Eshraq Zakri

تخصص المعلوماتية الحيوية · دفعة 2026

An automated pipeline for functional annotation and phenotype mapping

Interpreting the functional impact of genetic variants remains a fundamental challenge in genomics. Functional annotation and phenotype mapping resources represent different channels of evidence on the potential biological impact of genomic variants. These resources are heterogeneous in structure and format, requiring access to multiple independent databases. In this project, we build a pipeline to annotate sets of single-nucleotide polymorphisms (SNPs) with a focus on associations resulting from genome-wide association studies (GWAS). The pipeline generates variant-centric reports capturing functional annotation and phenotype mapping. Functional annotations are generated using ANNOVAR, Ensembl VEP, and SnpEff, which characterize variants across multiple biological dimensions, including predicted molecular consequences, clinical significance, and regulatory effects across diverse ancestries. Phenotype mapping is retrieved from the GWAS Catalog, a curated repository of published GWAS findings, and OpenGWAS, a large collection of GWAS summary statistics enabling phenome-wide variant queries. We applied the pipeline to 222 genome-wide significant variants from a trans-population osteoporosis GWAS, mapping SNPs to 19 genes including established osteoporosis and BMD loci such as ESR1, LRP5, SPP1, AXIN1, and COLEC10. Phenotype mapping retrieved 241 variant–trait associations from the GWAS Catalog and over 1,000 from OpenGWAS, with strong intersection with previously reported osteoporosis and bone mineral density associations. The results demonstrate that the pipeline successfully annotates GWAS-significant variants and retrieves biologically meaningful associations. The pipeline is generalisable to any SNP set, consolidating functional and phenotype evidence into structured variant-level summaries that support variant prioritisation, cross-trait interpretation, and downstream genetic analyses.

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