Copy number variation and gene rearrangements in CYP2D6 genotyping using multiplex ligation-dependent probe amplification in Koreans

Pharmacogenomics

Volumn 13, Issue 8, 2012, Pages 963-973

  Kim, Juwon ^a   Lee, Soo Youn ^b   Lee, Kyung A ^a  

^a Yonsei University College of Medicine   (South Korea)

^b Sungkyunkwan University   (South Korea)

Author keywords

CYP2D6 gene; genotyping; multiplex ligation dependent probe amplification

Indexed keywords

ACCURACY; ADULT; ALLELE; ANALYZER; ARTICLE; ASIAN; CAUCASIAN; CONSENSUS; CONTROLLED STUDY; COPY NUMBER VARIATION; CYP2D6 GENE; EXON; GENE; GENE DELETION; GENE DUPLICATION; GENE REARRANGEMENT; GENOTYPE; HETEROZYGOTE; HOMOZYGOTE; HUMAN; KOREAN; MALE; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; CYTOCHROME P-450 CYP2D6; DNA COPY NUMBER VARIATIONS; GENE REARRANGEMENT; GENES, DUPLICATE; GENOTYPING TECHNIQUES; HETEROZYGOTE; HUMANS; MALE; MULTIPLEX POLYMERASE CHAIN REACTION; REPUBLIC OF KOREA; SEQUENCE DELETION;

EID: 84862001602     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/pgs.12.58     Document Type: Article

References (30)

