Visual inspection of mapped reads from exome sequencing and examination of publicly-available data showed that the CNV showing the strongest association with asthma, overlapping the HLA-DQA1 and HLA-DQB1 genes, was likely to be an artefact of under-mapping of reads from reference-divergent HLA haplotypes, and that the duplications affecting the CHROMR/PRKRA and FBRSL1 genes were both likely to be artefacts of the polymorphic presence/absence of processed pseudogenes within the HLA region. Here, HLA-DQA1 is linked to asthma.