Dissertations

Addressing the SNPs associated with malaria treatment failure of King Faisal hospital patients

2026-05-28T18:22:12Z

Addressing the SNPs associated with malaria treatment failure of King Faisal hospital patients MUKANDAYISENGA, Esther Malaria is a major health burden nationally and regionally, especially in sub-Saharan Africa which experiencing more than 94% of cases and 95% of deaths attributed to malaria, and Plasmodium falciparum being the most lethal parasite species. Rwanda, continues to have a high transmission of malaria despite the national commitment and malaria control programs. The major cause of this failure to malaria control strategies includes the Resistance of Plasmodium falciparum to antimalarial drugs, affecting more treatment programs globally including the use of Artemisinin-based combination therapies (ACTs). There is therefore an urgent need to improve the control strategy. This study focused on addressing Single Nucleotide Polymorphisms (SNPs) associated with malaria treatment failure. P. falciparum, the deadliest malaria parasite species, and the gene mutation associated with it, specifically in the Plasmodium falciparum Kelch 13 (PfK13), Plasmodium falciparum chloroquine resistance transporter (Pfcrt) and Plasmodium falciparum multidrug resistance 1(Pfmdr1) genes were studied. These genetic markers are widely implicated in resistance to drugs like chloroquine, lumefantrine, and amodiaquine. In Rwanda, as many other countries adopted ACTs as the first line therapy but the presence of mutation associated with PfK13 and pfmdr1 caused reduced treatment efficacy of ACTs. In this study, validation of oxford nanopore technology (ONT) findings by sanger sequencing were performed. In total 64 samples (collected in 2024) were sequenced by ONT and validated by sanger sequencing. Results obtained revealed the concordance of results to be 92.05 % and Cohen’s Kappa k=0.479, chi-square test (x2 = 25.000), p < 0.001 confirms concordance and the Pearson Chi-Square test also confirms a strong association of the ONT and Sanger sequencing and finally the Likelihood Ratio Test confirms the concordance (x2 = 8.397, p = 0.015). Next, another cohort of 43 samples (collected in 2025) were analyzed for prevalence, 36/43(83.7%) of samples presented SNPs associated with malaria treatment failure, PfK13R561H (51.2%) and PfMDR1-Y184F (60.5%) were the most prevalence SNPs identified. These mutations compromise rapid malaria parasites clearance thus causing ACT failure and plays a role in multidrug resistance and reduce the efficacy of ArtemetherLumefantrine (Coartem). Master's Dissertation

Correlation between chemotherapy-induced peripheral neuropathy severity and CYP3A4 variations in Rwandan cancer patients receiving paclitaxel treatment

2026-05-28T18:09:22Z

Correlation between chemotherapy-induced peripheral neuropathy severity and CYP3A4 variations in Rwandan cancer patients receiving paclitaxel treatment TUYISENGE, Jean Paul Chemotherapy-induced peripheral neuropathy (CIPN) is a common and distressing complication experienced by cancer patients undergoing paclitaxel therapy. This study investigates the correlation between CIPN severity and genetic variations in the CYP3A4 enzyme among Rwandan cancer patients receiving paclitaxel-based chemotherapy. A cohort of 90 patients, predominantly female (96.5%) with breast cancer (88.37%), was enrolled at Butaro Cancer Center; 86 completed all clinical visits. Patients were followed across four chemotherapy cycles, with neuropathic symptoms systematically assessed at each visit using standardized scoring tool, EORTC QLQ-CIPN20 scale tailored for CIPN severity. Blood samples were collected for genetic analysis, and CYP3A4 genotyping was conducted using Infinium Global screening Array, a robust and validated approach for single nucleotide polymorphism detection. Genotyping revealed that 67.4% carried the wild-type allele (AA), 27.9% were heterozygous mutants (AT), and 4.7% were homozygous mutants (TT) of CYP3A4. Longitudinal assessment of neuropathic symptoms over four visits demonstrated a significant increase in CIPN severity, particularly after the second chemotherapy cycle. Linear mixed-effects modeling showed a statistically significant effect of CYP3A4 genotype on CIPN severity(p<0.001), with homozygous mutants exhibiting markedly higher symptom scores compared to wild-type carriers (p<0.001). No significant difference was observed between heterozygous mutants and wild-type patients. These findings highlight a potential genetic predisposition contributing to CIPN severity and underscore the importance of incorporating CYP3A4 genotyping in clinical oncology practice. Early and systematic neuropathy monitoring is recommended to optimize paclitaxel treatment and improve patient quality of life. Further studies in diverse African populations are warranted to validate these results. Master's Dissertation

