Genotyping TOMM40'523 Poly-T Polymorphisms Using Whole-Genome Sequencing.

ABSTRACT: The TOMM40'523 poly-T repeat polymorphism (rs10524523), located in the TOMM40 gene and in linkage disequilibrium with APOE, has been associated with cognitive decline and Alzheimer's disease (AD) progression. Accurate genotyping of this polymorphism is crucial for understanding its role in neurodegeneration. Challenges in processing whole-genome sequencing (WGS) data traditionally require additional PCR and targeted sequencing assays to genotype these polymorphisms. Here, we introduce a novel computational pipeline that integrates multiple short tandem repeat (STR) detection tools in an ensemble machine learning model using XGBoost. This approach leverages STR tool predictions, k-mer counts, and related features to enhance poly-T repeat length estimation. Using a sampl

SUBMITTER: Vialle RA 

PROVIDER: S-EPMC12045402 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature