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Marasanapalle VP, Masimirembwa C, Sivasubramanian R, Sayyed S, Weinzierl-Hinum A, Mehta D, Kapungu NN, Kanji C, Thelingwani R, Zack J. Investigation of the Differences in the Pharmacokinetics of CYP2D6 Substrates, Desipramine, and Dextromethorphan in Healthy African Subjects Carrying the Allelic Variants CYP2D6*17 and CYP2D6*29, When Compared with Normal Metabolizers. J Clin Pharmacol 2024; 64:578-589. [PMID: 37803948 DOI: 10.1002/jcph.2366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023]
Abstract
This study investigated the differences in the pharmacokinetics (PK) of dextromethorphan and desipramine in healthy African volunteers to understand the effect of allelic variants of the human cytochrome P450 2D6 (CYP2D6) enzyme, namely the diplotypes of CYP2D6*1/*2 (*1*1, *1*2, *2*2) and the genotypes of CYP2D6*17*17 and CYP2D6*29*29. Overall, 28 adults were included and split into 3 cohorts after genotype screening: CYP2D6*1/*2 (n = 12), CYP2D6*17*17 (n = 12), and CYP2D6*29*29 (n = 4). Each subject received a single oral dose of dextromethorphan 30 mg syrup on day 1 and desipramine 50 mg tablet on day 8. The PK parameters of area under the plasma concentration-time curve from time of dosing to time of last quantifiable concentration (AUClast), and extrapolated to infinity (AUCinf), and the maximum plasma concentration (Cmax) were determined. For both dextromethorphan and desipramine, AUCinf and Cmax were higher in subjects of the CYP2D6*29*29 and CYP2D6*17*17 cohorts, as compared with subjects in the CYP2D6*1/*2 diplotype cohort and with normal metabolizers from the literature. All PK parameters, including AUCinf, Cmax, and the elimination half-life, followed a similar trend: CYP2D6*17*17 > CYP2D6*29*29 > CYP2D6*1/*2. The plasma and urinary drug/metabolite exposure ratios of both drugs were higher in subjects of the CYP2D6*17*17 and CYP2D6*29*29 cohorts, when compared with subjects in the CYP2D6*1/*2 diplotype cohort. All adverse events were mild, except in 1 subject with CYP2D6*17*17 who had moderately severe headache with desipramine. These results indicate that subjects with CYP2D6*17*17 and CYP2D6*29*29 genotypes were 5-10 times slower metabolizers than those with CYP2D6*1/*2 diplotypes. These findings suggest that dose optimization may be required when administering CYP2D6 substrate drugs in African patients. Larger studies can further validate these findings.
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Affiliation(s)
| | - Collen Masimirembwa
- African Institute of Biomedical Science & Technology (AiBST), Harare, Zimbabwe
| | | | | | | | - Dheeraj Mehta
- Novartis Healthcare Private Limited, Hyderabad, India
| | | | - Comfort Kanji
- African Institute of Biomedical Science & Technology (AiBST), Harare, Zimbabwe
| | - Roslyn Thelingwani
- African Institute of Biomedical Science & Technology (AiBST), Harare, Zimbabwe
| | - Julia Zack
- Novartis Pharmaceutical Corporation, East Hanover, NJ, USA
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2
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Atiq MA, Peterson SE, Langman LJ, Baudhuin LM, Black JL, Moyer AM. Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach. J Pers Med 2023; 13:883. [PMID: 37373874 DOI: 10.3390/jpm13060883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
CYP2D6 duplication has important pharmacogenomic implications. Reflex testing with long-range PCR (LR-PCR) can resolve the genotype when a duplication and alleles with differing activity scores are detected. We evaluated whether visual inspection of plots from real-time-PCR-based targeted genotyping with copy number variation (CNV) detection could reliably determine the duplicated CYP2D6 allele. Six reviewers evaluated QuantStudio OpenArray CYP2D6 genotyping results and the TaqMan Genotyper plots for seventy-three well-characterized cases with three copies of CYP2D6 and two different alleles. Reviewers blinded to the final genotype visually assessed the plots to determine the duplicated allele or opt for reflex sequencing. Reviewers achieved 100% accuracy for cases with three CYP2D6 copies that they opted to report. Reviewers did not request reflex sequencing in 49-67 (67-92%) cases (and correctly identified the duplicated allele in each case); all remaining cases (6-24) were marked by at least one reviewer for reflex sequencing. In most cases with three copies of CYP2D6, the duplicated allele can be determined using a combination of targeted genotyping using real-time PCR with CNV detection without need for reflex sequencing. In ambiguous cases and those with >3 copies, LR-PCR and Sanger sequencing may still be necessary for determination of the duplicated allele.
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Affiliation(s)
- Mazen A Atiq
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Sandra E Peterson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Loralie J Langman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Linnea M Baudhuin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - John L Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street Southwest, Rochester, MN 55905, USA
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3
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Wang WY, Twesigomwe D, Nofziger C, Turner AJ, Helmecke LS, Broeckel U, Derezinski AD, Hazelhurst S, Gaedigk A. Characterization of Novel CYP2D6 Alleles across Sub-Saharan African Populations. J Pers Med 2022; 12:1575. [PMID: 36294714 PMCID: PMC9605556 DOI: 10.3390/jpm12101575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/11/2022] [Accepted: 09/19/2022] [Indexed: 07/16/2024] Open
Abstract
The CYP2D6 gene has been widely studied to characterize variants and/or star alleles, which account for a significant portion of variability in drug responses observed within and between populations. However, African populations remain under-represented in these studies. The increasing availability of high coverage genomes from African populations has provided the opportunity to fill this knowledge gap. In this study, we characterized computationally predicted novel CYP2D6 star alleles in 30 African subjects for whom DNA samples were available from the Coriell Institute. CYP2D6 genotyping and resequencing was performed using a variety of commercially available and laboratory-developed tests in a collaborative effort involving three laboratories. Fourteen novel CYP2D6 alleles and multiple novel suballeles were identified. This work adds to the growing catalogue of validated African ancestry CYP2D6 allelic variation in pharmacogenomic databases, thus laying the foundation for future functional studies and improving the accuracy of CYP2D6 genotyping, phenotype prediction, and the refinement of clinical pharmacogenomic implementation guidelines in African and global settings.
