Editorial For reprint orders, please contact: [email protected]
CYP2D6 and pharmacogenomics: where does future research need to focus? Part 1: technical aspects “Owing to the highly polymorphic nature of CYP2D6, genotype analysis of this gene and accurate prediction of a patient’s CYP2D6 phenotype status is therefore a challenging task.”
KEYWORDS: clinical implementation n CPIC n CYP2D6 n cytochrome P450 n drug-metabolizing enzymes n genetic variation n pharmacogenetics
Andrea Gaedigk The CYP2D6 enzyme contributes to the metabolism and bioactivation of approximately a quarter of drugs clinically used, including many antidepressants and antipsychotics, codeine and tramadol prescribed for pain, the estrogen receptor antagonist tamoxifen, a drug frequently used to treat women with breast cancer, and many others [1,2]. CYP2D6 activity is highly variable in most populations ranging from no activity in poor metabolizers (PMs) to reduced, normal and higher than normal activity in intermediate metabolizers (IMs), extensive metabolizers (EMs) and ultrarapid metabolizers (UMs), respectively. This variation is, in large part, attributable to the highly polymorphic nature of the CYP2D6 gene locus [3]. Among the known allelic variants, many contain one or multiple single nucleotide variations (SNVs) and/or insertions or deletions of multiple nucleotides. However, this gene locus is also hampered by extensive gene copy number variation, including the deletion of the entire gene as well as gene duplications and multiplication of functional, reduced function and nonfunctional genes [4,5]. Also, a growing number of rearrangement events involving the CYP2D7 pseudogene, which is located just upstream of CYP2D6 within the gene locus, have been described; these typically contain nonfunctional CYP2D7/2D6 hybrid genes [6,7]. Furthermore, the most complicated allelic variants may include a combination of SNVs and copy number variations as well as hybrid genes [7–9]. In addition, allele frequencies dramatically differ among ethnic populations. A comprehensive list of CYP2D6 allele frequencies is maintained by the author and can be found at [101]. To date over 100 allelic variants and subvariants have been defined by the Human
Cytochrome P450 (CYP) Allele Nomenclature database at [102]; however, not all have been functionally characterized. Also, numerous additional variants have been described in the literature, but have never been submitted to the nomenclature committee or are no longer assigned a star (*) allele designation because they fail to meet current criteria for designation [10]; such alleles are often labeled as ‘variants’ or ‘subvariants’ in respective publications and may be difficult to track.
10.2217/PGS.14.28 © 2014 Future Medicine Ltd
Pharmacogenomics (2014) 15(4), 407–410
“…the process of how a genotype result is translated into a predicted phenotype is not standardized and may lead to variable interpretations.” Owing to the highly polymorphic nature of CYP2D6, genotype analysis of this gene and accurate prediction of a patient’s CYP2D6 phenot ype status is therefore a challenging task [11]. As discussed by Hicks et al., not only does the level of testing offered by clinical test laboratories and investigator-designed platforms differ, the process of how a genotype result is translated into a predicted phenotype is not standardized and may lead to variable interpretations. For example, patients with certain CYP2D6 genotypes may be classified as EMs or IMs and may receive a normal or reduced dose of a drug depending on which guideline is followed, that is, those developed by the Clinical Pharmacogenetics Implementation Consortium (CPIC) or those published by the Dutch Pharmacogenetics Working Group (DPWG) [11]. This serious predicament causes inconsistencies of phenotype predictions among reference laboratory reports and research proceedings alike. As a consequence, difficulties may arise in the prediction
Author for correspondence: Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Hospital & Clinics & Department of Pediatrics, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA [email protected]
J Steven Leeder Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Hospital & Clinics & Department of Pediatrics, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA
part of
ISSN 1462-2416
407
Editorial
Gaedigk & Leeder
