents the Bonferroni-corrected significance threshold (−log(p-value) = 6.79). Inset: Corrected QQ plot confirms that the observed p-values of the best-associated markers have stronger association with the trait than expected by chance (null hypothesis, red line). (b) Genomic context of the associated locus on CFA 11 showing the association region and the lead SNP (red bar and arrow), the previously described region and lead SNP in OSA-affected greyhounds (blue bar and arrow) [16], the previously described region and lead SNPs in histiocytic sarcoma-affected Bernese mountain dogs, flat-coated retrievers and Rottweilers (orange bar and arrows) [19], as well as the candidate genes CDKN2A/B.

Figure 3

Posterior estimates of the total proportion of the estimated genetic variance explained by each SNP. The 38 canine autosomes are plotted on the x-axis and the estimated proportion of the total genetic variance explained is presented on the y-axis. Each dot represents a single SNP or overlapping SNPs.