1. Zhou SF. Polymorphism of human cytochrome P450 2D6 and its clinical significance: part I. Clin. Pharmacokinet. 48(11), 689-723 (2009).
2. Gough AC, Smith CA, Howell SM, Wolf CR, Bryant SP, Spurr NK. Localization of the CYP2D gene locus to human chromosome 22q13.1 by polymerase chain reaction, in situ hybridization, and linkage ana lysis. Genomics 15(2), 430-432 (1993).
3. Kimura S, Umeno M, Skoda RC, Meyer UA, Gonzalez FJ. The human debrisoquine 4-hydroxylase (CYP2D) locus: sequence and identification of the polymorphic CYP2D6 gene, a related gene, and a pseudogene. Am. J. Hum. Genet. 45(6), 889-904 (1989).
4. Kim K, Johnson JA, Derendorf H. Differences in drug pharmacokinetics between East Asians and Caucasians and the role of genetic polymorphisms. J. Clin. Pharmacol. 44(10), 1083-1105 (2004).
5. Hersberger M, Marti-Jaun J, Rentsch K, Hanseler E. Rapid detection of the CYP2D6*3, CYP2D6*4, and CYP2D6*6 alleles by tetra-primer PCR and of the CYP2D6*5 allele by multiplex long PCR. Clin. Chem. 46(8 Pt 1), 1072-1077 (2000).
6. Lovlie R, Daly AK, Molven A, Idle JR, Steen VM. Ultrarapid metabolizers of debrisoquine: characterization and PCR-based detection of alleles with duplication of the CYP2D6 gene. FEBS Lett. 392(1), 30-34 (1996).
7. Hosono N, Kato M, Kiyotani K et al. CYP2D6 genotyping for functional-gene dosage ana lysis by allele copy number detection. Clin. Chem. 55(8), 1546-1554 (2009).
8. Beer B, Erb R, Pitterl F et al. CYP2D6 genotyping by liquid chromatography-electrospray ionization mass spectrometry. Anal. Bioanal. Chem. 400(8), 2361-2370 (2011).
9. 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 20(7), 451-454 (2010).
10. Soderback E, Zackrisson AL, Lindblom B, Alderborn A. Determination of CYP2D6 gene copy number by pyrosequencing. Clin. Chem. 51(3), 522-531 (2005).
11. Suwannasri P, Thongnoppakhun W, Pramyothin P, Assawamakin A, Limwongse C. Combination of multiplex PCR and DHPLC-based strategy for CYP2D6 genotyping scheme in Thais. Clin. Biochem. 44(13), 1144-1152 (2011).
12. Kim EY, Lee SS, Jung HJ et al. Robust CYP2D6 genotype assay including copy number variation using multiplex single-base extension for Asian populations. Clin. Chim. Acta; Int. J. Clin. Chem. 411(23-24), 2043-2048 (2010).
13. Soyama A, Saito Y, Kubo T et al. Sequence-based ana lysis of the CYP2D6*36-CYP2D6*10 tandem-type arrangement, a major CYP2D6*10 haplotype in the Japanese population. Drug Metab. Pharmacokinet. 21(3), 208-216 (2006). Provided genotype frequency of the tandem type arrangement in Asian populations.
14. Patrinos GP, Ansorge W. Molecular Diagnostics (2nd Edition). Academic Press, London, UK (2010).
15. Kiyotani K, Shimizu M, Kumai T, Kamataki T, Kobayashi S, Yamazaki H. Limited effects of frequent CYP2D6*36-*10 tandem duplication allele on in vivo dextromethorphan metabolism in a Japanese population. Eur. J. Clin. Pharmacol. 66(10), 1065-1068 (2010).
16. Armour JA, Barton DE, Cockburn DJ, Taylor GR. The detection of large deletions or duplications in genomic DNA. Hum. Mutat. 20(5), 325-337 (2002).
17. Sellner LN, Taylor GR. MLPA and MAPH: new techniques for detection of gene deletions. Hum. Mutat. 23(5), 413-419 (2004).
18. Sorensen KM, El-Segaier M, Fernlund E et al. Screening of congenital heart disease patients using multiplex ligation-dependent probe amplification: early diagnosis of syndromic patients. Am. J. Med. Genet. Part A 158A(4), 720-725 (2012).
19. Chan JE, Kolodner RD. Rapid analysis of Saccharomyces cerevisiae genome rearrangements by multiplex ligation-dependent probe amplification. PLoS Genet. 8(3), e1002539 (2012).
20. Abdool A, Donahue AC, Wohlgemuth JG, Yeh CH. Detection, ana lysis and clinical validation of chromosomal aberrations by multiplex ligation-dependent probe amplification in chronic leukemia. PLoS ONE 5(10), e15407 (2010).
21. Al Zaabi EA, Fernandez LA, Sadek IA, Riddell DC, Greer WL. Multiplex ligation-dependent probe amplification versus multiprobe fluorescence in situ hybridization to detect genomic aberrations in chronic lymphocytic leukemia: a tertiary center experience. J. Mol. Diagn. 12(2), 197-203 (2010).
22. Wolf NI, Sistermans EA, Cundall M et al. Three or more copies of the proteolipid protein gene PLP1 cause severe Pelizaeus-Merzbacher disease. Brain 128(Pt 4), 743-751 (2005).
23. Gaedigk A, Bradford LD, Alander SW, Leeder JS. CYP2D6*36 gene arrangements within the cyp2d6 locus: association of CYP2D6*36 with poor metabolizer status. Drug Metab. Dispos. 34(4), 563-569 (2006).
24. Gaedigk A, Twist GP, Leeder JS. CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR. Pharmacogenomics 13(1), 91-111 (2012).
25. Gaedigk A, Fuhr U, Johnson C, Berard LA, Bradford D, Leeder JS. CYP2D7-2D6 hybrid tandems: identification of novel CYP2D6 duplication arrangements and implications for phenotype prediction. Pharmacogenomics 11(1), 43-53 (2010). Identified a tandem hybrid of CYP2D6, which was not detected with the methods previously used to genotype CYP2D6 and provided evidence for a new classification of the CYP2D6 allele.
26. Rodriguez-Antona C, Gurwitz D, de Leon J et al. CYP2D6 genotyping for psychiatric patients treated with risperidone: considerations for cost-effectiveness studies. Pharmacogenomics 10(4), 685-699 (2009).
27. Ramamoorthy A, Skaar TC. Gene copy number variations: it is important to determine which allele is affected. Pharmacogenomics 12(3), 299-301 (2011).
28. CYP2D6 allele nomenclature. www.cypalleles.ki.se/cyp2d6.htm (Accessed 8 March 2012)
29. MLPA®. www.mlpa.com (Accessed 10 December 2011)
30. Genetic Testing Reference Materials Coordination Program (GeT-RM). wwwn.cdc.gov/dls/genetics/RMMaterials (Accessed 8 March 2012)