of drug clearance in an individual patient, and thus the dose that is required to achieve a particular therapeutic goal. Therefore, a universal system for CYP2D6 phenotype assignment is warranted. However, in order to develop a universal CYP2D6 phenotype assignment system, a number of major challenges need to be overcome [11]. The first challenge is to ascertain the functional significance of novel CYP2D6 variant alleles, that is, to develop a universal approach to assign a value to each CYP2D6 allele that accurately reflects its predicted activity. Scoring systems have been introduced [12,13] and are increasingly utilized, but are still relatively crude. The second challenge is substrate specificity, that is, to quantify substrate-specific differences in the activity that is conveyed by different allelic variants or particular genotypes. The third challenge is phenocopy and drug interactions, that is, recognition that concomitant drug administration or the influence of other environmental factors may impact a patient’s phenotype and is different from that predicted by genotype. The fourth challenge is to convert a continuum of CYP2D6 activity into the four ‘traditional’ phenotype categories, that is, to categorize the ever growing number of CYP2D6 alleles and corresponding diplotypes representing a continuum of activity into the discrete PM, IM, EM and ultrarapid metabolizer phenotype groups. Phenotype assignments are also mostly based on the association between genotype and urinary metabolic ratios of a probe drug such as dextromethorphan/dextrorphan, which is a phenotype that translates poorly to clearance of individual CYP2D6 substrates. Clearly, pharmacokinetic studies measuring drug clearance represent a superior method for defining the relationship between CYP2D6 genotype and phenotype. Additional challenges not covered by our recent review articles [3,11] include the need of a database that collects and annotates all known CYP2D6 allelic variants and a standardized procedure or ‘checklist’ of how CYP2D6 genotyping is reported. Regarding the first point, a user-friendly CYP2D6 variation database is not only important for, for example, the interpretation of test results that produced ‘no-calls’ or triggered other ‘red flags’ owing to discordant SNP and/or SNV patterns or the presence of complex diplotypes that interfere with particular test platforms [14,15], but also for the development of improved and more robust genotyping platforms. Moreover, as next-generation sequencing (NGS)-based testing is being developed for CYP2D6 characterization, novel variants will 408
Pharmacogenomics (2014) 15(4)
be discovered that need to be functionally characterized and catalogued for public access. For NGS in particular, the development of reference sequences that span the entire CYP2D gene locus (CYP2D6, 7 and 8) will be necessary in order to accurately align the relatively short sequence reads generated by NGS. Regarding the second point, it is often cumbersome, or even impossible, to delineate from published reports how CYP2D6 genotyping was performed, which sequence variations were specifically tested and which allelic variants were unequivocally determined and which were assigned by default. To interpret in vitro and in vivo studies for evidence to support clinical guidelines, for example those developed by CPIC for the CYP2D6/codeine [16], CYP2D6/tricyclic antidepressants [17] and gene/drug pairs (a third guideline for CYP2D6/ selective serotonin re-uptake inhibitors is underway), well-described genotype methods are essential. A checklist collecting essential testspecific information similar to those prescribed by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines for quantitative PCR [18], would be immensely valuable for any standardization efforts for the translation of genotype data at large into phenotype assignments.
“…pharmacokinetic studies measuring drug clearance represent a superior method for defining the relationship between CYP2D6 genotype and phenotype.”
While many clinical studies often focus on the more common CYP2D6 allelic variants and also investigate only one gene at a time, future investigations need not only to include subjects with less-well characterized allelic variants or diplotypes, but be more pathway-oriented and include other genes that contribute to interindividual variability in the absorption, distribution, metabolism, excretion and response of the drug of interest. As exemplified by the CPIC guideline for the CYP2D6/tricyclic antidepressants gene/drug pair, there is a void of information of how to interpret a combination of CYP2D6 and CYP2C19 genotypes to guide clinical action for cases where genotype information is available for both genes. Finally, in addition to the barriers discussed above that hinder efforts of clinical implementation of pharmacogenetics, other barriers that have to be addressed in the future for successful clinical implementation of CYP2D6 and other pharmacogenes include the lack of knowledge future science group
CYP2D6 & pharmacogenomics: where does future research need to focus?
and education of health professionals who are/will be involved with the interpretation of genotype data and individualized clinical decision-making, the integration of pharmacogenomics data into the medical record system to facilitate appropriate interpretation, the utility genotype data versus the cost of genotyping and coverage of pharmacogenomics tests by medical health plans.