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Affiliation(s)
- Wendy Y. Wang
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | | | - Amy J. Turner
- Section of Genomic Pediatrics, Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- RPRD Diagnostics LLC, Milwaukee, WI 53226, USA
| | - Lena-Sophie Helmecke
- PharmGenetix GmbH, A-5020 Niederalm, Austria
- Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
- RPRD Diagnostics LLC, Milwaukee, WI 53226, USA
| | - Ashley D. Derezinski
- Section of Genomic Pediatrics, Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Research Institute, Kansas City, MO 64108, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
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4
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Rubben K, Tilleman L, Deserranno K, Tytgat O, Deforce D, Van Nieuwerburgh F. Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping. PLoS Genet 2022; 18:e1010176. [PMID: 36149915 PMCID: PMC9534437 DOI: 10.1371/journal.pgen.1010176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/05/2022] [Accepted: 09/10/2022] [Indexed: 11/19/2022] Open
Abstract
CYP2D6 is a very important pharmacogene as it is responsible for the metabolization or bioactivation of 20 to 30% of the clinically used drugs. However, despite its relatively small length of only 4.4 kb, it is one of the most challenging pharmacogenes to genotype due to the high similarity with its neighboring pseudogenes and the frequent occurrence of CYP2D6-CYP2D7 hybrids. Unfortunately, most current genotyping methods are therefore not able to correctly determine the complete CYP2D6-CYP2D7 sequence. Therefore, we developed a genotyping assay to generate complete allele-specific consensus sequences of complex regions by optimizing the PCR-free nanopore Cas9-targeted sequencing (nCATS) method combined with adaptive sequencing, and developing a new comprehensive long read genotyping (CoLoRGen) pipeline. The CoLoRGen pipeline first generates consensus sequences of both alleles and subsequently determines both large structural and small variants to ultimately assign the correct star-alleles. In reference samples, our genotyping assay confirms the presence of CYP2D6-CYP2D7 large structural variants, single nucleotide variants (SNVs), and small insertions and deletions (INDELs) that go undetected by most current assays. Moreover, our results provide direct evidence that the CYP2D6 genotype of the NA12878 DNA should be updated to include the CYP2D6-CYP2D7 *68 hybrid and several additional single nucleotide variants compared to existing references. Ultimately, the nCATS-CoLoRGen genotyping assay additionally allows for more accurate gene function predictions by enabling the possibility to detect and phase de novo mutations in addition to known large structural and small variants. During the last decades, the usefulness of personalized medicine has become increasingly apparent. Directly linked to that is the need for accurate genotyping assays to determine the pharmacogenetic profile of patients. Continuing research has led to the development of genotyping assays that perform quite robustly. However, complex genes remain an issue when it comes to determining the complete sequence correctly. An example of such a complex but very important pharmacogene is CYP2D6. Therefore, we developed a genotyping assay in an attempt to generate complete allele-specific consensus sequences of CYP2D6, by optimizing a targeted amplification-free long-read sequencing method and developing a new analysis pipeline. In reference samples, we showed that our genotyping assay performed accurately and confirmed the presence of variants that go undetected by most current assays. However, the implementation of this assay in practice is still hampered as the selected enrichment strategies inherently lead to a low percentage of on-target reads, resulting in low on-target sequencing depths. Further optimization and validation of the assay is thus needed, but definitely worth considering for follow-up research as we already demonstrated the added value for generating more complete genotypes, which on its turn will result in more accurate gene function predictions.
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Affiliation(s)
- Kaat Rubben
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Koen Deserranno
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
- Department of Life Science Technologies, Imec, Leuven, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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5
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Genetic Variation among Pharmacogenes in the Sardinian Population. Int J Mol Sci 2022; 23:ijms231710058. [PMID: 36077453 PMCID: PMC9456055 DOI: 10.3390/ijms231710058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022] Open
Abstract
Pharmacogenetics (PGx) aims to identify the genetic factors that determine inter-individual differences in response to drug treatment maximizing efficacy while decreasing the risk of adverse events. Estimating the prevalence of PGx variants involved in drug response, is a critical preparatory step for large-scale implementation of a personalized medicine program in a target population. Here, we profiled pharmacogenetic variation in fourteen clinically relevant genes in a representative sample set of 1577 unrelated sequenced Sardinians, an ancient island population that accounts for genetic variation in Europe as a whole, and, at the same time is enriched in genetic variants that are very rare elsewhere. To this end, we used PGxPOP, a PGx allele caller based on the guidelines created by the Clinical Pharmacogenetics Implementation Consortium (CPIC), to identify the main phenotypes associated with the PGx alleles most represented in Sardinians. We estimated that 99.43% of Sardinian individuals might potentially respond atypically to at least one drug, that on average each individual is expected to have an abnormal response to about 17 drugs, and that for 27 drugs the fraction of the population at risk of atypical responses to therapy is more than 40%. Finally, we identified 174 pharmacogenetic variants for which the minor allele frequency was at least 10% higher among Sardinians as compared to other European populations, a fact that may contribute to substantial interpopulation variability in drug response phenotypes. This study provides baseline information for further large-scale pharmacogenomic investigations in the Sardinian population and underlines the importance of PGx characterization of diverse European populations, such as Sardinians.
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6
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Boucenna A, Boudaoud K, Hireche A, Rezgoune ML, Abadi N, Filali T, Satta D. Influence of CYP2D6, CYP2C19 and CYP3A5 polymorphisms on plasma levels of tamoxifen metabolites in Algerian women with ER+ breast cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Background
Tamoxifen, a selective estrogen receptor modulator, is indicated for breast cancer developed in response to estrogen.
Findings
In the current study we explored the relationship between the different variants of CYP2D6, CYP2C19, CYP3A5 and plasma Endoxifen levels in Algerian patients with ER + breast cancer. We further conducted the relationship between the candidate genes and the recurrences rate. Endoxifen levels differed significantly (p < .005) between carriers of two functional alleles and patients genotyped as CYP2D6*10, CYP2D6*17, CYP2D6*41 or CYP2D6*5/*5. Patients with elevated Endoxifen concentrations were significantly more likely to not report recurrences than patients with reduced or nul alleles. Such nul/nul, red/red, and red/nul diplotypes have been associated with a higher rate of recurrences than other genotypes during treatment.
Conclusion
Our findings suggest that the CYP2D6 genotype should be considered in tamoxifen-treated women. While quantitatively, CYP2D6 represents only a minor fraction of the total drug metabolizing capacity of the liver, it is polymorphic and, therefore, may alter the balance of metabolism of tamoxifen toward the activation pathways. Breast cancer patients with the CYP2D6 nul/nul or red/nul diplotype may benefit less from Tamoxifen treatment and are more likely to develop recurrences. Comprehensive CYP2D6 genotyping has a good predictive value for CYP2D6 activity. Common variants in CYP2C19 and CYP3A5 did not have a significant impact on the recurrences in this cohort of patients with ER + breast cancer.
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7
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Wen YF, Gaedigk A, Boone EC, Wang WY, Straka RJ. The Identification of Novel CYP2D6 Variants in US Hmong: Results From Genome Sequencing and Clinical Genotyping. Front Pharmacol 2022; 13:867331. [PMID: 35387332 PMCID: PMC8979107 DOI: 10.3389/fphar.2022.867331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Hmong individuals represent a unique East Asian subpopulation in whom limited information concerning pharmacogenetic variation exists. The objectives of this study were to comprehensively characterize the highly polymorphic CYP2D6 gene in Hmong, estimate allele and phenotype frequencies and to compare results between two testing platforms. Methods: DNA from 48 self-identified Hmong participants were sequenced using a targeted next-generation sequencing (NGS) panel. Star allele calls were made using Astrolabe, manual inspection of NGS variant calls and confirmatory Sanger sequencing. Structural variation was determined by long-range (XL)-PCR and digital droplet PCR (ddPCR). The consensus diplotypes were subsequently translated into phenotype utilizing the activity score system. Clinical grade pharmacogenetic testing was obtained for 12 of the 48 samples enabling an assessment of concordance between the consensus calls and those determined by clinical testing platforms. Results: A total of 13 CYP2D6 alleles were identified. The most common alleles were CYP2D6*10 and its structural arrangements (37.5%, 36/96) and the *5 gene deletion (13.5%, 13/96). Three novel suballeles (*10.007, *36.004, and *75.002) were also identified. Phenotype frequencies were as follows: ultrarapid metabolizers (4.2%, 2/48), normal metabolizers (41.7%, 20/48) and intermediate metabolizers (52.1%, 25/48); none of the 48 participants were predicted to be poor metabolizers. Concordance of diplotype and phenotype calls between the consensus and clinical testing were 66.7 and 50%, respectively. Conclusion: Our study to explore CYP2D6 genotypes in the Hmong population suggests that this subpopulation is unique regarding CYP2D6 allelic variants; also, a higher portion of Hmong participants (50%) are predicted to have an intermediate metabolizer phenotype for CYP2D6 compared to other East Asians which range between 27 and 44%. Results from different testing methods varied considerably. These preliminary findings underscore the importance of thoroughly interrogating unique subpopulations to accurately predict a patient's CYP2D6 metabolizer status.
