1
|
Just KS, Pott LM, Sommer J, Scholl C, Steffens M, Denkinger MD, Rothenbacher D, Dallmeier D, Stingl J. Association of Polymorphic Cytochrome P450 Enzyme Pathways With Falls in Multimedicated Older Adults. J Am Med Dir Assoc 2024:105235. [PMID: 39236770 DOI: 10.1016/j.jamda.2024.105235] [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: 11/14/2023] [Revised: 06/27/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
OBJECTIVES Dose exposure is considered relevant for drug-associated falls in older adults, pointing to an importance of drug metabolism. Aim was to analyze individual factors altering drug metabolism such as enzyme saturation by drug exposure and pharmacogenetics in the context of drug-associated falls. DESIGN Prospective population-based study (ActiFE-Ulm study). SETTING AND PARTICIPANTS Community-dwelling older adults. METHODS Focus was laid on the metabolism by polymorphic cytochrome P450 (CYP) enzymes CYP2C19, 2C9, and 2D6. Relevant variants of pharmacogenes were analyzed. Logistic binary regression analysis was used to calculate odds ratios (ORs) and 95% CIs for falls observed prospectively over a 1-year period with drug metabolism characteristics. RESULTS In total, 1377 participants were included in the analysis. Although the phenotype predicted by the genotype was not, the use of drugs metabolized by CYP2C19 was associated with falls. Drugs not known as fall risk-increasing drugs (FRIDs; ie, non-FRIDs), but metabolized by CYP2C19, showed an OR of 1.46 (1.11-1.93) in adjusted analysis. Significant effect modification was observed for a reduced CYP2C19 activity phenotype with non-FRIDs metabolized by CYP2C19. CONCLUSIONS AND IMPLICATIONS This study suggests an association between the occurrence of falls in older adults and the metabolic capacity of CYP2C19. Thus, an important step toward prevention of falls might be to personalize dosage and treatment length of the main drug classes known to be CYP2C19 substrates, such as many antidepressants, opioids, and sedatives, but also proton pump inhibitors in particular in poor and intermediate metabolizers.
Collapse
Affiliation(s)
- Katja S Just
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Aachen, Germany.
| | - Laura M Pott
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Aachen, Germany
| | - Jakob Sommer
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Aachen, Germany
| | - Catharina Scholl
- Research Department, Federal Institute of Drugs and Medical Devices, Bonn, Germany
| | - Michael Steffens
- Research Department, Federal Institute of Drugs and Medical Devices, Bonn, Germany
| | - Michael D Denkinger
- AGAPLESION Bethesda Clinic, Ulm, Germany; Geriatric Centre Ulm, Ulm, Germany; Institute for Geriatric Research, Ulm University Medical Center, Ulm Germany
| | | | - Dhayana Dallmeier
- AGAPLESION Bethesda Clinic, Ulm, Germany; Geriatric Centre Ulm, Ulm, Germany; Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Julia Stingl
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Aachen, Germany
| |
Collapse
|
2
|
Frear S, Sherman A, Rule D, Marcath LA. Prevalence of CYP2D6 structural variation in large retrospective study. Pharmacogenet Genomics 2024; 34:135-138. [PMID: 38372405 DOI: 10.1097/fpc.0000000000000525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
CYP2D6 is a highly polymorphic gene with clinically important structural variations. Commonly, only exon 9 is assayed on clinical pharmacogenomics panels, as it allows for accurate functional characterization even in the presence of a CYP2D6::CYP2D7 conversion. However, this method does not capture CYP2D7::CYP2D6 (CYP2D6*13) conversions, possibly leading to inaccurate phenotype assignment. The study's purpose was to determine the frequency of structural variations in CYP2D6 utilizing multiple copy number variation (CNV) assay locations to quantify the potential impact on clinical phenotype classification. A retrospective analysis was conducted of de-identified pharmacogenomics data submitted through the Translational Software, Inc. platform. Samples with CYP2D6 CNV data for exon 9 and at least one additional CNV location (5'UTR, exon 1, intron 2, exon 5 or intron 6) were included. CYP2D7::CYP2D6 and CYP2D6::CYP2D7 conversions were classified according to PharmVar nomenclature. The CYP2D6 copies were capped at four total copies to account for assay limitations in detecting more than four copies. A total of 106,474 samples were included for analysis. CYP2D7::CYP2D6 conversions were present in approximately 2.44% of samples, and 5.84% of samples had CYP2D6::CYP2D7 conversions. Many samples did not have a CYP2D7 conversion detected (91.5%; 97,462/106,474). A full gene deletion was detected in 0.15%, and 5.98% had a duplication or multiplication present. This retrospective study underscores the importance of testing more than one CNV site for CYP2D6 . Over 2% of patients were found to have a CYP2D7::CYP2D6 conversion. This translates into potentially misclassified phenotype classification and incongruent clinical recommendations.