Genomic characterization of antimalarial drug resistance markers in plasmodium falciparum using selective whole genome amplification and the nomad Nanopore sequencing in Huye, Gisagara, and Kirehe districts

2026-05-28T18:04:13Z

Genomic characterization of antimalarial drug resistance markers in plasmodium falciparum using selective whole genome amplification and the nomad Nanopore sequencing in Huye, Gisagara, and Kirehe districts IRANKUNDA, Laetitia Malaria remains a major public health challenge, with increasing cases and emerging drug resistance threatening global control efforts. This study evaluates and compares two DNA amplification strategies selective whole genome amplification (sWGA) and MVP within the nomadic sequencing (NOMAD) nanopore sequencing protocol to enhance genomic surveillance of Plasmodium falciparum in Rwanda. Our findings demonstrate that sWGA produces significantly higher sequencing reads compared to MVP, although it does not markedly improve genome coverage or depth. The NOMAD protocol delivers robust performance across multiple key resistance and vaccine target genes, maintaining high sequencing depth and coverage even with varying DNA input levels from clinical field samples. Molecular surveillance identified mutations in crucial resistance markers including pfkelch13, pfcrt, pfmdr1, pfdhfr, and pfdhps, providing actionable insights into regional parasite populations and drug resistance dynamics. This work underscores the practical utility of rapid, field-deployable nanopore sequencing combined with selective amplification methods to support real-time malaria control efforts. Strategic use of sWGA should balance increased throughput benefits against higher costs and longer processing times, while MVP may suit rapid, low-bias applications. Continued optimization and nationwide scale-up of this protocol, alongside sustained molecular surveillance and functional validation of emerging mutations, will strengthen Rwanda’s capacity for adaptive malaria control and elimination Master's Dissertation

Genetic architecture of plasmodium falciparum and impacts on Prophylaxies in Rwanda and Cameroon

2026-05-28T18:00:45Z

Genetic architecture of plasmodium falciparum and impacts on Prophylaxies in Rwanda and Cameroon UWASE, Emelyne Malaria remains a major public health challenge in sub-Saharan Africa. Increasing resistance to antimalarial drugs such as Malarone (atovaquone–proguanil) and Lariam (mefloquine) threatens the effectiveness of chemoprophylaxis, particularly in mobile populations. This study aimed to assess molecular markers associated with resistance to proguanil, atovaquone, and mefloquine by analyzing mutations in the dhfr, cytb, and pfmdr1 genes of Plasmodium falciparum isolates from Rwanda and Cameroon. A total of 339 samples were included in this study. Among them, 170 isolates from Rwanda were analyzed for mutations in the dhfr, cytb, and pfmdr1 genes, while 169 isolates from Cameroon were analyzed exclusively for cytb mutations. Targeted PCR amplification and Sanger sequencing combined to Oxford Nanopore Technology were used to detect key point mutations: N51I, C59R, S108N, and I164L in dhfr; Y268S in cytb; and Y184F in pfmdr1. In Rwanda, dhfr mutations were highly prevalent: N51I (97.1%), C59R (94.7%), S108N (98.2%), and I164L (30.6%). Cameroonian samples showed a similar triple mutant profile based on previous data, though I164L was not detected. No Y268S mutation was found in cytb from either country, indicating continued atovaquone efficacy. The Y184F mutation in pfmdr1 was observed in 48.8% of Rwandan isolates, while recent studies indicate a prevalence of approximately 60% in Cameroon. These findings suggest that proguanil resistance is near fixation, while atovaquone remains effective but at risk. The growing presence of pfmdr1 mutations raises concerns about declining mefloquine efficacy. The study highlights the urgent need for region-specific prophylaxis policies and continuous molecular surveillance Master's Dissertation