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Affiliation(s)
- Ya Feng Wen
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Twin Cities, MN, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, MO, United States.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, MO, United States
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute, Kansas City, MO, United States
| | - Robert J Straka
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Twin Cities, MN, United States
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8
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Dinh JC, Boone EC, Staggs VS, Pearce RE, Wang WY, Gaedigk R, Leeder JS, Gaedigk A. The Impact of the CYP2D6 "Enhancer" Single Nucleotide Polymorphism on CYP2D6 Activity. Clin Pharmacol Ther 2022; 111:646-654. [PMID: 34716917 PMCID: PMC8825689 DOI: 10.1002/cpt.2469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/21/2021] [Indexed: 11/10/2022]
Abstract
rs5758550 has been associated with enhanced transcription and suggested to be a useful marker of CYP2D6 activity. As there are limited and inconsistent data regarding the utility of this distant "enhancer" single nucleotide polymorphism (SNP), our goal was to further assess the impact of rs5758550 on CYP2D6 activity toward two probe substrates, atomoxetine (ATX) and dextromethorphan (DM), using in vivo urinary metabolite (DM; n = 188) and pharmacokinetic (ATX; n = 70) and in vitro metabolite formation (ATX and DM; n = 166) data. All subjects and tissues were extensively genotyped, the "enhancer" SNP phased with established CYP2D6 haplotypes either computationally or experimentally, and the impact on CYP2D6 activity investigated using several linear models of varying complexity to determine the proportion of variability in CYP2D6 activity captured by each model. For all datasets and models, the "enhancer" SNP had no or only a modest impact on CYP2D6 activity prediction. An increased effect, when present, was more pronounced for ATX than DM suggesting potential substate-dependency. In addition, CYP2D6*2 alleles with the "enhancer" SNP were associated with modestly higher metabolite formation rates in vitro, but not in vivo; no effect was detected for CYP2D6*1 alleles with "enhancer" SNP. In summary, it remains inconclusive whether the small effects detected in this investigation are indeed caused by the "enhancer" SNP or are rather due to its incomplete linkage with other variants within the gene. Taken together, there does not appear to be sufficient evidence to warrant the "enhancer" SNP be included in clinical CYP2D6 pharmacogenetic testing.
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Affiliation(s)
- Jean C Dinh
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Vincent S Staggs
- Biostatistics and Epidemiology Core, Health Services and Outcomes Research, Children's Mercy Kansas City, Kansas City, Missouri, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Robin E Pearce
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Roger Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - James Steven Leeder
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
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9
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Chan ER, Mehlotra RK, Pirani KA, Ratsimbasoa AC, Williams SM, Gaedigk A, Zimmerman PA. CYP2D6 gene resequencing in the Malagasy, a population at the crossroads between Asia and Africa: a pilot study. Pharmacogenomics 2022; 23:315-325. [PMID: 35230160 PMCID: PMC8965795 DOI: 10.2217/pgs-2021-0146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background: Plasmodium vivax malaria is endemic in Madagascar, where populations have genetic inheritance from Southeast Asia and East Africa. Primaquine, a drug of choice for vivax malaria, is metabolized principally via CYP2D6. CYP2D6 variation was characterized by locus-specific gene sequencing and was compared with TaqMan™ genotype data. Materials & methods: Long-range PCR amplicons were generated from 96 Malagasy samples and subjected to next-generation sequencing. Results: The authors observed high concordance between TaqMan™-based CYP2D6 genotype calls and the base calls from sequencing. In addition, there are new variants and haplotypes present in the Malagasy. Conclusion: Sequencing unique admixed populations provides more detailed and accurate insights regarding CYP2D6 variability, which may help optimize primaquine treatment across human genetic diversity.
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Affiliation(s)
- E Ricky Chan
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Rajeev K Mehlotra
- Center for Global Health & Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Karim A Pirani
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Arsene C Ratsimbasoa
- University of Fianarantsoa, Fianarantsoa, Madagascar.,CNARP (Centre National d'Application de Recherche Pharmaceutique), Antananarivo, Madagascar
| | - Scott M Williams
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Peter A Zimmerman
- Center for Global Health & Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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10
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Sicko RJ, Romitti PA, Browne ML, Brody LC, Stevens CF, Mills JL, Caggana M, Kay DM. Rare Variants in RPPH1 Real-Time Quantitative PCR Control Assay Binding Sites Result in Incorrect Copy Number Calls. J Mol Diagn 2022; 24:33-40. [PMID: 34656763 PMCID: PMC8802765 DOI: 10.1016/j.jmoldx.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 01/03/2023] Open
Abstract
Real-time quantitative PCR (qPCR) using RPPH1 as a reference gene is a standard method for assessment and validation of genomic copy number variations. However, variants in the reference amplicon may cause errors, which was investigated herein. While conducting copy number variation validations for birth defects research studies, 13 of 1634 specimens with multiple loci that appeared to be present as three copies were unexpectedly detected. This apparent trisomy was hypothesized to be an amplification artifact caused by a variant in the RPPH1 amplicon. Sequencing revealed all 13 individuals carried one of the four different variants within the RPPH1 amplicon. These variants could produce allelic dropout or altered reaction efficiency, causing an inaccurate measurement of copy number. Additional genotyping predicted a low frequency of the most common variant (rs3093876; 14/3562 alleles; minor allele frequency, 0.39%). Laboratories should recognize the potential for inaccurate results when using a single qPCR control assay. Overestimated CFTR and SMN2 copy numbers identified during newborn screening that otherwise would have been incorrectly called were also detected. Variants in reference loci may produce false-negative normal results for test loci when real deletions are present. For clinical laboratories screening for heterozygous deletions for diagnostic testing or prenatal/carrier screening via qPCR, the most cost-effective solution to maximize sensitivity is to run triplex reactions targeting the region of interest with two control genes.
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Affiliation(s)
- Robert J Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L Browne
- Birth Defects Registry, New York State Department of Health, Albany, New York; University at Albany School of Public Health, Rensselaer, New York
| | - Lawrence C Brody
- Genetics and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Colleen F Stevens
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York.
