Abstract
To determine the role of CYP450 copy number variation (CNV) beyond CYP2D6, 11 CYP450 genes were interrogated by multiplex ligation-dependent probe amplification and quantitative PCR in 542 African-American, Asian, Caucasian, Hispanic and Ashkenazi Jewish individuals. The CYP2A6, CYP2B6 and CYP2E1 combined deletion/duplication allele frequencies ranged from 2 to 10% in these populations. High-resolution microarray-based comparative genomic hybridization (aCGH) localized CYP2A6, CYP2B6 and CYP2E1 breakpoints to directly oriented low-copy repeats. Sequencing localized the CYP2B6 breakpoint to a 529-bp intron 4 region with high homology to CYP2B7P1, resulting in the CYP2B6*29 partial deletion allele and the reciprocal, and novel, CYP2B6/2B7P1 duplicated fusion allele (CYP2B6*30). Together, these data identified novel CYP450 CNV alleles (CYP2B6*30 and CYP2E1*1Cx2) and indicate that common CYP450 CNV formation is likely mediated by non-allelic homologous recombination resulting in both full gene and gene-fusion copy number imbalances. Detection of these CNVs should be considered when interrogating these genes for pharmacogenetic drug selection and dosing.
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References
Rovelet-Lecrux A, Hannequin D, Raux G, Le Meur N, Laquerriere A, Vital A et al. APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat Genet 2006; 38: 24–26.
McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn’s disease. Nat Genet 2008; 40: 1107–1112.
Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 2010; 466: 368–372.
Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y et al. Detection of large-scale variation in the human genome. Nat Genet 2004; 36: 949–951.
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P et al. Large-scale copy number polymorphism in the human genome. Science 2004; 305: 525–528.
Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU et al. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005; 77: 78–88.
Pinto D, Marshall C, Feuk L, Scherer SW . Copy-number variation in control population cohorts. Hum Mol Genet 2007; 16 Spec No. 2: R168–R173.
Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y et al. Origins and functional impact of copy number variation in the human genome. Nature 2010; 464: 704–712.
Johansson AC, Feuk L . Characterization of copy number-stable regions in the human genome. Hum Mutat 2011; 32: 947–955.
Feuk L, Carson AR, Scherer SW . Structural variation in the human genome. Nat Rev Genet 2006; 7: 85–97.
Hastings PJ, Lupski JR, Rosenberg SM, Ira G . Mechanisms of change in gene copy number. Nat Rev Genet 2009; 10: 551–564.
Zhang F, Khajavi M, Connolly AM, Towne CF, Batish SD, Lupski JR . The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 2009; 41: 849–853.
Hebbring SJ, Adjei AA, Baer JL, Jenkins GD, Zhang J, Cunningham JM et al. Human SULT1A1 gene: copy number differences and functional implications. Hum Mol Genet 2007; 16: 463–470.
Huang RS, Chen P, Wisel S, Duan S, Zhang W, Cook EH et al. Population-specific GSTM1 copy number variation. Hum Mol Genet 2009; 18: 366–372.
Gaedigk A, Twist GP, Leeder JS . CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR. Pharmacogenomics 2012; 13: 91–111.
McGraw J, Waller D . Cytochrome P450 variations in different ethnic populations. Expert Opin Drug Metab Toxicol 2012; 8: 371–382.
He Y, Hoskins JM, McLeod HL . Copy number variants in pharmacogenetic genes. Trends Mol Med 2011; 17: 244–251.
Ramamoorthy A, Skaar TC . Gene copy number variations: it is important to determine which allele is affected. Pharmacogenomics 2011; 12: 299–301.
Gaedigk A, Hernandez J, Garcia-Solaesa V, Sanchez S, Isidoro-Garcia M . Detection and characterization of the CYP2D6*9 × 2 gene duplication in two Spanish populations: resolution of AmpliChip CYP450 test no-calls. Pharmacogenomics 2011; 12: 1617–1622.
Ramamoorthy A, Flockhart DA, Hosono N, Kubo M, Nakamura Y, Skaar TC . Differential quantification of CYP2D6 gene copy number by four different quantitative real-time PCR assays. Pharmacogenet Genomics 2010; 20: 451–454.
Gaedigk A, Jaime LK, Bertino JS, Berard A, Pratt VM, Bradfordand LD et al. Identification of novel CYP2D7-2D6 hybrids: non-functional and functional variants. Front Pharmacol 2010; 1: 121.
Fukami T, Nakajima M, Yamanaka H, Fukushima Y, McLeod HL, Yokoi T . A novel duplication type of CYP2A6 gene in African-American population. Drug Metab Dispos 2007; 35: 515–520.
Nakajima M, Yoshida R, Fukami T, McLeod HL, Yokoi T . Novel human CYP2A6 alleles confound gene deletion analysis. FEBS Lett 2004; 569: 75–81.
Johansson I, Lundqvist E, Bertilsson L, Dahl ML, Sjoqvist F, Ingelman-Sundberg M . Inherited amplification of an active gene in the cytochrome P450 CYP2D locus as a cause of ultrarapid metabolism of debrisoquine. Proc Natl Acad Sci USA 1993; 90: 11825–11829.
