Risk of false positive genetic associations in complex traits with underlying population structure: a case study.

•Variants in PIK3C3, RIT2 and SYT4 uncovered in this study are not causative for equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy.•Inadequate sample size and underlying population structure may lead to false positive genome-wide associations.•40–50,000 single nucleotide polymorphisms may not be enough markers to perform genome-wide association studies of complex traits in the horse.