# Whole-Exome Sequencing (WES) Analysis

This repository contains the files and scripts used for the WES analysis presented in:

Lettera et al., 2025
Molecular and phenotypic blueprint of the hematopoietic compartment reveals proliferation stress as a driver of age-associated human stem cell dysfunctions

## Study Context

Whole-exome sequencing (WES) was performed to evaluate potential genomic alterations in human hematopoietic stem cells during aging. The analysis focused on variant detection and functional annotation.

## Repository Description

OncoPrint.R: contains the code to process, filter, and create an oncoprint plot from VCF files.

ClonalHema_Jakobsen_et_al.txt: contains the list of clonal hematopoiesis–associated genes from Jakobsen et al.

Metadata.txt: contains information about the samples.

Mutect2_variants.txt: contains the already computed and filtered matrix of variants called using the Mutect2 pipeline.

VarDict_variants.txt: contains the already computed and filtered matrix of variants called using the VarDict pipeline.

## Data Availability

Raw FASTQ files are available in the European Nucleotide Archive (ENA), accession code: PRJEB93902.

## Tools and Notes

Variants are called using both Mutect2 and VarDict to select a set of high-confidence variants.

Variants were then filtered for quality, coverage, presence in a panel of genes related to clonal hematopoiesis, and effect on the harboring gene.

The oncoprint was generated using the ComplexHeatmap R package to explore variant distributions across genes and samples.

## Citation

If you use this repository or data, please cite:

Lettera et al., Molecular and phenotypic blueprint of the hematopoietic compartment reveals proliferation stress as a driver of age-associated human stem cell dysfunctions

Thank you.