Sachse C, Brockmoller J, Hildebrand M, Muller K, Roots I . Correctness of prediction of the CYP2D6 phenotype confirmed by genotyping 47 intermediate and poor metabolizers of debrisoquine. Pharmacogenetics 1998; 8: 181–185.
Ishiguro A, Kubota T, Ishikawa H, Iga T . Metabolic activity of dextromethorphan O-demethylation in healthy Japanese volunteers carrying duplicated CYP2D6 genes: duplicated allele of CYP2D6*10 does not increase CYP2D6 metabolic activity. Clin Chim Acta 2004; 344: 201–204.
Scott SA, Jaremko M, Lubitz SA, Kornreich R, Halperin JL, Desnick RJ . CYP2C9*8 is prevalent among African-Americans: implications for pharmacogenetic dosing. Pharmacogenomics 2009; 10: 1243–1255.
Scott SA, Khasawneh R, Peter I, Kornreich R, Desnick RJ . Combined CYP2C9, VKORC1 and CYP4F2 frequencies among racial and ethnic groups. Pharmacogenomics 2010; 11: 781–791.
Martis S, Peter I, Hulot JS, Kornreich R, Desnick RJ, Scott SA . Multi-ethnic distribution of clinically relevant CYP2C genotypes and haplotypes. Pharmacogenomics J, e-pub ahead of print, 10 April 2012.
Scott SA, Edelmann L, Kornreich R, Erazo M, Desnick RJ . CYP2C9, CYP2C19 and CYP2D6 allele frequencies in the Ashkenazi Jewish population. Pharmacogenomics 2007; 8: 721–730.
Scott SA, Edelmann L, Kornreich R, Desnick RJ . Warfarin pharmacogenetics: CYP2C9 and VKORC1 genotypes predict different sensitivity and resistance frequencies in the Ashkenazi and Sephardi Jewish populations. Am J Hum Genet 2008; 82: 495–500.
Scott SA, Martis S, Peter I, Kasai Y, Kornreich R, Desnick RJ . Identification of CYP2C19*4B: pharmacogenetic implications for drug metabolism including clopidogrel responsiveness. Pharmacogenomics J 2012; 12: 297–305.
Scott SA, Cohen N, Brandt T, Toruner G, Desnick RJ, Edelmann L . Detection of low-level mosaicism and placental mosaicism by oligonucleotide array comparative genomic hybridization. Genet Med 2010; 12: 85–92.
Scott SA, Cohen N, Brandt T, Warburton PE, Edelmann L . Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome. Hum Mol Genet 2010; 19: 3383–3393.
Haberl M, Anwald B, Klein K, Weil R, Fuss C, Gepdiremen A et al. Three haplotypes associated with CYP2A6 phenotypes in Caucasians. Pharmacogenet Genomics 2005; 15: 609–624.
Rotger M, Saumoy M, Zhang K, Flepp M, Sahli R, Decosterd L et al. Partial deletion of CYP2B6 owing to unequal crossover with CYP2B7. Pharmacogenet Genomics 2007; 17: 885–890.
Ingelman-Sundberg M, Oscarson M, Daly AK, Garte S, Nebert DW . Human cytochrome P-450 (CYP) genes: a web page for the nomenclature of alleles. Cancer Epidemiol Biomarkers Prev 2001; 10: 1307–1308.
Sim SC, Ingelman-Sundberg M . The Human Cytochrome P450 (CYP) Allele Nomenclature website: a peer-reviewed database of CYP variants and their associated effects. Hum Genomics 2010; 4: 278–281.
Hu Y, Hakkola J, Oscarson M, Ingelman-Sundberg M . Structural and functional characterization of the 5′-flanking region of the rat and human cytochrome P450 2E1 genes: identification of a polymorphic repeat in the human gene. Biochem Biophys Res Commun 1999; 263: 286–293.
Tyndale RF, Sellers EM . Variable CYP2A6-mediated nicotine metabolism alters smoking behavior and risk. Drug Metab Dispos 2001; 29 (4 Pt 2): 548–552.
Kamataki T, Fujieda M, Kiyotani K, Iwano S, Kunitoh H . Genetic polymorphism of CYP2A6 as one of the potential determinants of tobacco-related cancer risk. Biochem Biophys Res Commun 2005; 338: 306–310.
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD et al. Global variation in copy number in the human genome. Nature 2006; 444: 444–454.
Rodriguez-Antona C, Gomez A, Karlgren M, Sim SC, Ingelman-Sundberg M . Molecular genetics and epigenetics of the cytochrome P450 gene family and its relevance for cancer risk and treatment. Hum Genet 2010; 127: 1–17.
Oscarson M, McLellan RA, Gullsten H, Yue QY, Lang MA, Bernal ML et al. Characterisation and PCR-based detection of a CYP2A6 gene deletion found at a high frequency in a Chinese population. FEBS Lett 1999; 448: 105–110.
van Binsbergen E . Origins and breakpoint analyses of copy number variations: up close and personal. Cytogenet Genome Res 2011; 135: 271–276.