Collapse
Affiliation(s)
- Samantha Frear
- Translational Software, Inc. Mercer Island, Washington, USA
| | | | | | | |
Collapse
|
3
|
Turner AJ, Nofziger C, Ramey BE, Ly RC, Bousman CA, Agúndez JAG, Sangkuhl K, Whirl-Carrillo M, Vanoni S, Dunnenberger HM, Ruano G, Kennedy MA, Phillips MS, Hachad H, Klein TE, Moyer AM, Gaedigk A. PharmVar Tutorial on CYP2D6 Structural Variation Testing and Recommendations on Reporting. Clin Pharmacol Ther 2023; 114:1220-1237. [PMID: 37669183 PMCID: PMC10840842 DOI: 10.1002/cpt.3044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus and a comprehensive summary of structural variation. CYP2D6 contributes to the metabolism of numerous drugs and, thus, genetic variation in its gene impacts drug efficacy and safety. To accurately predict a patient's CYP2D6 phenotype, testing must include structural variants including gene deletions, duplications, hybrid genes, and combinations thereof. This tutorial offers a comprehensive overview of CYP2D6 structural variation, terms, and definitions, a review of methods suitable for their detection and characterization, and practical examples to address the lack of standards to describe CYP2D6 structural variants or any other pharmacogene. This PharmVar tutorial offers practical guidance on how to detect the many, often complex, structural variants, as well as recommends terms and definitions for clinical and research reporting. Uniform reporting is not only essential for electronic health record-keeping but also for accurate translation of a patient's genotype into phenotype which is typically utilized to guide drug therapy.
Collapse
Affiliation(s)
- Amy J Turner
- Department of Pediatrics, Children’s Research Institute, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- RPRD Diagnostics LLC, Wauwatosa, Wisconsin, USA
| | | | | | - Reynold C Ly
- Department of Medical and Molecular Genetics, Division of Diagnostic Genomics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Chad A Bousman
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - José AG Agúndez
- University of Extremadura, Cáceres, Spain
- Institute of Molecular Pathology Biomarkers, Cáceres, Spain
| | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | | | | | - Henry M Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University Health System, Evanston, Illinois, USA
| | - Gualberto Ruano
- Institute of Living, Hartford Hospital (Hartford CT) and Department of Psychiatry, University of Connecticut School of Medicine (Farmington CT), USA
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Houda Hachad
- Houda Hachad, Department of Clinical Operations, AccessDx Laboratories, Houston, Texas, USA
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine (BMIR), Stanford University, Stanford, California, USA
| | - Ann M Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrea Gaedigk
- Children’s Mercy Research Institute (CMRI), Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| |
Collapse
|
4
|
Turner AJ, Derezinski AD, Gaedigk A, Berres ME, Gregornik DB, Brown K, Broeckel U, Scharer G. Characterization of complex structural variation in the CYP2D6-CYP2D7-CYP2D8 gene loci using single-molecule long-read sequencing. Front Pharmacol 2023; 14:1195778. [PMID: 37426826 PMCID: PMC10324673 DOI: 10.3389/fphar.2023.1195778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Complex regions in the human genome such as repeat motifs, pseudogenes and structural (SVs) and copy number variations (CNVs) present ongoing challenges to accurate genetic analysis, particularly for short-read Next-Generation-Sequencing (NGS) technologies. One such region is the highly polymorphic CYP2D loci, containing CYP2D6, a clinically relevant pharmacogene contributing to the metabolism of >20% of common drugs, and two highly similar pseudogenes, CYP2D7 and CYP2D8. Multiple complex SVs, including CYP2D6/CYP2D7-derived hybrid genes are known to occur in different configurations and frequencies across populations and are difficult to detect and characterize accurately. This can lead to incorrect enzyme activity assignment and impact drug dosing recommendations, often disproportionally affecting underrepresented populations. To improve CYP2D6 genotyping accuracy, we developed a PCR-free CRISPR-Cas9 based enrichment method for targeted long-read sequencing that fully characterizes the entire CYP2D6-CYP2D7-CYP2D8 loci. Clinically relevant sample types, including blood, saliva, and liver tissue were sequenced, generating high coverage sets of continuous single molecule reads spanning the entire targeted region of up to 52 kb, regardless of SV present (n = 9). This allowed for fully phased dissection of the entire loci structure, including breakpoints, to accurately resolve complex CYP2D6 diplotypes with a single assay. Additionally, we identified three novel CYP2D6 suballeles, and fully characterized 17 CYP2D7 and 18 CYP2D8 unique haplotypes. This method for CYP2D6 genotyping has the potential to significantly improve accurate clinical phenotyping to inform drug therapy and can be adapted to overcome testing limitations of other clinically challenging genomic regions.