“…future investigations need not only to include subjects with less-well characterized allelic variants or diplotypes, but be more pathway-oriented and include other genes that contribute to interindividual variability in the absorption, distribution, metabolism, excretion and response of the drug of interest.” Despite extensive efforts for CYP2D6 gene locus characterization, only part of the observed inter- and intra-individual variability can be explained by variation in the genetic code. Recently, Wang et al. discovered an enhancer region approximately 100 kb downstream of the CYP2D6 gene and SNPs therein, which appear to modulate gene transcription [19]. These authors also provided new evidence that a particular nonsynonymous SNP may play a greater role in References 1
Zhou SF. Polymorphism of human cytochrome P450 2D6 and its clinical significance: part I. Clin. Pharmacokinet. 48(11), 689–723 (2009).
2
Zhou SF. Polymorphism of human cytochrome P450 2D6 and its clinical significance: part II. Clin. Pharmacokinet. 48(12), 761–804 (2009).
3
Gaedigk A. Complexities of CYP2D6 gene analysis and interpretation. Int. Rev. Psychiatry 25(5), 534–553 (2013).
4
5
6
Gaedigk A, Twist GP, Leeder JS. CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR. Pharmacogenomics 13(1), 91–111 (2012). Gaedigk A, Ndjountche L, Divakaran K et al. Cytochrome P4502D6 (CYP2D6 ) gene locus heterogeneity: characterization of gene duplication events. Clin. Pharmacol. Ther. 81(2), 242–251 (2007). Gaedigk A, Jaime LK, Bertino JS Jr et al. Identification of novel CYP2D7–2D6 hybrids: non-functional and functional variants. Front. Pharmacol. 1, 121 (2010).
future science group
splicing than previously assumed. Other factors that are still relatively under investigated involve gene regulation by small noncoding RNAs such as miRNAs that may directly or indirectly influence gene expression [20] or epigenetic factors. Although much is known about CYP2D6 pharmacogenetics, clinical implementation is only in its infancy owing to numerous challenges and barriers that still need to be overcome. Solving the technical aspects of CYP2D6 testing is, however, only one aspect required of future research; the translation of genotype into actual dose adjustments is another, which will be discussed in detail in the second part of this editorial miniseries. The technical and clinical challenges of CYP2D6 pharmacogenetics make it an excellent model to find solutions and further the clinical utilization of pharmacogenetic testing. Financial & competing interests disclosure The authors are members of the Clinical Pharmacogenetics Implementation Consortium and contribute to the development of guidelines published by this group. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.
7
Sim SC, Daly AK, Gaedigk A. CYP2D6 update: revised nomenclature for CYP2D7/2D6 hybrid genes. Pharmacogenet. Genomics 22(9), 692–694 (2012).
8
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).
9
Editorial
Kramer WE, Walker DL, O’Kane DJ et al. CYP2D6: novel genomic structures and alleles. Pharmacogenet. Genomics 19(10), 813–822 (2009).
10 Sim SC, Ingelman-Sundberg M. Update on
Allele Nomenclature for Human Cytochromes P450 and the Human Cytochrome P450 Allele (CYP-Allele) Nomenclature Database. Methods Mol. Biol. 987, 251–259 (2013). 11 Hicks JK, Swen JJ, Gaedigk A. Challenges in
CYP2D6 phenotype assignment from genotype data: a critical assessment and call for standardization. Curr. Drug Metab. doi:10.2174/1389200215666140202215316 (2014) (Epub ahead of print). 12 Gaedigk A, Simon SD, Pearce RE, Bradford
LD, Kennedy MJ, Leeder JS. The CYP2D6
www.futuremedicine.com
activity score: translating genotype information into a qualitative measure of phenotype. Clin. Pharmacol. Ther. 83(2), 234–242 (2008). 13 Steimer W, Zopf K, von Amelunxen S et al.
