A Curated Pharmacogenomic Allele Catalog for Sub-Saharan African Populations

Abstract

Sub-Saharan African populations carry pharmacogenomic alleles poorly represented in the European-derived reference panels underlying most clinical genotyping tools. We present a curated, machine-readable catalog of nine actionable alleles across six pharmacogenes (CYP2D6, CYP2B6, CYP2C9, CYP2C19, CYP3A5, NAT2) with African-specific frequency ranges, functional annotations, and evidence levels derived from reanalysis of 661 high-coverage whole-genome sequences across seven 1000 Genomes Project African populations. Direct comparison against PharmCAT v3.4.0 shows that CYP2D6 produces zero diplotype calls (0/661 samples callable) due to monomorphic reference positions absent from standard variant-only VCF output, a known limitation whose consequences for African allele carriers had not been reported. afripharmagens reduced-position strategy identifies 243 CYP2D6 *17 and 134 CYP2D6 *29 carriers from the same input. For CYP2B6, CYP2C9, CYP2C19, and NAT2, both tools show concordance of 95-100%. Frequency gradients (CYP2B6 *6: 30-50%; CYP2D6 *17: 15-35% in West Africa; CYP3A5 *1: 60-95%) translate directly into prescribing risk for efavirenz, tramadol, tacrolimus, and isoniazid. Pharmacogenomic decision support in African settings must incorporate population-specific allele definitions and input-format-aware strategies.

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BibTeX RIS

BibTeX

@misc{sulaiman2026curated,
  title = {{A Curated Pharmacogenomic Allele Catalog for Sub-Saharan African Populations}},
  author = {M. A. SULAIMAN and B. F. Oyeyemi},
  howpublished = {medRxiv},
  year = {2026},
  month = aug,
  doi = {10.64898/2026.08.25.26361354},
  url = {https://www.medrxiv.org/content/10.64898/2026.08.25.26361354v1},
  note = {CC BY},
}

RIS

TY  - UNPB
TI  - A Curated Pharmacogenomic Allele Catalog for Sub-Saharan African Populations
AU  - M. A. SULAIMAN
AU  - B. F. Oyeyemi
PY  - 2026
DA  - 2026/08/25
PB  - medRxiv
DO  - 10.64898/2026.08.25.26361354
UR  - https://www.medrxiv.org/content/10.64898/2026.08.25.26361354v1
AB  - Sub-Saharan African populations carry pharmacogenomic alleles poorly represented in the European-derived reference panels underlying most clinical genotyping tools. We present a curated, machine-readable catalog of nine actionable alleles across six pharmacogenes (CYP2D6, CYP2B6, CYP2C9, CYP2C19, CYP3A5, NAT2) with African-specific frequency ranges, functional annotations, and evidence levels derived from reanalysis of 661 high-coverage whole-genome sequences across seven 1000 Genomes Project African populations. Direct comparison against PharmCAT v3.4.0 shows that CYP2D6 produces zero diplotype calls (0/661 samples callable) due to monomorphic reference positions absent from standard variant-only VCF output, a known limitation whose consequences for African allele carriers had not been reported. afripharmagens reduced-position strategy identifies 243 CYP2D6 *17 and 134 CYP2D6 *29 carriers from the same input. For CYP2B6, CYP2C9, CYP2C19, and NAT2, both tools show concordance of 95-100%. Frequency gradients (CYP2B6 *6: 30-50%; CYP2D6 *17: 15-35% in West Africa; CYP3A5 *1: 60-95%) translate directly into prescribing risk for efavirenz, tramadol, tacrolimus, and isoniazid. Pharmacogenomic decision support in African settings must incorporate population-specific allele definitions and input-format-aware strategies.
ER  -

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