Browsing by Author "Baez, Pablo"
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- ItemAmerindian ancestry proportion as a risk factor for inflammatory bowel diseases: results from a Latin American Andean cohort(2023) Pérez Jeldres, Tamara De Lourdes; Magne, Fabien; Ascui, Gabriel; Alvares, Danilo; Orellana, Matias; Álvarez Lobos Manuel Marcelo; Hernández Rocha, Cristián Antonio; Azocar, Lorena; Aguilar, Nataly; Espino, Alberto; Estela, Ricardo; Escobar, Sergio; Zazueta, Alejandra; Baez, Pablo; Silva, Veronica; de la Vega, Andres; Arriagada, Elizabeth; Pávez Ovalle, Carolina Denisse; Diaz-Asencio, Alejandro; Travisany, Dante; Miquel Poblete, Juan Francisco; Villablanca, Eduardo J.; Kronenberg, Mitchell; Bustamante, Maria LeonorBackground and aimsLatin American populations remain underrepresented in genetic studies of inflammatory bowel diseases (IBDs). Most genetic association studies of IBD rely on Caucasian, African, and Asian individuals. These associations have yet to be evaluated in detail in the Andean region of South America. We explored the contribution of IBD-reported genetic risk variants to a Chilean cohort and the ancestry contribution to IBD in this cohort.MethodsA total of 192 Chilean IBD patients were genotyped using Illumina's Global Screening Array. Genotype data were combined with similar information from 3,147 Chilean controls. The proportions of Aymara, African, European, and Mapuche ancestries were estimated using the software ADMIXTURE. We calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for gender, age, and ancestry proportions. We also explored associations with previously reported IBD-risk variants independently and in conjunction with genetic ancestry.ResultsThe first and third quartiles of the proportion of Mapuche ancestry in IBD patients were 24.7 and 34.2%, respectively, and the corresponding OR was 2.30 (95%CI 1.52-3.48) for the lowest vs. the highest group. Only one variant (rs7210086) of the 180 reported IBD-risk SNPs was associated with IBD risk in the Chilean cohort (adjusted P = 0.01). This variant is related to myeloid cells.ConclusionThe type and proportion of Native American ancestry in Chileans seem to be associated with IBD risk. Variants associated with IBD risk in this Andean region were related to myeloid cells and the innate immune response.
- ItemEntity normalization in a Spanish medical corpus using a UMLS-based lexicon: findings and limitations(2024) Baez, Pablo; Campillos-Llanos, Leonardo; Nunez, Fredy; Dunstan, JocelynEntity normalization is a common strategy to resolve ambiguities by mapping all the synonym mentions to a single concept identifier in standard terminology. Normalizing medical entities is challenging, especially for languages other than English, where lexical variation is considerably under-represented. Here, we report a new linguistic resource for medical entity normalization in Spanish. We applied a UMLS-based medical lexicon (MedLexSp) to automatically normalize mentions from 2000 medical referrals of the Chilean Waiting List Corpus. Three medical students manually revised the automatic normalization. The inter-coder agreement was computed, and the distribution of concepts, errors, and linguistic sources of variation was analyzed. The automatic method normalized 52% of the mentions, compared to 91% after manual revision. The lowest agreement between automatic and automatic-manual normalization was observed for Finding, Disease, and Procedure entities. Errors in normalization were associated with ortho-typographic, semantic, and grammatical linguistic inadequacies, mainly of the hyponymy/hyperonymy, polysemy/metonymy, and acronym-abbreviation types. This new resource can enrich dictionaries and lexicons with new mentions to improve the functioning of modern entity normalization methods. The linguistic analysis offers insight into the sources of lexical variety in the Spanish clinical environment related to error generation using lexicon-based normalization methods. This article also introduces a workflow that can serve as a benchmark for comparison in studies replicating our analysis in Romance languages.