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Botton MR, Lu X, Zhao G, Repnikova E, Seki Y, Gaedigk A, Schadt EE, Edelmann L, Scott SA. Structural variation at the CYP2C locus: Characterization of deletion and duplication alleles. Hum Mutat 2020; 40:e37-e51. [PMID: 31260137 DOI: 10.1002/humu.23855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/11/2019] [Accepted: 06/25/2019] [Indexed: 12/27/2022]
Abstract
The human CYP2C locus harbors the polymorphic CYP2C18, CYP2C19, CYP2C9, and CYP2C8 genes, and of these, CYP2C19 and CYP2C9 are directly involved in the metabolism of ~15% of all medications. All variant CYP2C19 and CYP2C9 star (*) allele haplotypes currently cataloged by the Pharmacogene Variation (PharmVar) Consortium are defined by sequence variants. To determine if structural variation also occurs at the CYP2C locus, the 10q23.33 region was interrogated across deidentified clinical chromosomal microarray (CMA) data from 20,642 patients tested at two academic medical centers. Fourteen copy number variants that affected the coding region of CYP2C genes were detected in the clinical CMA cohorts, which ranged in size from 39.2 to 1,043.3 kb. Selected deletions and duplications were confirmed by MLPA or ddPCR. Analysis of the clinical CMA and an additional 78,839 cases from the Database of Genomic Variants (DGV) and ClinGen (total n = 99,481) indicated that the carrier frequency of a CYP2C structural variant is ~1 in 1,000, with ~1 in 2,000 being a CYP2C19 full gene or partial-gene deletion carrier, designated by PharmVar as CYP2C19*36 and *37, respectively. Although these structural variants are rare in the general population, their detection will likely improve metabolizer phenotype prediction when interrogated for research and/or clinical testing.
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Affiliation(s)
- Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Xingwu Lu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Geping Zhao
- Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Elena Repnikova
- Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, Missouri.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | | | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, Missouri
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Sema4, A Mount Sinai venture, Stamford, Connecticut
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Vijzelaar R, Botton MR, Stolk L, Martis S, Desnick RJ, Scott SA. Multi-ethnic SULT1A1 copy number profiling with multiplex ligation-dependent probe amplification. Pharmacogenomics 2018; 19:761-770. [PMID: 29790428 PMCID: PMC6021911 DOI: 10.2217/pgs-2018-0047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/30/2018] [Indexed: 02/03/2023] Open
Abstract
AIM To develop a SULT1A1 multiplex ligation-dependent probe amplification assay and to investigate multi-ethnic copy number variant frequencies. METHODS A novel multiplex ligation-dependent probe amplification assay was developed and tested on 472 African-American, Asian, Caucasian, Hispanic and Ashkenazi Jewish individuals. RESULTS The frequencies of atypical total copy number (i.e., greater or less than two) were 38.7% for Hispanics, 38.9% for Ashkenazi Jewish, 43.2% for Caucasians, 53.6% for Asians and 64.1% for African-Americans. Heterozygous SULT1A1 deletion carriers (slow sulfators) were most common among Caucasians (8.4%), whereas African-Americans had the highest frequencies of three or more copies (rapid sulfators; 60.9%). CONCLUSION Different ethnic and racial populations have varying degrees of SULT1A1-mediated sulfation activity, which warrants further research and that may have utility for drug response prediction among SULT1A1-metabolized medications.
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Affiliation(s)
- Raymon Vijzelaar
- MRC-Holland, Willem Schoutenstraat 1, Amsterdam, The Netherlands
| | - 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
| | - Lisette Stolk
- MRC-Holland, Willem Schoutenstraat 1, Amsterdam, The Netherlands
| | - Suparna Martis
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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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Gaedigk A, Twist GP, Leeder JS. CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR. Pharmacogenomics 2012; 13:91-111. [DOI: 10.2217/pgs.11.135] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Among the genes of drug-metabolizing enzymes, CYP2D6 is notoriously difficult to characterize owing to the complexity of gene deletions, duplications, multiplications and the presence of hybrid genes composed of CYP2D6 and CYP2D7. For SULT1A1 up to five gene copies have been reported, while UGT2B17 is known for gene deletions only. Different platforms exist for copy number variation (CNV) detection; however, there are no gold standards. Robust methods are required that address specific challenges to accurately determine gene CNVs in complex gene loci. Materials & methods: Quantitative multiplex PCR amplification (MPA) was performed on a diverse set of genomic DNA samples. Resulting PCR fragments were separated on an ABI 3730 instrument and analyzed with GeneMapper. CYP2D6 was targeted at four different gene regions and either normalized against CYP2D8 or UGT2B15 and SULT1A2. Inconsistent observations and CNVs contrasting genotype data were further characterized by long-range PCR and/or DNA sequence analysis. UGT2B17 and SULT1A1 were normalized against UGT2B15 and SULT1A2, respectively. Results: MPA detected 0–5, 1–5 and 0–2 copies for CYP2D6, SULT1A1 and UGT2B17, respectively. The interrogation of four CYP2D6 regions resulted in robust copy number assignments that were in agreement with genotype, sequencing and extra long PCR-based data. Gene deletions, duplication, and multiplications among known and novel hybrid genes were reliably identified. Novel findings regarding allelic variation include nonfunctional CYP2D6/2D7 hybrids such as CYP2D6*4N and *68, which were consistently identified on a subset of CYP2D6*4 alleles. In addition, a novel variant, designated CYP2D6*83, was discovered. For SULT1A1, we report the first six-copy case and for UGT2B15 and UGT2B17 we have evidence for rare deletion and duplication events, respectively. Conclusion: This MPA-based copy number platform not only allowed us to determine CNVs, but also served as a tool for allele discovery and characterization in a diverse panel of samples in a fast and reliable manner. Original submitted 6 July 2011; Revision submitted 24 August 2011
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Affiliation(s)
| | - Greyson P Twist
- Division of Pediatric Pharmacology & Medical Toxicology, The Children’s Mercy Hospital & Clinics, 2401 Gillham Rd, Kansas City, MO 64108, USA
| | - J Steven Leeder
- Division of Pediatric Pharmacology & Medical Toxicology, The Children’s Mercy Hospital & Clinics, 2401 Gillham Rd, Kansas City, MO 64108, USA
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Huin V, Drouot N, Chambon P, Le Meur N, Frébourg T, Tosi M, Saugier-Veber P. Development of a Nonfluorescent Multiplex Semiquantitative Polymerase Chain Reaction to Confirm Rearrangements Detected by Array-Comparative Genomic Hybridization. Genet Test Mol Biomarkers 2011; 15:469-74. [DOI: 10.1089/gtmb.2010.0144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Vincent Huin
- Department of Genetics, Rouen University Hospital, Rouen, France
| | - Nathalie Drouot
- Department of Genetics, Rouen University Hospital, Rouen, France
| | - Pascal Chambon
- Inserm U614, Faculty of Medicine, University of Rouen, Rouen, France
- Department of Cytogenetics, Rouen University Hospital, Rouen, France
| | - Nathalie Le Meur
- Department of Cytogenetics, Etablissement Français du Sang, Bois-Guillaume, France
| | - Thierry Frébourg
- Department of Genetics, Rouen University Hospital, Rouen, France
- Inserm U614, Faculty of Medicine, University of Rouen, Rouen, France
| | - Mario Tosi
- Inserm U614, Faculty of Medicine, University of Rouen, Rouen, France
| | - Pascale Saugier-Veber
- Department of Genetics, Rouen University Hospital, Rouen, France
- Inserm U614, Faculty of Medicine, University of Rouen, Rouen, France
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