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11
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Carvalho Henriques B, Buchner A, Hu X, Wang Y, Yavorskyy V, Wallace K, Dong R, Martens K, Carr MS, Behroozi Asl B, Hague J, Sivapalan S, Maier W, Dernovsek MZ, Henigsberg N, Hauser J, Souery D, Cattaneo A, Mors O, Rietschel M, Pfeffer G, Hume S, Aitchison KJ. Methodology for clinical genotyping of CYP2D6 and CYP2C19. Transl Psychiatry 2021; 11:596. [PMID: 34811360 PMCID: PMC8608805 DOI: 10.1038/s41398-021-01717-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 10/28/2021] [Indexed: 01/10/2023] Open
Abstract
Many antidepressants, atomoxetine, and several antipsychotics are metabolized by the cytochrome P450 enzymes CYP2D6 and CYP2C19, and guidelines for prescribers based on genetic variants exist. Although some laboratories offer such testing, there is no consensus regarding validated methodology for clinical genotyping of CYP2D6 and CYP2C19. The aim of this paper was to cross-validate multiple technologies for genotyping CYP2D6 and CYP2C19 against each other, and to contribute to feasibility for clinical implementation by providing an enhanced range of assay options, customizable automated translation of data into haplotypes, and a workflow algorithm. AmpliChip CYP450 and some TaqMan single nucleotide variant (SNV) and copy number variant (CNV) data in the Genome-based therapeutic drugs for depression (GENDEP) study were used to select 95 samples (out of 853) to represent as broad a range of CYP2D6 and CYP2C19 genotypes as possible. These 95 included a larger range of CYP2D6 hybrid configurations than have previously been reported using inter-technology data. Genotyping techniques employed were: further TaqMan CNV and SNV assays, xTAGv3 Luminex CYP2D6 and CYP2C19, PharmacoScan, the Ion AmpliSeq Pharmacogenomics Panel, and, for samples with CYP2D6 hybrid configurations, long-range polymerase chain reactions (L-PCRs) with Sanger sequencing and Luminex. Agena MassARRAY was also used for CYP2C19. This study has led to the development of a broader range of TaqMan SNV assays, haplotype phasing methodology with TaqMan adaptable for other technologies, a multiplex genotyping method for efficient identification of some hybrid haplotypes, a customizable automated translation of SNV and CNV data into haplotypes, and a clinical workflow algorithm.
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Affiliation(s)
| | - Avery Buchner
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Xiuying Hu
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Yabing Wang
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Vasyl Yavorskyy
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Keanna Wallace
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Rachael Dong
- grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Kristina Martens
- grid.22072.350000 0004 1936 7697Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Michael S. Carr
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Pharmacology, University of Alberta, Edmonton, Canada
| | - Bahareh Behroozi Asl
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Joshua Hague
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Sudhakar Sivapalan
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada
| | - Wolfgang Maier
- grid.10388.320000 0001 2240 3300Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | | | - Neven Henigsberg
- grid.4808.40000 0001 0657 4636Croatian Institute for Brain Research, Centre for Excellence for Basic, Clinical and Translational Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Joanna Hauser
- grid.22254.330000 0001 2205 0971Departnent of Psychiatry, Poznan University of Medical Sciences, Poznań, Poland
| | - Daniel Souery
- grid.4989.c0000 0001 2348 0746Laboratoire de Psychologie Médicale, Université Libre de Bruxelles and Psy Pluriel, Centre Européen de Psychologie Médicale, Brussels, Belgium
| | - Annamaria Cattaneo
- grid.419422.8Biological Psychiatry Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy ,grid.4708.b0000 0004 1757 2822Department of Pharmacological and Biomolecular Sciences, University of Milan, via Balzaretti 9, 20133 Milan, Italy
| | - Ole Mors
- grid.154185.c0000 0004 0512 597XPsychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Marcella Rietschel
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty of Mannheim, Heidelberg University, Mannheim, Germany
| | - Gerald Pfeffer
- grid.22072.350000 0004 1936 7697Department of Clinical Neurosciences, Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, Canada ,grid.22072.350000 0004 1936 7697Alberta Child Health Research Institute & Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Stacey Hume
- grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, University of Alberta, Edmonton, Canada ,Alberta Precision Laboratories, Edmonton, Canada
| | - Katherine J. Aitchison
- grid.17089.370000 0001 2190 316XDepartment of Psychiatry, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XNeuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada ,grid.17089.370000 0001 2190 316XDepartment of Medical Genetics, University of Alberta, Edmonton, Canada ,grid.413574.00000 0001 0693 8815Alberta Health Services, Edmonton, Canada ,grid.13097.3c0000 0001 2322 6764King’s College London, London, UK
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Pratt VM, Cavallari LH, Del Tredici AL, Gaedigk A, Hachad H, Ji Y, Kalman LV, Ly RC, Moyer AM, Scott SA, van Schaik RHN, Whirl-Carrillo M, Weck KE. Recommendations for Clinical CYP2D6 Genotyping Allele Selection: A Joint Consensus Recommendation of the Association for Molecular Pathology, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, and the European Society for Pharmacogenomics and Personalized Therapy. J Mol Diagn 2021; 23:1047-1064. [PMID: 34118403 DOI: 10.1016/j.jmoldx.2021.05.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/11/2021] [Accepted: 05/25/2021] [Indexed: 01/14/2023] Open
Abstract
The goals of the Association for Molecular Pathology Clinical Practice Committee's Pharmacogenomics (PGx) Working Group are to define the key attributes of pharmacogenetic alleles recommended for clinical testing, and to determine a minimal set of variants that should be included in clinical PGx genotyping assays. This document series provides recommendations on a minimal panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories in designing assays for PGx testing. When developing these recommendations, the Association for Molecular Pathology PGx Working Group considered the functional impact of the variant alleles, allele frequencies in multiethnic populations, the availability of reference materials, as well as other technical considerations with regard to PGx testing. The ultimate goal of this Working Group is to promote standardization of PGx gene/allele testing across clinical laboratories. This document is focused on clinical CYP2D6 PGx testing that may be applied to all cytochrome P450 2D6-metabolized medications. These recommendations are not meant to be interpreted as prescriptive but to provide a reference guide for clinical laboratories that may be either implementing PGx testing or reviewing and updating their existing platform.
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Affiliation(s)
- Victoria M Pratt
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Larisa H Cavallari
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and Precision Medicine, University of Florida, Gainesville, Florida
| | - Andria L Del Tredici
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Millennium Health, LLC, San Diego, California
| | - Andrea Gaedigk
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Houda Hachad
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; private precision medicine consultancy, Seattle, Washington
| | - Yuan Ji
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Lisa V Kalman
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Reynold C Ly
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ann M Moyer
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stuart A Scott
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University, Stanford, California; Clinical Genomics Program, Stanford Health Care, Palo Alto, California
| | - R H N van Schaik
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Chemistry/IFCC Expert center Pharmacogenetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; European Society of Pharmacogenomics and Personalized Therapy
| | - Michelle Whirl-Carrillo
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Biomedical Data Science, Stanford University, Stanford, California
| | - Karen E Weck
- The Pharmacogenomics Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine and Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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Hongkaew Y, Wang WY, Gaedigk R, Sukasem C, Gaedigk A. Resolving discordant CYP2D6 genotyping results in Thai subjects: platform limitations and novel haplotypes. Pharmacogenomics 2021; 22:529-541. [PMID: 33998274 DOI: 10.2217/pgs-2021-0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: Several CYP2D6 Luminex xTAG genotype calls were identified as inconsistent or suspicious among Thai subjects and further characterized to identify the root causes. Material & methods: Forty-eight subjects were followed-up with long-range-PCR, quantitative copy number assays and/or Sanger sequencing. Results: Most of the Luminex-duplication calls were either negative or had hybrid structures involving CYP2D6*36 in various configurations. Ten samples were inaccurately called as CYP2D6*2, *29 or *35 alleles. Sequencing revealed three novel haplotypes, CYP2D6*142, *143 and *144 of which two are nonfunctional. Conclusion: The Luminex platform produced a relatively high number of false genotype calls for Thai subjects. Our findings underscore the need for the systematic characterization of the CYP2D6 locus in diverse populations and rigorous platform validation.