Allele-specific change of concentration and functional gene dose for the prediction of steady-state serum concentrations of amitriptyline and nortriptyline in CYP2C19 and CYP2D6 extensive and intermediate metabolizers. Clin. Chem. 50(9), 1623–1633 (2004). 14 Gaedigk A, Riffel AK, Garcia Berrocal B,
Garcia-Solaesa V, Davila I, Isidoro-Garcia M. Characterization of a complex CYP2D6 genotype that caused an AmpliChip CYP450 Test ® no-call in the clinical setting. Clin. Chem. Lab. Med. doi:10.1515/ cclm-2013-0943 (2014) (Epub ahead of print). 15 Gaedigk A, Isidoro-Garcia M, Pearce RE
et al. Discovery of the nonfunctional CYP2D6*31 allele in Spanish, Puerto Rican, and US Hispanic populations. Eur. J. Clin. Pharmacol. 66(9), 859–864 (2010). 16 Crews KR, Gaedigk A, Dunnenberger HM
et al. Clinical Pharmacogenetics Implementation Consortium (CPIC)
409
Editorial
Gaedigk & Leeder
guidelines for cytochrome P450 2D6 (CYP2D6) genotype and codeine therapy: 2014 update. Clin. Pharmacol. Ther. doi:10.1038/clpt.2013.254 (2014) (Epub ahead of print). 17 Hicks JK, Swen JJ, Thorn CF et al. Clinical
Pharmacogenetics Implementation Consortium Guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants. Clin. Pharmacol. Ther. 93(5), 402–408 (2013). 18 Bustin SA, Benes V, Garson J et al. The need
for transparency and good practices in the
410
qPCR literature. Nat. Methods 10(11), 1063–1067 (2013). 19 Wang D, Poi MJ, Sun X, Gaedigk A, Leeder
JS, Sadee W. Common CYP2D6 polymorphisms affecting alternative splicing and transcription: long-range haplotypes with two regulatory variants modulate CYP2D6 activity. Hum. Mol. Genet. 23(1), 268–278 (2013). 20 Ramamoorthy A, Li L, Gaedigk A et al.
In silico and in vitro identification of microRNAs that regulate hepatic nuclear factor 4alpha expression. Drug metabolism
Pharmacogenomics (2014) 15(4)
and disposition: the biological fate of chemicals. Drug Metab. Dispos. 40(4), 726–733 (2012).
Websites 101 CYP2D6 allele frequency table on
PharmGKB Knowledge Base. www.pharmgkb.org/download. action?filename=CYP2D6_Literature_Table_ and_Legend.pdf 102 The Human Cytochrome P450 (CYP) Allele
Nomenclature Database. www.cypalleles.ki.se
future science group
CYP2D6 and pharmacogenomics: where does future research need to focus? Part 1: technical aspects “Owing to the highly polymorphic nature of CYP2D6, genotype analysis of this gene and accurate prediction of a patient’s CYP2D6 phenotype status is therefore a challenging task.”
KEYWORDS: clinical implementation n CPIC n CYP2D6 n cytochrome P450 n drug-metabolizing enzymes n genetic variation n pharmacogenetics
Andrea Gaedigk The CYP2D6 enzyme contributes to the metabolism and bioactivation of approximately a quarter of drugs clinically used, including many antidepressants and antipsychotics, codeine and tramadol prescribed for pain, the estrogen receptor antagonist tamoxifen, a drug frequently used to treat women with breast cancer, and many others [1,2]. CYP2D6 activity is highly variable in most populations ranging from no activity in poor metabolizers (PMs) to reduced, normal and higher than normal activity in intermediate metabolizers (IMs), extensive metabolizers (EMs) and ultrarapid metabolizers (UMs), respectively. This variation is, in large part, attributable to the highly polymorphic nature of the CYP2D6 gene locus [3]. Among the known allelic variants, many contain one or multiple single nucleotide variations (SNVs) and/or insertions or deletions of multiple nucleotides. However, this gene locus is also hampered by extensive gene copy number variation, including the deletion of the entire gene as well as gene duplications and multiplication of functional, reduced function and nonfunctional genes [4,5]. Also, a growing number of rearrangement events involving the CYP2D7 pseudogene, which is located just upstream of CYP2D6 within the gene locus, have been described; these typically contain nonfunctional CYP2D7/2D6 hybrid genes [6,7]. Furthermore, the most complicated allelic variants may include a combination of SNVs and copy number variations as well as hybrid genes [7–9]. In addition, allele frequencies dramatically differ among ethnic populations. A comprehensive list of CYP2D6 allele frequencies is maintained by the author and can be found at [101]. To date over 100 allelic variants and subvariants have been defined by the Human
Cytochrome P450 (CYP) Allele Nomenclature database at [102]; however, not all have been functionally characterized. Also, numerous additional variants have been described in the literature, but have never been submitted to the nomenclature committee or are no longer assigned a star (*) allele designation because they fail to meet current criteria for designation [10]; such alleles are often labeled as ‘variants’ or ‘subvariants’ in respective publications and may be difficult to track.
