Fine-Mapping of Loci Contributing to Sarcoid Tumor Developments in Horses

Equine sarcoid, the most common tumor of domestic equids, is caused by Bovine Papilloma Virus (BPV) or closely related equine variants.  While sarcoids are usually non-malignant, their location around eyes, ears or the girth area can interfere with usefulness of the horses.  Prior studies indicate a genetic association with the equine Major Histocompatibility Complex (MHC), but few have assessed other contributing loci.

Previous allelic analysis using PLINK V1.07 (Purcell, 2007) revealed several candidate loci including two hits on ECA20 in the MHC as well as loci on ECA22, ECA1, and ECA4 (P = 1.375e-5 to 9.61e-5) for GWA.  Two fine-mapping panels were developed to investigate the candidate loci in genome-wide and MHC regions.  DNA from 54 cases and 87 controls for genome-wide identified regions and DNA from 39 cases and 48 controls for MHC were genotyped using the Sequenom MassARRAY® at the Cornell University Core Laboratories Center (Ithaca, NY) and the Genotyping Shared Resource at the Mayo Clinic (Rochester, MN). SNPs with low genotyping rates and MAF<.05 were removed for quality control.

Bayesian analysis of the GWA data using the GenSel platform (http://bigs.ansci.iastate.edu) verified candidate loci on ECA20 and ECA22 identified in the prior allelic analysis.  Allelic analysis using PLINK V1.07 of SNP markers from our two custom genotyping panels identified two highly significant loci on ECA22 and two significant loci on ECA20 (P=2.14e-6, 7.34e-6, 1.12e-4, and 4.64e-6).  Future work will include sequencing of candidate genes within identified regions.