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Affiliation(s)
- Yaowaluck Hongkaew
- Department of Laboratory, Division of Advance Research & Development Laboratory, Bumrungrad International Hospital, Bangkok, Thailand
| | - Wendy Y Wang
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Roger Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Chonlaphat Sukasem
- Department of Pathology, Division of Pharmacogenomics & Personalized Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
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14
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Turner AJ, Aggarwal P, Boone EC, Haidar CE, Relling MV, Derezinski AD, Broeckel U, Gaedigk A. Identification of CYP2D6 Haplotypes that Interfere with Commonly Used Assays for Copy Number Variation Characterization. J Mol Diagn 2021; 23:577-588. [PMID: 33631352 DOI: 10.1016/j.jmoldx.2021.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) copy number (CN) variation affects the metabolism of numerous prescribed drugs. Sequence variation within primer or probe target regions of hydrolysis probe CN assays can generate false-positive calls for CN loss. Furthermore, CYP2D6-CYP2D7 hybrids and gene conversions can cause difficult to interpret discordant CN calls. The identification of haplotypes with CN variations and structural arrangements is important to predict phenotype accurately. During clinical testing with hydrolysis probe assays targeting three CYP2D6 regions (intron 2, intron 6, and exon 9), samples with haplotypes causing inconsistent CN calls were identified. To resolve these cases, next-generation sequencing and allele-specific Sanger sequencing was performed. Sequence analysis of 16 samples, all but one from subjects of African descent, identified six novel suballeles containing single-nucleotide polymorphisms, which cause false-positive calls for CN loss in introns 2 and 6. Five samples with an exon 9 CN loss contained CYP2D6/CYP2D7 hybrids (∗13 or ∗36) and one sample was found to have a novel haplotype, CYP2D6∗141. Interestingly, CYP2D6∗141 contains a CYP2D7-derived exon 9 conversion and core single-nucleotide polymorphisms that are otherwise found in CYP2D6∗17 and ∗27. Although these variants are rare, they can cause inconsistent CN calls that typically are reported as no calls or indeterminant, and thus may deprive patients, particularly those of African descent, from taking full benefit of pharmacogenetic testing.
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Affiliation(s)
- Amy J Turner
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Right Patient Right Drug Diagnostics, Wauwatosa, Wisconsin
| | - Praful Aggarwal
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Right Patient Right Drug Diagnostics, Wauwatosa, Wisconsin
| | - Erin C Boone
- Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri
| | - Cyrine-Eliana Haidar
- Pharmaceutical Science Department, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mary V Relling
- Pharmaceutical Science Department, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Ulrich Broeckel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Right Patient Right Drug Diagnostics, Wauwatosa, Wisconsin
| | - Andrea Gaedigk
- Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri.
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15
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Determination of novel CYP2D6 haplotype using the targeted sequencing followed by the long-read sequencing and the functional characterization in the Japanese population. J Hum Genet 2020; 66:139-149. [PMID: 32759992 DOI: 10.1038/s10038-020-0815-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/08/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) has identified variations in cytochrome P450 (CYP) 2D6 associated with drug responses. However, determination of novel haplotypes is difficult because of the short reads generated by NGS. We aimed to identify novel CYP2D6 variants in the Japanese population and predict the CYP2D6 phenotype based on in vitro metabolic studies. Using a targeted NGS panel (PKSeq), 990 Japanese genomes were sequenced, and then novel CYP2D6 haplotypes were determined. Km, Vmax, and intrinsic clearance (Vmax/Km) of N-desmethyl-tamoxifen 4-hydroxylation were calculated by in vitro metabolic studies using cDNA-expressed CYP2D6 proteins. After determination of the CYP2D6 diplotypes, phenotypes of the individuals were predicted based on the in vitro metabolic activities. Targeted NGS identified 14 CYP2D6 variants not registered in the Pharmacogene Variation Consortium (PharmVar) database. Ten novel haplotypes were registered as CYP2D6*128 to *137 alleles in the PharmVar database. Based on the Vmax/Km value of each allele, *128, *129, *130, *131, *132, and *133 were predicted to be nonfunctional alleles. According to the results of the present study, six normal metabolizers (NM) and one intermediate (IM) metabolizers were designated as IM and poor metabolizers (PM), respectively. Our findings provide important insights into novel haplotypes and haplotypes of CYP2D6 and the effects on in vitro metabolic activities.
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Liau Y, Maggo S, Miller AL, Pearson JF, Kennedy MA, Cree SL. Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications. Pharmacogenomics 2020; 20:1033-1047. [PMID: 31559921 DOI: 10.2217/pgs-2019-0080] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the whole CYP2D6 gene using nanopore sequencing. Materials and methods: 32 samples covering various haplotypes including gene duplication were sequenced on the GridION platform. Results: Haplotypes of 52 alleles matched accurately to known star (*) allele subvariants, with the remaining 12 being assigned as new alleles, or new subvariants of known alleles. Duplicated alleles could be detected by analyzing the allelic balance. Conclusion: Nanopore sequencing of CYP2D6 offers a high throughput method for accurate haplotyping, detection of new variants and determination of duplicated alleles.
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Affiliation(s)
- Yusmiati Liau
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simran Maggo
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Allison L Miller
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L Cree
- Department of Pathology & Biomedical Science, University of Otago, Christchurch, New Zealand
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17
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Boone EC, Wang WY, Gaedigk R, Cherner M, Bérard A, Leeder JS, Miller NA, Gaedigk A. Long-Distance Phasing of a Tentative "Enhancer" Single-Nucleotide Polymorphism With CYP2D6 Star Allele Definitions. Front Pharmacol 2020; 11:486. [PMID: 32457600 PMCID: PMC7226225 DOI: 10.3389/fphar.2020.00486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The CYP2D6 gene locus has been extensively studied over decades, yet a portion of variability in CYP2D6 activity cannot be explained by known sequence variations within the gene, copy number variation, or structural rearrangements. It was proposed that rs5758550, located 116 kb downstream of the CYP2D6 gene locus, increases gene expression and thus contributes to variability in CYP2D6 activity. This finding has, however, not been validated. The purpose of the study was to address a major technological barrier, i.e., experimentally linking rs5758550, also referred to as the "enhancer" single-nucleotide polymorphism (SNP), to CYP2D6 haplotypes >100 kb away. To overcome this challenge is essential to ultimately determine the contribution of the "enhancer" SNP to interindividual variability in CYP2D6 activity. METHODS A large ethnically mixed population sample (n=3,162) was computationally phased to determine linkage between the "enhancer" SNP and CYP2D6 haplotypes (or star alleles). To experimentally validate predicted linkages, DropPhase2D6, a digital droplet PCR (ddPCR)-based method was developed. 10X Genomics Linked-Reads were utilized as a proof of concept. RESULTS Phasing predicted that the "enhancer" SNP can occur on numerous CYP2D6 haplotypes including CYP2D6*1, *2, *5, and *41 and suggested that linkage is incomplete, i.e., a portion of these alleles do not have the "enhancer" SNP. Phasing also revealed differences among the European and African ancestry data sets regarding the proportion of alleles with and without the "enhancer" SNP. DropPhase2D6 was utilized to confirm or refute the predicted "enhancer" SNP location for individual samples, e.g., of n=3 samples genotyped as *1/*41, rs5758550 was on the *41 allele of two samples and on the *1 allele of one sample. Our findings highlight that the location of the "enhancer" SNP must not be assigned by "default." Furthermore, linkage between the "enhancer" SNP and CYP2D6 star allele haplotypes was confirmed with 10X Genomics technology. CONCLUSIONS Since the "enhancer" SNP can be present on a portion of normal, decreased, or no function alleles, the phase of the "enhancer" SNP must be considered when investigating the impact of the "enhancer" SNP on CYP2D6 activity.
