Next-Generation Sequencing and Bioinformatics-Based Protocol for the Full-Length CYP2E1 Gene Polymorphism Analysis
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Date
2022
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Abstract
Introduction: Pharmacogenetics studies provide clinically relevant information on the identified associations between genetic variants and individual variability in drug response, which, in turn, offers great promise for guiding personalized drug therapy and clinical trial design. However, there is a lack of information concerning the evidence-based clinical annotations of specific CYP2E1 genetic variants. Aim: To design and evaluate the next-generation sequencing-based method for full-length CYP2E1 gene polymorphism analysis. Materials and Methods: Seven gene-specific oligonucleotide primer pairs targeting overlapping CYP2E1 gene fragments spanning all nine gene exons with interleaving introns, untranslated (UTR) and intergenic regions were designed. Human DNA samples (n = 3) were used as a training set to check the primer performance and to optimize the PCR conditions. The effectiveness of the developed target amplification and sequencing protocol was evaluated using the test set comprising human DNA samples (n = 3) obtained from tuberculosis patients. Sequencing data analysis was performed on the Galaxy online-based platform. Results: The sequencing data quality was sufficient for the detection of genetic variants dispersed throughout the CYP2E1 gene with a high degree of confidence in fully covered regions achieving optimal reading depth of the targeted fragment with high base call accuracy. Conclusion: Developed protocol can be applied in subpopulation-level association studies to determine whether single nucleotide variants (SNVs) or variant combinations from multiple regions of the CYP2E1 gene are of clinical significance.
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Funding Information: This study was supported by FLP Program/Ministry of Education and Science, Republic of Latvia, project No lzp2020/ 1-0050. This funding source had no role in the design of this study, analyses, interpretation of the data, or decision to submit results. Publisher Copyright: © 2022 Igumnova et al.
Keywords
CYP2E1, cytochrome P450, next-generation sequencing, pharmacogenetics, single nucleotide variants, 3.1 Basic medicine, 1.1. Scientific article indexed in Web of Science and/or Scopus database, Molecular Medicine, Pharmacology, SDG 3 - Good Health and Well-being
Citation
Igumnova, V, Kivrane, A, Viksna, A, Norvaisa, I & Ranka, R 2022, 'Next-Generation Sequencing and Bioinformatics-Based Protocol for the Full-Length CYP2E1 Gene Polymorphism Analysis', Pharmacogenomics and Personalized Medicine, vol. 15, pp. 959-965. https://doi.org/10.2147/PGPM.S371709