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Shugg T, Ly RC, Osei W, Rowe EJ, Granfield CA, Lynnes TC, Medeiros EB, Hodge JC, Breman AM, Schneider BP, Sahinalp SC, Numanagić I, Salisbury BA, Bray SM, Ratcliff R, Skaar TC. Computational pharmacogenotype extraction from clinical next-generation sequencing. Front Oncol 2023; 13:1199741. [PMID: 37469403 PMCID: PMC10352904 DOI: 10.3389/fonc.2023.1199741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/22/2023] [Indexed: 07/21/2023] Open
Abstract
Background Next-generation sequencing (NGS), including whole genome sequencing (WGS) and whole exome sequencing (WES), is increasingly being used for clinic care. While NGS data have the potential to be repurposed to support clinical pharmacogenomics (PGx), current computational approaches have not been widely validated using clinical data. In this study, we assessed the accuracy of the Aldy computational method to extract PGx genotypes from WGS and WES data for 14 and 13 major pharmacogenes, respectively. Methods Germline DNA was isolated from whole blood samples collected for 264 patients seen at our institutional molecular solid tumor board. DNA was used for panel-based genotyping within our institutional Clinical Laboratory Improvement Amendments- (CLIA-) certified PGx laboratory. DNA was also sent to other CLIA-certified commercial laboratories for clinical WGS or WES. Aldy v3.3 and v4.4 were used to extract PGx genotypes from these NGS data, and results were compared to the panel-based genotyping reference standard that contained 45 star allele-defining variants within CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP3A4, CYP3A5, CYP4F2, DPYD, G6PD, NUDT15, SLCO1B1, TPMT, and VKORC1. Results Mean WGS read depth was >30x for all variant regions except for G6PD (average read depth was 29 reads), and mean WES read depth was >30x for all variant regions. For 94 patients with WGS, Aldy v3.3 diplotype calls were concordant with those from the genotyping reference standard in 99.5% of cases when excluding diplotypes with additional major star alleles not tested by targeted genotyping, ambiguous phasing, and CYP2D6 hybrid alleles. Aldy v3.3 identified 15 additional clinically actionable star alleles not covered by genotyping within CYP2B6, CYP2C19, DPYD, SLCO1B1, and NUDT15. Within the WGS cohort, Aldy v4.4 diplotype calls were concordant with those from genotyping in 99.7% of cases. When excluding patients with CYP2D6 copy number variation, all Aldy v4.4 diplotype calls except for one CYP3A4 diplotype call were concordant with genotyping for 161 patients in the WES cohort. Conclusion Aldy v3.3 and v4.4 called diplotypes for major pharmacogenes from clinical WES and WGS data with >99% accuracy. These findings support the use of Aldy to repurpose clinical NGS data to inform clinical PGx.
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Affiliation(s)
- Tyler Shugg
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Reynold C. Ly
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Wilberforce Osei
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elizabeth J. Rowe
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Caitlin A. Granfield
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Ty C. Lynnes
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Elizabeth B. Medeiros
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Jennelle C. Hodge
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Amy M. Breman
- Division of Diagnostic Genetics and Genomics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bryan P. Schneider
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - S. Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Ibrahim Numanagić
- Department of Computer Science, University of Victoria, Victoria, BC, Canada
| | | | | | | | - Todd C. Skaar
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
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Li J, Chen T, Jie F, Xiang H, Huang L, Jiang H, Lu F, Zhu S, Wu L, Tang Y. Impact of VKORC1, CYP2C9, CYP1A2, UGT1A1, and GGCX polymorphisms on warfarin maintenance dose: Exploring a new algorithm in South Chinese patients accept mechanical heart valve replacement. Medicine (Baltimore) 2022; 101:e29626. [PMID: 35866816 PMCID: PMC9302374 DOI: 10.1097/md.0000000000029626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Warfarin is the most recommended oral anticoagulant after artificial mechanical valve replacement therapy. However, the narrow therapeutic window and varying safety and efficacy in individuals make dose determination difficult. It may cause adverse events such as hemorrhage or thromboembolism. Therefore, advanced algorithms are urgently required for the use of warfarin. OBJECTIVE To establish a warfarin dose model for patients after prosthetic mechanical valve replacement in southern China in combination with clinical and genetic variables, and to improve the accuracy and ideal prediction percentage of the model. METHODS Clinical data of 476 patients