Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx
Background<p>To generate an ancestry-resolved pharmacogenomic (PGx) landscape for Colombia by integrating all PharmGKB variant-drug annotations with local allele-frequency data, thereby quantifying inter-ancestry differences of clinical relevance and exposing evidence gaps that hinder equitabl...
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2025
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| author | Andy A. Acosta-Monterrosa (22141996) |
| author2 | Kevin Fernando Montoya-Quintero (22141999) Johana Galván-Barrios (22142002) Indiana Luz Rojas Torres (22142005) |
| author2_role | author author author |
| author_facet | Andy A. Acosta-Monterrosa (22141996) Kevin Fernando Montoya-Quintero (22141999) Johana Galván-Barrios (22142002) Indiana Luz Rojas Torres (22142005) |
| author_role | author |
| dc.creator.none.fl_str_mv | Andy A. Acosta-Monterrosa (22141996) Kevin Fernando Montoya-Quintero (22141999) Johana Galván-Barrios (22142002) Indiana Luz Rojas Torres (22142005) |
| dc.date.none.fl_str_mv | 2025-08-29T05:41:42Z |
| dc.identifier.none.fl_str_mv | 10.3389/fphar.2025.1636451.s002 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Table_2_Pharmacogenomics_and_genetic_ancestry_in_Colombia_a_study_on_all_variant_drug_annotations_of_PharmGKB_xlsx/30007708 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Pharmacology pharmacogenomic variants precision medicine pharmacogenetics genomics Colombia |
| dc.title.none.fl_str_mv | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | Background<p>To generate an ancestry-resolved pharmacogenomic (PGx) landscape for Colombia by integrating all PharmGKB variant-drug annotations with local allele-frequency data, thereby quantifying inter-ancestry differences of clinical relevance and exposing evidence gaps that hinder equitable precision medicine.</p>Methods<p>We conducted a cross-sectional analysis of 4,462 PharmGKB variant annotations (1994–2024), retaining 1,216 significant single-nucleotide polymorphisms (SNPs) reported in 552 studies. Allele frequencies were extracted for five Colombian populations: two predominantly African (Palenque [PLQ], Chocó [CHG]) and three predominantly European (ATQCES, ATQPGC, CLM), from the CÓDIGO database. Spearman correlations compared population-specific PGx profiles; SNPs with >25 percentage-point frequency differentials were tabulated.</p>Results<p>European ancestry dominated the global evidence base, representing 51.5% of 651,532 participants, while African ancestry accounted for only 0.46% (n = 3,031). Strong correlations were observed among European-leaning Antioquians (r<sup>2</sup> ≥ 0.90), whereas PLQ exhibited inverse or negligible correlations with those groups (r<sup>2</sup> = −0.20 to −0.02) and minimal similarity with CHG (r<sup>2</sup> = 0.12). Twenty-eight SNPs were frequent in PLQ (>75%) but rare in Europeans (<50%), and 44 showed the opposite pattern. Notable examples include CYP3A4 rs3735451-C (rivaroxaban; 87.1% vs. 23.2%), CYP3A5 rs776746-T (tacrolimus; 85% vs. 23.5%), and rs55881666-C (duloxetine; 15% vs. 84%). Globally, 71.5% of PGx studies originated in high-income countries.</p>Conclusion<p>Large, clinically actionable allele-frequency contrasts and pronounced discovery biases confirm the need for ancestry-aware PGx testing and locally calibrated dosing algorithms in Colombia. The analytic framework and variant catalogue generated knowledge to operationalize precision pharmacotherapy across admixed Latin-American populations.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_5a9a6ed3e1f3cbcea2da89b2e3cefa41 |
| identifier_str_mv | 10.3389/fphar.2025.1636451.s002 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30007708 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsxAndy A. Acosta-Monterrosa (22141996)Kevin Fernando Montoya-Quintero (22141999)Johana Galván-Barrios (22142002)Indiana Luz Rojas Torres (22142005)Pharmacologypharmacogenomic variantsprecision medicinepharmacogeneticsgenomicsColombiaBackground<p>To generate an ancestry-resolved pharmacogenomic (PGx) landscape for Colombia by integrating all PharmGKB variant-drug annotations with local allele-frequency data, thereby quantifying inter-ancestry differences of clinical relevance and exposing evidence gaps that hinder equitable precision medicine.</p>Methods<p>We conducted a cross-sectional analysis of 4,462 PharmGKB variant annotations (1994–2024), retaining 1,216 significant single-nucleotide polymorphisms (SNPs) reported in 552 studies. Allele frequencies were extracted for five Colombian populations: two predominantly African (Palenque [PLQ], Chocó [CHG]) and three predominantly European (ATQCES, ATQPGC, CLM), from the CÓDIGO database. Spearman correlations compared population-specific PGx profiles; SNPs with >25 percentage-point frequency differentials were tabulated.</p>Results<p>European ancestry dominated the global evidence base, representing 51.5% of 651,532 participants, while African ancestry accounted for only 0.46% (n = 3,031). Strong correlations were observed among European-leaning Antioquians (r<sup>2</sup> ≥ 0.90), whereas PLQ exhibited inverse or negligible correlations with those groups (r<sup>2</sup> = −0.20 to −0.02) and minimal similarity with CHG (r<sup>2</sup> = 0.12). Twenty-eight SNPs were frequent in PLQ (>75%) but rare in Europeans (<50%), and 44 showed the opposite pattern. Notable examples include CYP3A4 rs3735451-C (rivaroxaban; 87.1% vs. 23.2%), CYP3A5 rs776746-T (tacrolimus; 85% vs. 23.5%), and rs55881666-C (duloxetine; 15% vs. 84%). Globally, 71.5% of PGx studies originated in high-income countries.</p>Conclusion<p>Large, clinically actionable allele-frequency contrasts and pronounced discovery biases confirm the need for ancestry-aware PGx testing and locally calibrated dosing algorithms in Colombia. The analytic framework and variant catalogue generated knowledge to operationalize precision pharmacotherapy across admixed Latin-American populations.</p>2025-08-29T05:41:42ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fphar.2025.1636451.s002https://figshare.com/articles/dataset/Table_2_Pharmacogenomics_and_genetic_ancestry_in_Colombia_a_study_on_all_variant_drug_annotations_of_PharmGKB_xlsx/30007708CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/300077082025-08-29T05:41:42Z |
| spellingShingle | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx Andy A. Acosta-Monterrosa (22141996) Pharmacology pharmacogenomic variants precision medicine pharmacogenetics genomics Colombia |
| status_str | publishedVersion |
| title | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| title_full | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| title_fullStr | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| title_full_unstemmed | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| title_short | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| title_sort | Table 2_Pharmacogenomics and genetic ancestry in Colombia: a study on all variant drug annotations of PharmGKB.xlsx |
| topic | Pharmacology pharmacogenomic variants precision medicine pharmacogenetics genomics Colombia |