A. Gaedigk, E. Repnikova, L. Cooley, J. S. Leeder; Children's Mercy Hospital, Kansas City, MO

BACKGROUND: The CYP2D6 gene is associated with multiple copy number variation (CNV) events some of which involve the highly similar CYP2D7 gene. This study aimed to characterize loss or gain CNVs in the Chr 22q13.1 region discovered by clinical-grade microarray-based genomic profiling using established methods.
METHODS: The CytoScan® HD Array (Affymetrix) includes over 2.6 million markers to detect 25-50 kb copy number changes and absence of heterozygosity across the genome. We identified 18 cases with gains/losses affecting Chr 22q13.1 for which DNA was available for CYP2D6 genotype analysis and CNV determination using quantitative multiplex PCR probing 4 CYP2D6 regions and 2 regions each of CYP2D7 and CYP2D8. Deletions and duplications were further examined by XL-PCR.
RESULTS: Losses (n=14) ranged from 661 bp to 8.9 Mbp. 12 subjects produced a 2.9 kb XL-PCR indicative of the CYP2D6*5 gene deletion; one subject with 0 or 1 copy per CytoScan was homozygous for *5. Two subjects did not amplify CYP2D6*5-specific 2.9 or 5 kb XL-PCR products and had inconsistent CNV calls with quantitative PCR suggesting the presence of a hybrid gene. Finally, one subject with a large 0.59 Mbp loss had the *5 allele, but also carried a *68+*4 tandem. Gains (n=4) ranged from 3.3 kb to 210 kb. CYP2D6*1x2 and *2x2 duplications were found in 2 subjects with 3.3 kb and 3.8 kb gains and a *36+*10 tandem in a subject with a 1.4 kb gain. Unexpectedly, the subject with the largest gain was negative for duplication, hybrid or tandem events, but revealed a *5 gene deletion.
CONCLUSION: Large structural variants can affect the human CYP2D locus. Microarray-based gain and loss CNVs do not necessarily correlate with known CYP2D6 gene deletion and duplication events and need to be further characterized for accurate CNV assignments.