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Affiliation(s)
- Erin C. Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Wendy Y. Wang
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Roger Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Mariana Cherner
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Anick Bérard
- Faculty of Pharmacy, University of Montreal, Montreal, QC, Canada
- Research Center, CHU Sainte-Justine, Montreal, QC, Canada
| | - J. Steven Leeder
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
| | - Neil A. Miller
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO, United States
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18
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CYP2D6 haplotypes with enhancer single-nucleotide polymorphism rs5758550 and rs16947 (*2 allele): implications for CYP2D6 genotyping panels. Pharmacogenet Genomics 2020; 29:39-47. [PMID: 30520769 DOI: 10.1097/fpc.0000000000000363] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION CYP2D6 metabolizes ∼25% of all clinically used drugs, with numerous genetic polymorphisms affecting enzyme activity and drug response. Clinical utility of current CYP2D6 genotyping is partially compromised the unresolved complex haplotype structure of the CYP2D6 locus. We have identified a distal enhancer single-nucleotide polymorphism rs5758550 that robustly increases CYP2D6 expression, whereas rs16947 (CYP2D6*2), previously considered inert, reduces correct mRNA splicing and expression, thereby affecting presumed activity of other alleles on the *2 haplotype. OBJECTIVE This study aims to determine the structure and frequency of haplotypes containing either rs5758550 or rs16947, or both, together with other relevant CYP2D6 alleles, assigning predictive enzyme activity scores to each, and addressing ambiguities in estimating diplotypes in different populations. METHODS The structure and frequency of haplotypes containing rs5758550 and/or rs16947 in different populations were determined by using phased genotype data from 'The 1000 Genomes Project'. The assigned haplotype-phenotype relationship was tested by associating assigned CYP2D6 activity score with CYP2D6 enzyme activity in a cohort of 122 human liver microsomes. RESULTS Addition of enhancer single-nucleotide polymorphism rs5758550 and *2 to a CYP2D6 panel improves prediction of CYP2D6 activity. Moreover, the haplotype containing rs5758550 and rs16947 predict extensive CYP2D6 activity more accurately than CYP2D6*2A, a surrogate marker for extensive activity. CONCLUSION With further studies, the results support possible incorporation of rs5758550 and rs16947 into CYP2D6 biomarker panels for more accurate prediction of CYP2D6 metabolizer status.
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Nofziger C, Turner AJ, Sangkuhl K, Whirl-Carrillo M, Agúndez JAG, Black JL, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Gaedigk A. PharmVar GeneFocus: CYP2D6. Clin Pharmacol Ther 2020; 107:154-170. [PMID: 31544239 PMCID: PMC6925641 DOI: 10.1002/cpt.1643] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 01/13/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocus provides a comprehensive overview and summary of CYP2D6 genetic variation and describes how the information provided by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
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Affiliation(s)
| | - Amy J. Turner
- Department of Pediatrics, Section of Genomic Pediatrics and Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - José A. G. Agúndez
- University Institute of Molecular Pathology Biomarkers, UEx, Cáceres; ARADyAL Instituto de Salud Carlos III. Spain
| | - John L. Black
- Personalized Genomics Laboratory, Division of Laboratory Genetics and Genomics, Mayo Clinic laboratories, Mayo Clinic, Rochester MN (200 1st Street SW, Rochester MN 55902)
| | - Henry M. Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanton, IL, USA
| | - Gualberto Ruano
- Institute of Living at Hartford Hospital, Genomas Laboratory of Personalized Health, Hartford, Connecticut (67 Jefferson Street, Hartford, Connecticut 06106)
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science, University Otago, Christchurch, New Zealand
| | - Michael S. Phillips
- Sequence Bioinformatics Inc., 139 Water Street, 2 Floor, St. John’s NL, A1C 1B2, Canada
| | | | - Teri E. Klein
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
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20
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Dalton R, Lee SB, Claw KG, Prasad B, Phillips BR, Shen DD, Wong LH, Fade M, McDonald MG, Dunham MJ, Fowler DM, Rettie AE, Schuetz E, Thornton TA, Nickerson DA, Gaedigk A, Thummel KE, Woodahl EL. Interrogation of CYP2D6 Structural Variant Alleles Improves the Correlation Between CYP2D6 Genotype and CYP2D6-Mediated Metabolic Activity. Clin Transl Sci 2019; 13:147-156. [PMID: 31536170 PMCID: PMC6951848 DOI: 10.1111/cts.12695] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 01/03/2023] Open
Abstract
The cytochrome P450 2D6 (CYP2D6) gene locus is challenging to accurately genotype due to numerous single nucleotide variants and complex structural variation. Our goal was to determine whether the CYP2D6 genotype‐phenotype correlation is improved when diplotype assignments incorporate structural variation, identified by the bioinformatics tool Stargazer, with next‐generation sequencing data. Using CYP2D6 activity measured with substrates dextromethorphan and metoprolol, activity score explained 40% and 34% of variability in metabolite formation rates, respectively, when diplotype calls incorporated structural variation, increasing from 36% and 31%, respectively, when diplotypes did not incorporate structural variation. We also investigated whether the revised Clinical Pharmacogenetics Implementation Consortium (CPIC) recommendations for translating genotype to phenotype improve CYP2D6 activity predictions over the current system. Although the revised recommendations do not improve the correlation between activity score and CYP2D6 activity, perhaps because of low frequency of the CYP2D6*10 allele, the correlation with metabolizer phenotype group was significantly improved for both substrates. We also measured the function of seven rare coding variants: one (A449D) exhibited decreased (44%) and another (R474Q) increased (127%) activity compared with reference CYP2D6.1 protein. Allele‐specific analysis found that A449D is part of a novel CYP2D6*4 suballele, CYP2D6*4.028. The novel haplotype containing R474Q was designated CYP2D6*138 by PharmVar; another novel haplotype containing R365H was designated CYP2D6*139. Accuracy of CYP2D6 phenotype prediction is improved when the CYP2D6 gene locus is interrogated using next‐generation sequencing coupled with structural variation analysis. Additionally, revised CPIC genotype to phenotype translation recommendations provides an improvement in assigning CYP2D6 activity.
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Affiliation(s)
- Rachel Dalton
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
| | - Seung-Been Lee
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Katrina G Claw
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Brian R Phillips
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Danny D Shen
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Lai Hong Wong
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Mitch Fade
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Matthew G McDonald
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Maitreya J Dunham
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Douglas M Fowler
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Erin Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Departments of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic Innovation, Children's Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA
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21
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CYP2D6 Polymorphisms and the Safety and Gametocytocidal Activity of Single-Dose Primaquine for Plasmodium falciparum. Antimicrob Agents Chemother 2019; 63:AAC.00538-19. [PMID: 31383656 PMCID: PMC6761544 DOI: 10.1128/aac.00538-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
Single-dose primaquine (PQ) clears mature gametocytes and reduces the transmission of Plasmodium falciparum after artemisinin combination therapy. Genetic variation in CYP2D6, the gene producing the drug-metabolizing enzyme cytochrome P450 2D6 (CYP2D6), influences plasma concentrations of PQ and its metabolites and is associated with PQ treatment failure in Plasmodium vivax malaria. Single-dose primaquine (PQ) clears mature gametocytes and reduces the transmission of Plasmodium falciparum after artemisinin combination therapy. Genetic variation in CYP2D6, the gene producing the drug-metabolizing enzyme cytochrome P450 2D6 (CYP2D6), influences plasma concentrations of PQ and its metabolites and is associated with PQ treatment failure in Plasmodium vivax malaria. Using blood and saliva samples of varying quantity and quality from 8 clinical trials across Africa (n = 1,076), we were able to genotype CYP2D6 for 774 samples (72%). We determined whether genetic variation in CYP2D6 has implications for PQ efficacy in individuals with gametocytes at the time of PQ administration (n = 554) and for safety in glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals treated with PQ (n = 110). Individuals with a genetically inferred CYP2D6 poor/intermediate metabolizer status had a higher gametocyte prevalence on day 7 or 10 after PQ than those with an extensive/ultrarapid CYP2D6 metabolizer status (odds ratio [OR] = 1.79 [95% confidence interval {CI}, 1.10, 2.90]; P = 0.018). The mean minimum hemoglobin concentrations during follow-up for G6PD-deficient individuals were 11.8 g/dl for CYP2D6 extensive/ultrarapid metabolizers and 12.1 g/dl for CYP2D6 poor/intermediate metabolizers (P = 0. 803). CYP2D6 genetically inferred metabolizer status was also not associated with anemia following PQ treatment (P = 0.331). We conclude that CYP2D6 poor/intermediate metabolizer status may be associated with prolonged gametocyte carriage after treatment with single-low-dose PQ but not with treatment safety.
