Maherjerry/Population_Genetics_Analysis-Malaria

Integrated Bioinformatics Analysis Reveals Selection Signatures and Transmission Dynamics in Plasmodium falciparum Populations from Guinea and Sierra Leone to understand the evolutionary dynamics and transmission patterns of Plasmodium falciparum is crucial for malaria control and elimination efforts. # Population Genetics Analysis of *Plasmodium falciparum* in West Africa ## Overview Comprehensive population genetics analysis of **325 *P. falciparum* isolates** from Guinea and Sierra Leone (2011-2020) using MalariaGEN whole-genome vcf data. **Key Findings:** - Minimal temporal differentiation within Guinea (FST = 0.0008) despite intensifying selection - Moderate spatial differentiation between countries (FST = 0.020-0.024) - 931 SNPs under positive selection at drug resistance loci (*pfcrt*, *pfmdr1*, *pfkelch13*) - Structured transmission networks with zero cross-border highly-related pairs --- ## Repository Structure ``` ├── Manuscript/ # Full technical manuscript (PDF) ├── Scripts/ # R analysis scripts (8 files) ├── Figures/ # Publication-ready plots (9 files) └── Data/ # Sample metadata & gene coordinates ``` **Scripts:** `pca_analysis.R`, `fst_analysis.R`, `ibd_network_analysis.R`, `fws_analysis.R`, `ihs_analysis.R`, `tajima_d_analysis.R`, `tajima_d_gene_analysis.R`, `plot_missingness.R` --- ## Data - **Source:** MalariaGEN Pf Community Project - **Samples:** CONWAY (Guinea 2011, n=178), LAMA (Guinea 2020, n=97), NGWA-SM (Sierra Leone 2020, n=20) - **Final Dataset:** 30,803 SNPs × 295 samples --- ## Requirements ```r install.packages(c("vcfR", "hierfstat", "ggraph", "rehh", "qqman", "dplyr")) BiocManager::install(c("SeqArray", "gdsfmt")) devtools::install_github("bahlolab/moimix") ``` --- ## Author **Muhammed Bah** — Bioinformatician, MRCG@LSHTM ## Acknowledgments Prof. Alfred Ngwa (PI) and Mattu Kroma (PhD Student) for guidance on population genetics methods. --- ## Citation > Bah, M. (2025). Population Genetics Analysis of *P. falciparum* in West Africa. github.com