were tracked and recorded in detail. The gene polymorphisms of VKORC1 (rs9923231, rs9934438, rs7196161, and rs7294), CYP2C9 (rs1057910), CYP1A2 (rs2069514), GGCX (rs699664), and UGT1A1 (rs887829) were determined using Sanger sequencing. Multiple linear regressions were used to analyze the gene polymorphisms and the contribution of clinical data variables; the variables that caused multicollinearity were screened stepwise and excluded to establish an algorithm model for predicting the daily maintenance dose of warfarin. The ideal predicted percentage was used to test clinical effectiveness. RESULTS A total of 395 patients were included. Univariate linear regression analysis suggested that CYP1A2 (rs2069514) and UGT1A1 (rs887829) were not associated with the daily maintenance dose of warfarin. The new algorithm model established based on multiple linear regression was as follows: Y = 1.081 - 0.011 (age) + 1.532 (body surface area)-0.807 (rs9923231 AA) + 1.788 (rs9923231 GG) + 0.530 (rs1057910 AA)-1.061 (rs1057910 AG)-0.321 (rs699664 AA). The model accounted for 61.7% of individualized medication differences, with an ideal prediction percentage of 69%. CONCLUSION GGCX (rs699664) may be a potential predictor of warfarin dose, and our newly established model is expected to guide the individualized use of warfarin in clinical practice in southern China.
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Affiliation(s)
- Jin Li
- Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Chen
- School of Science, Nanchang University, Nanchang, China
| | - Fangfang Jie
- School of Science, Nanchang University, Nanchang, China
| | - Haiyan Xiang
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Li Huang
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongfa Jiang
- Department of Cardiothoracic Surgery, Jiangxi Chest Hospital, Nanchang, China
| | - Fei Lu
- Comprehensive Intervention Department of the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shuqiang Zhu
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lidong Wu
- Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, China
- * Correspondence: Lidong Wu, Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: ); Yanhua Tang, Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: )
| | - Yanhua Tang
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
- * Correspondence: Lidong Wu, Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: ); Yanhua Tang, Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: )
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Tzveova R, Dimitrova-Karamfilova A, Saraeva R, Solarova T, Naydenova G, Petrova I, Hristova N, Popov I, Nachev G, Mitev V, Kaneva R. Estimation and validation of acenocoumarol dosing algorithms in Bulgarian patients with cardiovascular diseases. Per Med 2015; 12:209-220. [PMID: 29771648 DOI: 10.2217/pme.14.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim & Methods: A total of 169 Bulgarian patients were genotyped for CYP2C9*2,*3, VKORC1-1639G>A and VKORC11173C>T. The effect of genetic and nongenetic factors on acenocoumarol dose variability was tested in a derivation cohort of patients and the obtained algorithm was validated in a test cohort. RESULTS & DISCUSSION It was found that VKORC-1639G>A (25.5%), CYP2C9*2 (7.8%), CYP2C9*3 (6.1%), age (13.6%) and diagnosis (6.0%) significantly affected acenocoumarol dose variability in the derivation cohort. These factors with additional factors, such as sex (0.1%, p = 0.76), weight (2.6%, p = 0.14) and amiodarone use (3.0%, p = 0.059) accounted for 46.5% and 23.0% of the dose variability for genetic and clinical models, respectively. CONCLUSION Based on the results of this investigation, validated clinical and pharmacogenetic algorithms for the prediction of a stable anticoagulant dose were developed, specifically designed for the Bulgarian population.
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Affiliation(s)
- Reni Tzveova
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Antoaneta Dimitrova-Karamfilova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Radoslava Saraeva
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Tanya Solarova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Galya Naydenova
- Second Department of Cardiology, University NationalMulti-profile Active Treatment Hospital "Dr. G. Stansky"- Pleven, 8A Georgi Kochev str., Pleven 5800, Bulgaria
| | - Irina Petrova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Nataliya Hristova
- Department of Clinical Laboratory, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Ivan Popov
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Gencho Nachev
- Department of Cardiac Surgery, University National Multi-profile Active Treatment Hospital "St. Ekaterina"- Sofia, 52A Pencho Slaveykov bul., Sofia 1431, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry & Biochemistry, Medical Faculty, Medical University - Sofia, 2 Zdrave str, Sofia 1431, Bulgaria
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