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22
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Gaedigk A, Turner A, Everts RE, Scott SA, Aggarwal P, Broeckel U, McMillin GA, Melis R, Boone EC, Pratt VM, Kalman LV. Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles: A GeT-RM Collaborative Project. J Mol Diagn 2019; 21:1034-1052. [PMID: 31401124 DOI: 10.1016/j.jmoldx.2019.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 06/13/2019] [Indexed: 11/25/2022] Open
Abstract
Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. Testing included the recharacterization of 137 genomic DNAs that were genotyped in previous Genetic Testing Reference Material Coordination Program studies and 42 additional samples that had not been characterized previously. DNA samples were distributed to volunteer testing laboratories for genotyping using a variety of commercially available and laboratory-developed tests. These publicly available samples will support the quality-assurance and quality-control programs of clinical laboratories performing CYP2D6 testing.
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Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Amy Turner
- Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD (Right Patient Right Drug) Diagnostics, LLC, Wauwatosa, Wisconsin
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, Stamford, Connecticut
| | - Praful Aggarwal
- Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD (Right Patient Right Drug) Diagnostics, LLC, Wauwatosa, Wisconsin
| | - Ulrich Broeckel
- Medical College of Wisconsin, Milwaukee, Wisconsin; RPRD (Right Patient Right Drug) Diagnostics, LLC, Wauwatosa, Wisconsin
| | | | | | - Erin C Boone
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Victoria M Pratt
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lisa V Kalman
- Informatics and Data Science Branch, Division of Laboratory Systems, Office of Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, Georgia.
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23
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Qiao W, Martis S, Mendiratta G, Shi L, Botton MR, Yang Y, Gaedigk A, Vijzelaar R, Edelmann L, Kornreich R, Desnick RJ, Scott SA. Integrated CYP2D6 interrogation for multiethnic copy number and tandem allele detection. Pharmacogenomics 2018; 20:9-20. [PMID: 30730286 DOI: 10.2217/pgs-2018-0135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM To comprehensively interrogate CYP2D6 by integrating genotyping, copy number analysis and novel strategies to identify CYP2D6*36 and characterize CYP2D6 duplications. METHODS Genotyping of 16 CYP2D6 alleles, multiplex ligation-dependent probe amplification (MLPA) and CYP2D6*36 and duplication allele-specific genotyping were performed on 427 African-American, Asian, Caucasian, Hispanic, and Ashkenazi Jewish individuals. RESULTS A novel PCR strategy determined that almost half of all CYP2D6*10 (100C>T) alleles are actually *36 (isolated or in tandem with *10) and all identified duplication alleles were characterized. Integrated results from all testing platforms enabled the refinement of genotype frequencies across all studied populations. CONCLUSION The polymorphic CYP2D6 gene requires comprehensive interrogation to characterize allelic variation across ethnicities, which was enabled in this study by integrating multiplexed genotyping, MLPA copy number analysis, novel PCR strategies and duplication allele-specific genotyping.
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Affiliation(s)
- Wanqiong Qiao
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Suparna Martis
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Geetu Mendiratta
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Lisong Shi
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Mariana R Botton
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Yao Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Raymon Vijzelaar
- MRC-Holland, Willem Schoutenstraat 6, Amsterdam, The Netherlands
| | - Lisa Edelmann
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Ruth Kornreich
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Robert J Desnick
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart A Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
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24
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Mukerjee G, Huston A, Kabakchiev B, Piquette-Miller M, van Schaik R, Dorfman R. User considerations in assessing pharmacogenomic tests and their clinical support tools. NPJ Genom Med 2018; 3:26. [PMID: 30210808 PMCID: PMC6133969 DOI: 10.1038/s41525-018-0065-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 12/18/2022] Open
Abstract
Pharmacogenomic (PGx) testing is gaining recognition from physicians, pharmacists and patients as a tool for evidence-based medication management. However, seemingly similar PGx testing panels (and PGx-based decision support tools) can diverge in their technological specifications, as well as the genetic factors that determine test specificity and sensitivity, and hence offer different values for users. Reluctance to embrace PGx testing is often the result of unfamiliarity with PGx technology, a lack of knowledge about the availability of curated guidelines/evidence for drug dosing recommendations, and an absence of wide-spread institutional implementation efforts and educational support. Demystifying an often confusing and variable PGx marketplace can lead to greater acceptance of PGx as a standard-of-care practice that improves drug outcomes and provides a lifetime value for patients. Here, we highlight the key underlying factors of a PGx test that should be considered, and discuss the current progress of PGx implementation.
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Affiliation(s)
| | - Andrea Huston
- GeneYouIn Inc., 156 Front St. W., Toronto, ON Canada
| | - Boyko Kabakchiev
- GeneYouIn Inc., 156 Front St. W., Toronto, ON Canada.,2Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | | | - Ron van Schaik
- 4International Expert Center Pharmacogenetics, Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
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25
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Nofziger C, Paulmichl M. Accurately genotyping CYP2D6: not for the faint of heart. Pharmacogenomics 2018; 19:999-1002. [PMID: 30020016 DOI: 10.2217/pgs-2018-0105] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Markus Paulmichl
- Center for Health & Bioresources, Austrian Institute of Technology, Vienna, Austria.,NESMOS Department, University of Rome Sapienza, Rome, Italy
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26
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Ten Years' Experience with the CYP2D6 Activity Score: A Perspective on Future Investigations to Improve Clinical Predictions for Precision Therapeutics. J Pers Med 2018; 8:jpm8020015. [PMID: 29673183 PMCID: PMC6023391 DOI: 10.3390/jpm8020015] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 12/20/2022] Open
Abstract
The seminal paper on the CYP2D6 Activity Score (AS) was first published ten years ago and, since its introduction in 2008, it has been widely accepted in the field of pharmacogenetics. This scoring system facilitates the translation of highly complex CYP2D6 diplotype data into a patient’s phenotype to guide drug therapy and is at the core of all CYP2D6 gene/drug pair guidelines issued by the Clinical Pharmacogenetics Implementation Consortium (CPIC). The AS, however, only explains a portion of the variability observed among individuals and ethnicities. In this review, we provide an overview of sources in addition to CYP2D6 genotype that contribute to the variability in CYP2D6-mediated drug metabolism and discuss other factors, genetic and non-genetic, that likely contribute to the observed variability in CYP2D6 enzymatic activity.