10.2217/PGS.14.28 © 2014 Future Medicine Ltd
Pharmacogenomics (2014) 15(4), 407–410
“…the process of how a genotype result is translated into a predicted phenotype is not standardized and may lead to variable interpretations.” Owing to the highly polymorphic nature of CYP2D6, genotype analysis of this gene and accurate prediction of a patient’s CYP2D6 phenot ype status is therefore a challenging task [11]. As discussed by Hicks et al., not only does the level of testing offered by clinical test laboratories and investigator-designed platforms differ, the process of how a genotype result is translated into a predicted phenotype is not standardized and may lead to variable interpretations. For example, patients with certain CYP2D6 genotypes may be classified as EMs or IMs and may receive a normal or reduced dose of a drug depending on which guideline is followed, that is, those developed by the Clinical Pharmacogenetics Implementation Consortium (CPIC) or those published by the Dutch Pharmacogenetics Working Group (DPWG) [11]. This serious predicament causes inconsistencies of phenotype predictions among reference laboratory reports and research proceedings alike. As a consequence, difficulties may arise in the prediction
Author for correspondence: Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Hospital & Clinics & Department of Pediatrics, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA [email protected]
J Steven Leeder Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Hospital & Clinics & Department of Pediatrics, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA
part of
ISSN 1462-2416
407
Editorial
Gaedigk & Leeder
of drug clearance in an individual patient, and thus the dose that is required to achieve a particular therapeutic goal. Therefore, a universal system for CYP2D6 phenotype assignment is warranted. However, in order to develop a universal CYP2D6 phenotype assignment system, a number of major challenges need to be overcome [11]. The first challenge is to ascertain the functional significance of novel CYP2D6 variant alleles, that is, to develop a universal approach to assign a value to each CYP2D6 allele that accurately reflects its predicted activity. Scoring systems have been introduced [12,13] and are increasingly utilized, but are still relatively crude. The second challenge is substrate specificity, that is, to quantify substrate-specific differences in the activity that is conveyed by different allelic variants or particular genotypes. The third challenge is phenocopy and drug interactions, that is, recognition that concomitant drug administration or the influence of other environmental factors may impact a patient’s phenotype and is different from that predicted by genotype. The fourth challenge is to convert a continuum of CYP2D6 activity into the four ‘traditional’ phenotype categories, that is, to categorize the ever growing number of CYP2D6 alleles and corresponding diplotypes representing a continuum of activity into the discrete PM, IM, EM and ultrarapid metabolizer phenotype groups. Phenotype assignments are also mostly based on the association between genotype and urinary metabolic ratios of a probe drug such as dextromethorphan/dextrorphan, which is a phenotype that translates poorly to clearance of individual CYP2D6 substrates. Clearly, pharmacokinetic studies measuring drug clearance represent a superior method for defining the relationship between CYP2D6 genotype and phenotype. Additional challenges not covered by our recent review articles [3,11] include the need of a database that collects and annotates all known CYP2D6 allelic variants and a standardized procedure or ‘checklist’ of how CYP2D6 genotyping is reported. Regarding the first point, a user-friendly CYP2D6 variation database is not only important for, for example, the interpretation of test results that produced ‘no-calls’ or triggered other ‘red flags’ owing to discordant SNP and/or SNV patterns or the presence of complex diplotypes that interfere with particular test platforms [14,15], but also for the development of improved and more robust genotyping platforms. Moreover, as next-generation sequencing (NGS)-based testing is being developed for CYP2D6 characterization, novel variants will 408
Pharmacogenomics (2014) 15(4)
be discovered that need to be functionally characterized and catalogued for public access. For NGS in particular, the development of reference sequences that span the entire CYP2D gene locus (CYP2D6, 7 and 8) will be necessary in order to accurately align the relatively short sequence reads generated by NGS. Regarding the second point, it is often cumbersome, or even impossible, to delineate from published reports how CYP2D6 genotyping was performed, which sequence variations were specifically tested and which allelic variants were unequivocally determined and which were assigned by default. To interpret in vitro and in vivo studies for evidence to support clinical guidelines, for example those developed by CPIC for the CYP2D6/codeine [16], CYP2D6/tricyclic antidepressants [17] and gene/drug pairs (a third guideline for CYP2D6/ selective serotonin re-uptake inhibitors is underway), well-described genotype methods are essential. A checklist collecting essential testspecific information similar to those prescribed by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines for quantitative PCR [18], would be immensely valuable for any standardization efforts for the translation of genotype data at large into phenotype assignments.
