Genome wide association of sarcoid tumors in horses

Equine sarcoid, the most common tumor of horses and donkeys, is caused by Bovine Papilloma Virus (BPV) or closely related equine variants of BPV (EPV).  While sarcoids are usually non-malignant, their location around eyes, ears, girth or anus can interfere with use of and quality of life for affected horses.  Prior studies indicated an association with the equine Major Histocompatibility Complex (MHC) and sarcoid tumors, but did not assess other contributing loci. DNA from 59 horses affected with sarcoid and 118 controls were genotyped using the EquineSNP50 platform.  Control samples were obtained from other genotyping projects, and were therefore of unknown disease status.  However, as sarcoid tumors are fairly rare, few controls are likely to be miscategorized.  Controls were matched to cases (of unknown breed) by IBS, and SNPs filtered to remove those genotyping inconsistently between batches (genotyping performed at GeneSeek Inc, Lincoln, NE, Illumina Inc., San Diego CA, and the Genotyping Shared Resource at the Mayo Clinic, Rochester, MN). Allelic analysis using PLINK V1.07 (Purcell, 2007) revealed several candidate loci including 2 hits on ECA20 in the MHC as well as loci on ECA22, ECA1, and ECA4 (permuted p-value = 1.3e-05 to 1.1 e-04).  Genomic inflation was limited to a factor of 1.13, indicating adequate control of stratification due to batch or breed.  Ongoing work will include utilization of the GenSel platform to evaluate polygenic models (http://bigs.ansci.iastate.edu) and fine-mapping of regions of interest.