Biology subjects

Ibrahim, S.

Publications and source records attributed to Ibrahim, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-Cell Multimodal Profiling Reveals Maternal Diabetes-Nkx2-5 Interaction in Congenital Heart Disease in a Genetic Model Recapitulating Human Embryopathies

The etiological complexity of congenital heart disease (CHD) arises from the interaction between genetic and environmental factors. We hypothesized that environmental exposure could potentiate a genetic susceptibility, leading to an increased incidence of specific cardiac defects. To test this hypothesis, we used betaV59M+ female mice exhibiting severe hyperglycemia (>28 mmol/L) without dyslipidemia, a model we characterized that faithfully recapitulates human diabetic embryopathy. These females were crossed with males haploinsufficient for Nkx2-5, a transcription factor essential for cardiac development and implicated in human CHD. Our results show that the combination of genetic susceptibility and a hyperglycemic maternal environment (GxE) leads to a higher frequency and severity of cardiac malformations, including ventricular septal defects specifically involving the muscular septum, univentricular morphologies, and dilation with thinning of the myocardium. These structural abnormalities were associated with transcriptional changes affecting the contractile identity of the chamber myocardium. Single-nucleus multiomic profiling (snRNA-seq and snATAC-seq) of the E9.5 cardiac region revealed that the interaction between maternal diabetes and Nkx2-5 haploinsufficiency profoundly reshapes transcriptional and chromatin accessibility landscapes. These changes affect not only metabolic pathways, but also cell cycle progression in second heart field (SHF) progenitors, likely contributing to the observed structural cardiac defects. Multiomic integration further identifies a disrupted indirect Nkx2-5-Aldh1a2 regulatory axis in posterior SHF progenitors, while demonstrating that maternal diabetes selectively affects a restricted subset of Nkx2-5-dependent regulatory elements associated with cardiomyocyte maturation. Our findings establish a comprehensive single-cell multiomic resource that will facilitate the integration of human GWAS and other genomic datasets, enabling the identification and functional interpretation of disease-associated loci.

developmental biology↗

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2025

Epidemiological Survey of Snail Intermediate Hosts of Schistosomiasis in Zaria, Northwest Nigeria and Molluscicidal Screening of Ficus exasperata Extracts

Schistosomiasis is a Snail-borne parasitic disease transmitted through water contact activities in endemic areas. It is associated with serious morbidities including anaemia, bladder cancer and infertility. Vector control efforts rely on the use of synthetic molluscicide (Niclosamide) which has been attributed to environmental toxicity. Snail intermediate hosts of schistosomiasis were obtained from water bodies and channels around Zaria, morphologically identified and screened for cercarial shedding. F. exasperata leaves and stem bark were obtained from natural habitat in Zaria, authenticated, dried under shade, ground into powder and subjected to extraction with distilled water, ethanol and methanol. The extracts were evaluated for phytochemical constituents, DPPH and FRAP radical scavenging activities and Molluscicidal efficacy against Bulinus spp. Higher percentage yield (8.62%) was obtained in Methanolic extract. Phytochemical analysis revealed the presence of compounds such as alkaloids, flavonoids, saponins, cardiac glycosides and steroids. Tannins and Phenolics have higher concentration compared to other phytochemicals detected in all the extracts. In vitro antioxidant analysis demonstrated moderate activity, with DPPH radical scavenging activity of 62%, 60% and 47% for methanolic, aqueous and ethanolic extracts, respectively. Molluscicidal screening of the extracts revealed dose dependent toxicity against Bulinus snails, with LC50 value of 23.59ppm, 28.96ppm, 31.51ppm for ethanolic, methanolic and aqueous extracts, respectively. These findings suggest that F. exasperata stem bark extracts could be exploited for development of eco-friendly botanical molluscicide. Further research is needed to identify the bioactive compounds responsible for Molluscicidal efficacy, elucidate the possible mechanisms of action, evaluate the efficacy in field trials and environmental impact.

pharmacology and toxicology↗

bioRxiv2025

Gut Microbiota Modulates and Predicts Disease Severity in Experimental Pemphigoid Disease

