Novel CYP2A7/CYP2A6 germline hybrids associated with mutation burden in lung cancer revealed by whole-genome long-read sequencing

Nicotine is metabolized to cotinine by CYP2A6. CYP2A6 genotypes are associated with variations in enzymatic activity and increase the risk of developing tobacco-related diseases, including lung cancer. The high sequence similarity between CYP2A6 and CYP2A7, combined with frequent duplications, deletions, and structural variants (SVs), such as hybrids, complicate the accurate determination of CYP2A7/CYP2A6 sequence. In this study, we investigated CYP2A6 SVs in 20 Japanese patients with solid cancers using long-read whole-genome sequencing (lrWGS) and short-read whole-genome sequencing (srWGS). Combined lrWGS and srWGS facilitated the detection of copy number variations and SVs, including CYP2A7/CYP2A6 hybrids. Three novel CYP2A7/CYP2A6 hybrids were identified and validated via Sanger sequencing. Patients with CYP2A6 deletion exhibited a lower tumor mutation burden (TMB) than those with normal CYP2A6. There was no increase in TMB in tumors other than lung cancer in smokers, even when germline CYP2A6 was retained, indicating that the identified germline hybrids affect mutation accumulation in lung cancer in patients with a history of smoking. Overall, combined srWGS-lrWGS facilitated the precise determination of SVs between CYP2A6 and CYP2A7. This approach could contribute to SV identification in highly homologous chromosomal regions and elucidation of functions of germline SVs in cytochrome P450 in lung cancer.