This repository contains the files and scripts used for the WES analysis presented in:
**Conti et al., 2025**
*Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells*.
Published in **Cell Reports Medicine**.
## 🔬 Study Context
Whole-exome sequencing (WES) was performed to evaluate potential genomic alterations introduced by CRISPR-Cas9/AAV6 editing in human hematopoietic stem and progenitor cells (HSPCs). The analysis focused on variant detection, comparison across experimental conditions, and functional annotation.
## 📂 Repository Content
-`Variants/`
Contains filtered variant call files (VCFs) and summary tables per sample or condition.
-`callable_nt/`
BED files reporting callable nucleotide regions across samples, used to control for coverage and false negatives.
-`genePanels/`
Gene sets used for annotation and targeted analysis (e.g. DDR genes, myeloid panels).
-`Plot.R`
R script used to generate summary plots included in the manuscript. It includes variant counts, overlaps, and gene-level summaries.
## 📊 Data Availability
WES data supporting this analysis are available via the Gene Expression Omnibus (GEO), under the SuperSeries accession **[GSE244257](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE244257)**.
## 🧰 Tools and Notes
- Variant calling was performed using GATK best practices.
- Callable regions were computed to normalize comparisons across samples.
- Variant annotation was carried out using Ensembl VEP and custom gene panels.
## 📌 Citation
If you use this repository or data, please cite:
> Conti A., Giannetti K., Midena F., et al. (2025).
> *Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6 mediated gene editing in hematopoietic stem cells*.