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27
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de Andrés F, Sosa-Macías M, Ramos BPL, Naranjo MEG, LLerena A. CYP450 Genotype/Phenotype Concordance in Mexican Amerindian Indigenous Populations–Where to from Here for Global Precision Medicine? ACTA ACUST UNITED AC 2017; 21:509-519. [DOI: 10.1089/omi.2017.0101] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fernando de Andrés
- CICAB Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
- Department of Analytical Chemistry and Food Technology, Faculty of Pharmacy, University of Castilla-La Mancha, Albacete, Spain
| | | | | | - María-Eugenia G. Naranjo
- CICAB Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
| | - Adrián LLerena
- CICAB Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
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28
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Yang Y, Botton MR, Scott ER, Scott SA. Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics 2017; 18:673-685. [PMID: 28470112 DOI: 10.2217/pgs-2017-0033] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
CYP2D6 is one of the most studied enzymes in the field of pharmacogenetics. The CYP2D6 gene is highly polymorphic with over 100 catalogued star (*) alleles, and clinical CYP2D6 testing is increasingly accessible and supported by practice guidelines. However, the degree of variation at the CYP2D6 locus and homology with its pseudogenes make interrogating CYP2D6 by short-read sequencing challenging. Moreover, accurate prediction of CYP2D6 metabolizer status necessitates analysis of duplicated alleles when an increased copy number is detected. These challenges have recently been overcome by long-read CYP2D6 sequencing; however, such platforms are not widely available. This review highlights the genomic complexities of CYP2D6, current sequencing methods and the evolution of CYP2D6 from allele discovery to clinical pharmacogenetic testing.
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Affiliation(s)
- Yao Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mariana R Botton
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erick R Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart A Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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29
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Gaedigk A, Twist GP, Farrow EG, Lowry JA, Soden SE, Miller NA. In vivo characterization of CYP2D6*12, *29 and *84 using dextromethorphan as a probe drug: a case report. Pharmacogenomics 2017; 18:427-431. [PMID: 28290770 DOI: 10.2217/pgs-2016-0192] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CYP2D6*84 was first described in a Black South African subject, however, its function remains unknown. Astrolabe, a probabilistic scoring tool developed in our laboratory to call genotypes from whole genome sequence, identified CYP2D6*84 in a trio. The father presented with intermediate metabolism when challenged with the CYP2D6 probe drug dextromethorphan (DM/dextrorphan [DX] = 0.0839). Since his second allele, CYP2D6*12, is nonfunctional, the observed activity is derived by CYP2D6*84. This finding suggests that the allele's hallmark P267H causes decreased activity toward DM and that this allele should receive a value of 0.5 for Activity Score calculations. The mother's DM/DX of 0.0543 was consistent with the decreased activity classification of CYP2D6*29. The child, a critically ill neonate, was not phenotyped, but predicted to be a normal metabolizer.
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Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Greyson P Twist
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Jennifer A Lowry
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Sarah E Soden
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA
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30
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Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences. NPJ Genom Med 2016; 1:15007. [PMID: 29263805 PMCID: PMC5685293 DOI: 10.1038/npjgenmed.2015.7] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 12/30/2022] Open
Abstract
An important component of precision medicine-the use of whole-genome sequencing (WGS) to guide lifelong healthcare-is electronic decision support to inform drug choice and dosing. To achieve this, automated identification of genetic variation in genes involved in drug absorption, distribution, metabolism, excretion and response (ADMER) is required. CYP2D6 is a major enzyme for drug bioactivation and elimination. CYP2D6 activity is predominantly governed by genetic variation; however, it is technically arduous to haplotype. Not only is the nucleotide sequence of CYP2D6 highly polymorphic, but the locus also features diverse structural variations, including gene deletion, duplication, multiplication events and rearrangements with the nonfunctional, neighbouring CYP2D7 and CYP2D8 genes. We developed Constellation, a probabilistic scoring system, enabling automated ascertainment of CYP2D6 activity scores from 2×100 paired-end WGS. The consensus reference method included TaqMan genotyping assays, quantitative copy-number variation determination and Sanger sequencing. When compared with the consensus reference Constellation had an analytic sensitivity of 97% (59 of 61 diplotypes) and analytic specificity of 95% (116 of 122 haplotypes). All extreme phenotypes, i.e., poor and ultrarapid metabolisers were accurately identified by Constellation. Constellation is anticipated to be extensible to functional variation in all ADMER genes, and to be performed at marginal incremental financial and computational costs in the setting of diagnostic WGS.
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31
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Riffel AK, Dehghani M, Hartshorne T, Floyd KC, Leeder JS, Rosenblatt KP, Gaedigk A. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping. Front Pharmacol 2016; 6:312. [PMID: 26793106 PMCID: PMC4709848 DOI: 10.3389/fphar.2015.00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022] Open
Abstract
TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact the performance of PCR-based genotype assays, including TaqMan. Regardless of the test platform used, it is prudent to confirm rare allele calls by an independent method.
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Affiliation(s)
- Amanda K Riffel
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City Kansas City, MO, USA
| | - Mehdi Dehghani
- CompanionDx® Reference LabHouston, TX, USA; Division of Oncology, Department of Internal Medicine, University of Texas Health Science Center at HoustonHouston, TX, USA
| | - Toinette Hartshorne
- Genetic Analysis, Genetic Sciences Division, Thermo Fisher Scientific South San Francisco, CA, USA
| | | | - J Steven Leeder
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas CityKansas City, MO, USA; School of Medicine, University of Missouri-Kansas CityKansas City, MO, USA
| | - Kevin P Rosenblatt
- CompanionDx® Reference LabHouston, TX, USA; Division of Oncology, Department of Internal Medicine, University of Texas Health Science Center at HoustonHouston, TX, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas CityKansas City, MO, USA; School of Medicine, University of Missouri-Kansas CityKansas City, MO, USA
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32
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Qiao W, Yang Y, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, Scott SA. Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6. Hum Mutat 2015; 37:315-23. [PMID: 26602992 DOI: 10.1002/humu.22936] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/13/2015] [Indexed: 12/30/2022]
Abstract
The cytochrome P450-2D6 (CYP2D6) enzyme metabolizes ∼25% of common medications, yet homologous pseudogenes and copy number variants (CNVs) make interrogating the polymorphic CYP2D6 gene with short-read sequencing challenging. Therefore, we developed a novel long-read, full gene CYP2D6 single molecule real-time (SMRT) sequencing method using the Pacific Biosciences platform. Long-range PCR and CYP2D6 SMRT sequencing of 10 previously genotyped controls identified expected star (*) alleles, but also enabled suballele resolution, diplotype refinement, and discovery of novel alleles. Coupled with an optimized variant-calling pipeline, CYP2D6 SMRT sequencing was highly reproducible as triplicate intra- and inter-run nonreference genotype results were completely concordant. Importantly, targeted SMRT sequencing of upstream and downstream CYP2D6 gene copies characterized the duplicated allele in 15 control samples with CYP2D6 CNVs. The utility of CYP2D6 SMRT sequencing was further underscored by identifying the diplotypes of 14 samples with discordant or unclear CYP2D6 configurations from previous targeted genotyping, which again included suballele resolution, duplicated allele characterization, and discovery of a novel allele and tandem arrangement. Taken together, long-read CYP2D6 SMRT sequencing is an innovative, reproducible, and validated method for full-gene characterization, duplication allele-specific analysis, and novel allele discovery, which will likely improve CYP2D6 metabolizer phenotype prediction for both research and clinical testing applications.
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Affiliation(s)
- Wanqiong Qiao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri, 64108.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, 64108
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
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