An overview of the variants reduction procedure is illustrated in Figure 1. We first performed a gene-based annotation of all ∼4.7 million variants, and identified a total of 24 617 exonic SNVs or indels. Given that Miller syndrome is a rare Mendelian disease, in line with the Ng et al. study (3), we next focused on 11 166 exonic protein-changing variants only, and identified a subset of 4860 variants falling in highly conserved genomic regions. We note that both causal mutations for Miller syndrome sit in highly conserved regions, with normalized score of 505 and 445, respectively (the normalized scores for all types of annotations range from 0–1000 in UCSC Genome Browser). One of the mutations was predicted as ‘benign’ by PolyPhen in the Ng et al. study and would have been missed, had Ng et al. utilized PolyPhen predictions in their filtering procedure (3). We confirmed that it was predicted as benign by SIFT as well (SIFT score = 0.18). We next filtered the variants from the 1000 Genomes project and dbSNP version 130, assuming that variants observed in