Collapse
Affiliation(s)
| | | | - Andrea Gaedigk
- Children’s Mercy Research Institute, Kansas City, MO, United States
| | - Mark E. Berres
- Biotechnology Center, University of Wisconsin Madison, Madison, WI, United States
| | | | - Keith Brown
- Jumpcode Genomics, San Diego, CA, United States
| | | | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Twesigomwe D, Drögemöller BI, Wright GE, Adebamowo C, Agongo G, Boua PR, Matshaba M, Paximadis M, Ramsay M, Simo G, Simuunza MC, Tiemessen CT, Lombard Z, Hazelhurst S. Characterization of CYP2D6 Pharmacogenetic Variation in Sub-Saharan African Populations. Clin Pharmacol Ther 2023; 113:643-659. [PMID: 36111505 PMCID: PMC9957841 DOI: 10.1002/cpt.2749] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/11/2022] [Indexed: 11/07/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is a key enzyme in drug response owing to its involvement in the metabolism of ~ 25% of clinically prescribed medications. The encoding CYP2D6 gene is highly polymorphic, and many pharmacogenetics studies have been performed worldwide to investigate the distribution of CYP2D6 star alleles (haplotypes); however, African populations have been relatively understudied to date. In this study, the distributions of CYP2D6 star alleles and predicted drug metabolizer phenotypes-derived from activity scores-were examined across multiple sub-Saharan African populations based on bioinformatics analysis of 961 high-depth whole genome sequences. This was followed by characterization of novel star alleles and suballeles in a subset of the participants via targeted high-fidelity Single-Molecule Real-Time resequencing (Pacific Biosciences). This study revealed varying frequencies of known CYP2D6 alleles and predicted phenotypes across different African ethnolinguistic groups. Twenty-seven novel CYP2D6 star alleles were predicted computationally and two of them were further validated. This study highlights the importance of studying variation in key pharmacogenes such as CYP2D6 in the African context to better understand population-specific allele frequencies. This will aid in the development of better genotyping panels and star allele detection approaches with a view toward supporting effective implementation of precision medicine strategies in Africa and across the African diaspora.
Collapse
Affiliation(s)
- David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Britt I. Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Galen E.B. Wright
- Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Winnipeg Health Sciences Centre and Max Rady College of MedicineUniversity of ManitobaWinnipegManitobaCanada
- Department of Pharmacology and Therapeutics, Rady Faculty of Health SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Clement Adebamowo
- Institute for Human VirologyAbujaNigeria
- Division of Cancer Epidemiology, Department of Epidemiology and Public Health, and the Marlene and Stewart Greenebaum Comprehensive Cancer CentreUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Godfred Agongo
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
- C.K. Tedam University of Technology and Applied SciencesNavrongoGhana
| | - Palwendé R. Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Clinical Research Unit of NanoroInstitut de Recherche en Sciences de la SantéNanoroBurkina Faso
| | - Mogomotsi Matshaba
- Botswana‐Baylor Children's Clinical Centre of ExcellenceGaboroneBotswana
- RetrovirologyDepartment of Pediatrics, Baylor College of MedicineHoustonTexasUSA
| | - Maria Paximadis
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry, Faculty of ScienceUniversity of DschangDschangCameroon
| | - Martin C. Simuunza
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Caroline T. Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- School of Electrical and Information EngineeringUniversity of the WitwatersrandJohannesburgSouth Africa
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|