To train our machine learning model, we used seven well-established PD-associated genes from the PD GWAS (GBA1, LRRK2, SNCA, GCH1, MAPT, TMEM175 and VPS13C) as positive labels, and the remaining genes from the same loci (n = 205) were used as negative labels (i.e. genes that are unlikely to be involved in PD). Here, GCH1 is linked to Parkinson disease.