Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry

Pharmacogenomic testing may be used to improve treatment outcomes and reduce the frequency of adverse drug reactions (ADRs). Population specific, targeted pharmacogenetics (PGx) panel-based testing methods enable sensitive, accurate and economical implementation of precision medicine. We evaluated t...

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Autores principales: Kanji, Comfort Ropafadzo, Mbavha, Bianza Tinotenda, Masimirembwa, Collen, Thelingwani, Roslyn Stella
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10547200/
https://www.ncbi.nlm.nih.gov/pubmed/37788265
http://dx.doi.org/10.1371/journal.pone.0292131
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author Kanji, Comfort Ropafadzo
Mbavha, Bianza Tinotenda
Masimirembwa, Collen
Thelingwani, Roslyn Stella
author_facet Kanji, Comfort Ropafadzo
Mbavha, Bianza Tinotenda
Masimirembwa, Collen
Thelingwani, Roslyn Stella
author_sort Kanji, Comfort Ropafadzo
collection PubMed
description Pharmacogenomic testing may be used to improve treatment outcomes and reduce the frequency of adverse drug reactions (ADRs). Population specific, targeted pharmacogenetics (PGx) panel-based testing methods enable sensitive, accurate and economical implementation of precision medicine. We evaluated the analytical performance of the GenoPharm(®) custom open array platform which evaluates 120 SNPs across 46 pharmacogenes. Using commercially available reference samples (Coriell Biorepository) and in-house extracted DNA, we assessed accuracy, precision, and linearity of GenoPharm(®). We then used GenoPharm(®) on 218 samples from two Southern African black populations and determined allele and genotype frequencies for selected actionable variants. Across all assays, the GenoPharm(®) panel demonstrated 99.5% concordance with the Coriell reference samples, with 98.9% reproducibility. We observed high frequencies of key genetic variants in people of African ancestry: CYP2B6*6 (0.35), CYP2C9*8, *11 (0.13, 0.03), CYP2D6*17 (0.21) and *29 (0.11). GenoPharm(®) open array is therefore an accurate, reproducible and sensitive test that can be used for clinical pharmacogenetic testing and is inclusive of variants specific to the people of African ancestry.
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spelling pubmed-105472002023-10-04 Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry Kanji, Comfort Ropafadzo Mbavha, Bianza Tinotenda Masimirembwa, Collen Thelingwani, Roslyn Stella PLoS One Research Article Pharmacogenomic testing may be used to improve treatment outcomes and reduce the frequency of adverse drug reactions (ADRs). Population specific, targeted pharmacogenetics (PGx) panel-based testing methods enable sensitive, accurate and economical implementation of precision medicine. We evaluated the analytical performance of the GenoPharm(®) custom open array platform which evaluates 120 SNPs across 46 pharmacogenes. Using commercially available reference samples (Coriell Biorepository) and in-house extracted DNA, we assessed accuracy, precision, and linearity of GenoPharm(®). We then used GenoPharm(®) on 218 samples from two Southern African black populations and determined allele and genotype frequencies for selected actionable variants. Across all assays, the GenoPharm(®) panel demonstrated 99.5% concordance with the Coriell reference samples, with 98.9% reproducibility. We observed high frequencies of key genetic variants in people of African ancestry: CYP2B6*6 (0.35), CYP2C9*8, *11 (0.13, 0.03), CYP2D6*17 (0.21) and *29 (0.11). GenoPharm(®) open array is therefore an accurate, reproducible and sensitive test that can be used for clinical pharmacogenetic testing and is inclusive of variants specific to the people of African ancestry. Public Library of Science 2023-10-03 /pmc/articles/PMC10547200/ /pubmed/37788265 http://dx.doi.org/10.1371/journal.pone.0292131 Text en © 2023 Kanji et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kanji, Comfort Ropafadzo
Mbavha, Bianza Tinotenda
Masimirembwa, Collen
Thelingwani, Roslyn Stella
Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry
title Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry
title_full Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry
title_fullStr Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry
title_full_unstemmed Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry
title_short Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry
title_sort analytical validation of genopharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of african ancestry
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10547200/
https://www.ncbi.nlm.nih.gov/pubmed/37788265
http://dx.doi.org/10.1371/journal.pone.0292131
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