Accuracy and applications of sequencing and genotyping approaches for CYP2A6 and homologous genes.

TitleAccuracy and applications of sequencing and genotyping approaches for CYP2A6 and homologous genes.
Publication TypeJournal Article
Year of Publication2022
AuthorsLanglois, AWR, El-Boraie, A, Fukunaga, K, Mushiroda, T, Kubo, M, Lerman, C, Knight, J, Scherer, SE, Chenoweth, MJ, Tyndale, RF
JournalPharmacogenet Genomics
Date Published2022 Jun 01
KeywordsBase Sequence, Black People, Cytochrome P-450 CYP2A6, Exons, Gene Frequency, Genotype, Humans

OBJECTIVES: We evaluated multiple genotyping/sequencing approaches in a homologous region of chromosome 19, and investigated associations of two common 3'-UTR CYP2A6 variants with activity in vivo.

METHODS: Individuals (n = 1704) of European and African ancestry were phenotyped for the nicotine metabolite ratio (NMR), an index of CYP2A6 activity, and genotyped/sequenced using deep amplicon exon sequencing, SNP array, genotype imputation and targeted capture sequencing. Amplicon exon sequencing was the gold standard to which other methods were compared within-individual for CYP2A6, CYP2A7, CYP2A13, and CYP2B6 exons to identify highly discordant positions. Linear regression models evaluated the association of CYP2A6*1B and rs8192733 genotypes (coded additively) with logNMR.

RESULTS: All approaches were ≤2.6% discordant with the gold standard; discordant calls were concentrated at few positions. Fifteen positions were discordant in >10% of individuals, with 12 appearing in regions of high identity between homologous genes (e.g. CYP2A6 and CYP2A7). For six, allele frequencies in our study and online databases were discrepant, suggesting errors in online sources. In the European-ancestry group (n = 935), CYP2A6*1B and rs8192733 were associated with logNMR (P

CONCLUSION: Multiple genotyping/sequencing approaches used in this chromosome 19 region contain genotyping/sequencing errors, as do online databases. Gene-specific primers and SNP array probes must consider gene homology; short-read sequencing of related genes in a single reaction should be avoided. Using improved sequencing approaches, we characterized two gain-of-function 3'-UTR variants, including the relatively understudied rs8192733.

Alternate JournalPharmacogenet Genomics
PubMed ID35190513
PubMed Central IDPMC9081136
Grant ListR35 CA197461 / CA / NCI NIH HHS / United States
U01 DA020830 / DA / NIDA NIH HHS / United States
FDN-154294 / / CIHR / Canada
PJY-159710 / / CIHR / Canada