“…pharmacokinetic studies measuring drug clearance represent a superior method for defining the relationship between CYP2D6 genotype and phenotype.”
While many clinical studies often focus on the more common CYP2D6 allelic variants and also investigate only one gene at a time, future investigations need not only to include subjects with less-well characterized allelic variants or diplotypes, but be more pathway-oriented and include other genes that contribute to interindividual variability in the absorption, distribution, metabolism, excretion and response of the drug of interest. As exemplified by the CPIC guideline for the CYP2D6/tricyclic antidepressants gene/drug pair, there is a void of information of how to interpret a combination of CYP2D6 and CYP2C19 genotypes to guide clinical action for cases where genotype information is available for both genes. Finally, in addition to the barriers discussed above that hinder efforts of clinical implementation of pharmacogenetics, other barriers that have to be addressed in the future for successful clinical implementation of CYP2D6 and other pharmacogenes include the lack of knowledge future science group
CYP2D6 & pharmacogenomics: where does future research need to focus?
and education of health professionals who are/will be involved with the interpretation of genotype data and individualized clinical decision-making, the integration of pharmacogenomics data into the medical record system to facilitate appropriate interpretation, the utility genotype data versus the cost of genotyping and coverage of pharmacogenomics tests by medical health plans.
“…future investigations need not only to include subjects with less-well characterized allelic variants or diplotypes, but be more pathway-oriented and include other genes that contribute to interindividual variability in the absorption, distribution, metabolism, excretion and response of the drug of interest.” Despite extensive efforts for CYP2D6 gene locus characterization, only part of the observed inter- and intra-individual variability can be explained by variation in the genetic code. Recently, Wang et al. discovered an enhancer region approximately 100 kb downstream of the CYP2D6 gene and SNPs therein, which appear to modulate gene transcription [19]. These authors also provided new evidence that a particular nonsynonymous SNP may play a greater role in References 1
Zhou SF. Polymorphism of human cytochrome P450 2D6 and its clinical significance: part I. Clin. Pharmacokinet. 48(11), 689–723 (2009).
2
Zhou SF. Polymorphism of human cytochrome P450 2D6 and its clinical significance: part II. Clin. Pharmacokinet. 48(12), 761–804 (2009).
3
Gaedigk A. Complexities of CYP2D6 gene analysis and interpretation. Int. Rev. Psychiatry 25(5), 534–553 (2013).
4
5
6
Gaedigk A, Twist GP, Leeder JS. CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR. Pharmacogenomics 13(1), 91–111 (2012). Gaedigk A, Ndjountche L, Divakaran K et al. Cytochrome P4502D6 (CYP2D6 ) gene locus heterogeneity: characterization of gene duplication events. Clin. Pharmacol. Ther. 81(2), 242–251 (2007). Gaedigk A, Jaime LK, Bertino JS Jr et al. Identification of novel CYP2D7–2D6 hybrids: non-functional and functional variants. Front. Pharmacol. 1, 121 (2010).
future science group
splicing than previously assumed. Other factors that are still relatively under investigated involve gene regulation by small noncoding RNAs such as miRNAs that may directly or indirectly influence gene expression [20] or epigenetic factors. Although much is known about CYP2D6 pharmacogenetics, clinical implementation is only in its infancy owing to numerous challenges and barriers that still need to be overcome. Solving the technical aspects of CYP2D6 testing is, however, only one aspect required of future research; the translation of genotype into actual dose adjustments is another, which will be discussed in detail in the second part of this editorial miniseries. The technical and clinical challenges of CYP2D6 pharmacogenetics make it an excellent model to find solutions and further the clinical utilization of pharmacogenetic testing. Financial & competing interests disclosure The authors are members of the Clinical Pharmacogenetics Implementation Consortium and contribute to the development of guidelines published by this group. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.
