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Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach
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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10301474/ https://www.ncbi.nlm.nih.gov/pubmed/37373874 http://dx.doi.org/10.3390/jpm13060883 |
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author | Atiq, Mazen A. Peterson, Sandra E. Langman, Loralie J. Baudhuin, Linnea M. Black, John L. Moyer, Ann M. |
author_facet | Atiq, Mazen A. Peterson, Sandra E. Langman, Loralie J. Baudhuin, Linnea M. Black, John L. Moyer, Ann M. |
author_sort | Atiq, Mazen A. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10301474 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-103014742023-06-29 Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach Atiq, Mazen A. Peterson, Sandra E. Langman, Loralie J. Baudhuin, Linnea M. Black, John L. Moyer, Ann M. J Pers Med Article 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. MDPI 2023-05-24 /pmc/articles/PMC10301474/ /pubmed/37373874 http://dx.doi.org/10.3390/jpm13060883 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Atiq, Mazen A. Peterson, Sandra E. Langman, Loralie J. Baudhuin, Linnea M. Black, John L. Moyer, Ann M. Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach |
title | Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach |
title_full | Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach |
title_fullStr | Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach |
title_full_unstemmed | Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach |
title_short | Determination of the Duplicated CYP2D6 Allele Using Real-Time PCR Signal: An Alternative Approach |
title_sort | determination of the duplicated cyp2d6 allele using real-time pcr signal: an alternative approach |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10301474/ https://www.ncbi.nlm.nih.gov/pubmed/37373874 http://dx.doi.org/10.3390/jpm13060883 |
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