Most copy number variations are neutral, but some are deleterious and associated 
with various human diseases. Copy number variations are distributed non-randomly 
in vertebrate genomes, and it was recently reported that ohnologs, which are 
duplicated genes derived from whole genome duplication, are refractory to copy 
number variations. However, it is unclear what genomic factors affect the 
deleterious effects of copy number variations and the biological significance of 
the biased genomic distribution of copy number variations remains poorly 
understood. Here we show that non-ohnologs neighbouring ohnologs are unlikely to 
have copy number variations, resulting in ohnolog-rich regions in vertebrate 
genomes being copy number variation deserts. Our results suggest that the 
genomic location of ohnologs is a determining factor in the retention of copy 
number variations and that the dosage-balanced ohnologs are likely to cause the 
deleterious effects of copy number variations in these regions. We propose that 
investigating copy number variation of genes in regions that are typically copy 
number variation deserts is an efficient means to find disease-related copy 
number variations.