Mwenifumbo JC, Zhou Q, Benowitz NL, Sellers EM, Tyndale RF . New CYP2A6 gene deletion and conversion variants in a population of Black African descent. Pharmacogenomics 2010; 11: 189–198.
Lang T, Klein K, Fischer J, Nussler AK, Neuhaus P, Hofmann U et al. Extensive genetic polymorphism in the human CYP2B6 gene with impact on expression and function in human liver. Pharmacogenetics 2001; 11: 399–415.
Klein K, Lang T, Saussele T, Barbosa-Sicard E, Schunck WH, Eichelbaum M et al. Genetic variability of CYP2B6 in populations of African and Asian origin: allele frequencies, novel functional variants, and possible implications for anti-HIV therapy with efavirenz. Pharmacogenet Genomics 2005; 15: 861–873.
Gatanaga H, Hayashida T, Tsuchiya K, Yoshino M, Kuwahara T, Tsukada H et al. Successful efavirenz dose reduction in HIV type 1-infected individuals with cytochrome P450 2B6 *6 and *26. Clin Infect Dis 2007; 45: 1230–1237.
Batzer MA, Deininger PL . Alu repeats and human genomic diversity. Nat Rev Genet 2002; 3: 370–379.
Hesse LM, He P, Krishnaswamy S, Hao Q, Hogan K, von Moltke LL et al. Pharmacogenetic determinants of interindividual variability in bupropion hydroxylation by cytochrome P450 2B6 in human liver microsomes. Pharmacogenetics 2004; 14: 225–238.
Kirchheiner J, Klein C, Meineke I, Sasse J, Zanger UM, Murdter TE et al. Bupropion and 4-OH-bupropion pharmacokinetics in relation to genetic polymorphisms in CYP2B6. Pharmacogenetics 2003; 13: 619–626.
Rotger M, Tegude H, Colombo S, Cavassini M, Furrer H, Decosterd L et al. Predictive value of known and novel alleles of CYP2B6 for efavirenz plasma concentrations in HIV-infected individuals. Clin Pharmacol Ther 2007; 81: 557–566.
Grove J, Brown AS, Daly AK, Bassendine MF, James OF, Day CP . The RsaI polymorphism of CYP2E1 and susceptibility to alcoholic liver disease in Caucasians: effect on age of presentation and dependence on alcohol dehydrogenase genotype. Pharmacogenetics 1998; 8: 335–342.
Iwahashi K, Ameno S, Ameno K, Okada N, Kinoshita H, Sakae Y et al. Relationship between alcoholism and CYP2E1 C/D polymorphism. Neuropsychobiology 1998; 38: 218–221.
McCarver DG, Byun R, Hines RN, Hichme M, Wegenek W . A genetic polymorphism in the regulatory sequences of human CYP2E1: association with increased chlorzoxazone hydroxylation in the presence of obesity and ethanol intake. Toxicol Appl Pharmacol 1998; 152: 276–281.
Howard LA, Ahluwalia JS, Lin SK, Sellers EM, Tyndale RF . CYP2E1*1D regulatory polymorphism: association with alcohol and nicotine dependence. Pharmacogenetics 2003; 13: 321–328.
Khan AJ, Ruwali M, Choudhuri G, Mathur N, Husain Q, Parmar D . Polymorphism in cytochrome P450 2E1 and interaction with other genetic risk factors and susceptibility to alcoholic liver cirrhosis. Mutat Res 2009; 664: 55–63.
Beck JA, Campbell TA, Adamson G, Poulter M, Uphill JB, Molou E et al. Association of a null allele of SPRN with variant Creutzfeldt-Jakob disease. J Med Genet 2008; 45: 813–817.
McGuire MM, Bowden W, Engel NJ, Ahn HW, Kovanci E, Rajkovic A . Genomic analysis using high-resolution single-nucleotide polymorphism arrays reveals novel microdeletions associated with premature ovarian failure. Fertil Steril 2011; 95: 1595–1600.
Acknowledgements
This research was supported in part by the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), through Grant KL2TR000069 (SAS). The Cytochrome P-450 MLPA kit reagents used in this study were generously provided by MRC-Holland (Amsterdam, The Netherlands). We thank Dr Sarah Sim, Karolinska Institutet, Stockholm, Sweden, for critical reading of the manuscript; Ms Edith Gould, formerly of the Mount Sinai School of Medicine, New York, for her technical assistance with the MLPA assays; and Dr Minjie Luo, Mount Sinai School of Medicine, for assistance with the long-range PCR assays.
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One of the authors (RV) is an employee of MRC-Holland, Amsterdam, The Netherlands. The remaining authors declare no conflict of interest.
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Martis, S., Mei, H., Vijzelaar, R. et al. Multi-ethnic cytochrome-P450 copy number profiling: novel pharmacogenetic alleles and mechanism of copy number variation formation. Pharmacogenomics J 13, 558–566 (2013). https://doi.org/10.1038/tpj.2012.48
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DOI: https://doi.org/10.1038/tpj.2012.48
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