7
Sim SC, Daly AK, Gaedigk A. CYP2D6 update: revised nomenclature for CYP2D7/2D6 hybrid genes. Pharmacogenet. Genomics 22(9), 692–694 (2012).
8
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).
9
Editorial
Kramer WE, Walker DL, O’Kane DJ et al. CYP2D6: novel genomic structures and alleles. Pharmacogenet. Genomics 19(10), 813–822 (2009).
10 Sim SC, Ingelman-Sundberg M. Update on
Allele Nomenclature for Human Cytochromes P450 and the Human Cytochrome P450 Allele (CYP-Allele) Nomenclature Database. Methods Mol. Biol. 987, 251–259 (2013). 11 Hicks JK, Swen JJ, Gaedigk A. Challenges in
CYP2D6 phenotype assignment from genotype data: a critical assessment and call for standardization. Curr. Drug Metab. doi:10.2174/1389200215666140202215316 (2014) (Epub ahead of print). 12 Gaedigk A, Simon SD, Pearce RE, Bradford
LD, Kennedy MJ, Leeder JS. The CYP2D6
www.futuremedicine.com
activity score: translating genotype information into a qualitative measure of phenotype. Clin. Pharmacol. Ther. 83(2), 234–242 (2008). 13 Steimer W, Zopf K, von Amelunxen S et al.
Allele-specific change of concentration and functional gene dose for the prediction of steady-state serum concentrations of amitriptyline and nortriptyline in CYP2C19 and CYP2D6 extensive and intermediate metabolizers. Clin. Chem. 50(9), 1623–1633 (2004). 14 Gaedigk A, Riffel AK, Garcia Berrocal B,
Garcia-Solaesa V, Davila I, Isidoro-Garcia M. Characterization of a complex CYP2D6 genotype that caused an AmpliChip CYP450 Test ® no-call in the clinical setting. Clin. Chem. Lab. Med. doi:10.1515/ cclm-2013-0943 (2014) (Epub ahead of print). 15 Gaedigk A, Isidoro-Garcia M, Pearce RE
et al. Discovery of the nonfunctional CYP2D6*31 allele in Spanish, Puerto Rican, and US Hispanic populations. Eur. J. Clin. Pharmacol. 66(9), 859–864 (2010). 16 Crews KR, Gaedigk A, Dunnenberger HM
et al. Clinical Pharmacogenetics Implementation Consortium (CPIC)
409
Editorial
Gaedigk & Leeder
guidelines for cytochrome P450 2D6 (CYP2D6) genotype and codeine therapy: 2014 update. Clin. Pharmacol. Ther. doi:10.1038/clpt.2013.254 (2014) (Epub ahead of print). 17 Hicks JK, Swen JJ, Thorn CF et al. Clinical
Pharmacogenetics Implementation Consortium Guideline for CYP2D6 and CYP2C19 genotypes and dosing of tricyclic antidepressants. Clin. Pharmacol. Ther. 93(5), 402–408 (2013). 18 Bustin SA, Benes V, Garson J et al. The need
for transparency and good practices in the
410
qPCR literature. Nat. Methods 10(11), 1063–1067 (2013). 19 Wang D, Poi MJ, Sun X, Gaedigk A, Leeder
JS, Sadee W. Common CYP2D6 polymorphisms affecting alternative splicing and transcription: long-range haplotypes with two regulatory variants modulate CYP2D6 activity. Hum. Mol. Genet. 23(1), 268–278 (2013). 20 Ramamoorthy A, Li L, Gaedigk A et al.
In silico and in vitro identification of microRNAs that regulate hepatic nuclear factor 4alpha expression. Drug metabolism
Pharmacogenomics (2014) 15(4)
and disposition: the biological fate of chemicals. Drug Metab. Dispos. 40(4), 726–733 (2012).
Websites 101 CYP2D6 allele frequency table on
PharmGKB Knowledge Base. www.pharmgkb.org/download. action?filename=CYP2D6_Literature_Table_ and_Legend.pdf 102 The Human Cytochrome P450 (CYP) Allele
Nomenclature Database. www.cypalleles.ki.se
future science group