Pemphigoid diseases (PD) are autoimmune blistering diseases with reported alterations in skin and gut microbiota, though their causal contribution to disease pathophysiology remains unclear. Using a passive model of bullous pemphigoid-like epidermolysis bullosa acquisita (BP-like EBA), we compared C57BL/6J mice from two sources (in-house vs. Charles River) that differed in their baseline microbiota. Charles River mice developed significantly less severe disease. Co-housing led to partial homogenization of the gut microbiota, driven by asymmetric transfer of taxa from Charles River to in-house mice, which corresponded with reduced disease severity in the latter. The skin microbiota, however, showed limited exchange. Disease severity was inversely associated with gut microbial alpha diversity, with protective taxa such as Lactobacillus intestinalis and Parabacteroides distasonis enriched in Charles River mice, while pro-inflammatory taxa including Turicimonas muris and Muribaculum intestinale were enriched in in-house mice. A machine learning model further identified a gut taxon most closely matching the candidate genus Scatocola as a strong negative predictor of disease severity. Through experimental exposure and uptake of variable gut microbiota, these findings suggest a direct role of gut microbiota in mediating the severity of the experimental BP-like EBA and highlight the potential of microbiota-based strategies for therapeutic intervention in PD.

microbiology↗

bioRxiv2025

Prediction of physical characteristics of disordered proteins using molecular simulation and physics-informed multiple machine learning strategies

We introduce a novel hybrid machine learning (ML) framework to predict the radius of gyration and other conformational properties of intrinsically disordered proteins (IDPs). Our model integrates sequence information with physical features derived from a coarse-grained (CG) model validated by experimental data. Specifically, we combine hidden states from sequence-based models with 23 physical features projected into a shared latent space, and apply an attention mechanism that assigns weights to each residue to highlight the most informative regions of the sequence. This attention-guided fusion significantly improves predictive accuracy across multiple metrics, including MAPE and MSE, while also enhancing confidence in the predictions. We trained and evaluated our models on Brownian dynamics (BD) simulation results for approximately 7,000 IDPs from the MobiDB database (each with > 99% disorder score). We find that sequence-based models consistently outperform feature-only models, with the GRU achieving the best performance among sequence-only approaches. Moreover, combining sequence and feature information further improves accuracy across all architectures, with the hybrid biGRU model delivering the best overall predictive performance. SHAP analysis reveals the relative importance of physical features, offering model explainability and guiding feature selection. Notably, using a small number of top features often reduces model complexity and improves generalization. Furthermore an integrated gradient analysis reveals that apart from the length of the IDPs, the three parameters (SCD, SHD, and f *) play key role in ML predictions. Our framework provides a fast, interpretable, and scalable tool for predicting IDP behavior, enabling efficient initial screening prior to costly molecular simulations.

biophysics↗

bioRxiv2024

An Emirati pangenome incorporating a diploid telomere-to-telomere reference

Reference data on genomic variation form the basis of genetic research. Limitations in identifying genetic variation from single reference sequences have been recently overcome, as improvements in sequencing technologies have allowed the generation of pangenomic references from multiple accurate, chromosome-level de novo assemblies. Here, we present a comprehensive Emirati telomere-to-telomere (T2T) pangenome generated from 58 individuals, comprising 28 trio-based and 30 single-sample assemblies. The resulting 116 haplotype-resolved assemblies demonstrate high contiguity, with a median continuity of 150 Mb and a median quality value (QV) of 59, achieving T2T-level scaffold status for 71.9% of chromosomes. These assemblies form the foundation of the Emirati T2T pangenome graph. The graph reveals levels of genomic diversity comparable to those reported by the Human Pangenome Reference Consortium, while also capturing regionally enriched and difficult-to-assemble variation, uniquely accessible through the Emirati T2T assemblies. This reference makes a valuable global contribution to human pangenomics and serves as a critical resource for advancing precision medicine in the United Arab Emirates.

genomics↗

bioRxiv2024

Impact of variants and vaccination on nasal immunity across three waves of SARS-CoV-2

SARS-CoV-2 infection and COVID-19 disease vary with respect to viral variant and host vaccination status. However, how vaccines, emergent variants, and their intersection shift host responses in the human nasal mucosa remains uncharacterized. We and others have shown during the first SARS-CoV-2 wave that a muted nasal epithelial interferon response at the site of infection underlies severe COVID-19. We sought to further understand how upper airway cell subsets and states associate with COVID-19 phenotypes across viral variants and vaccination. Here, we integrated new single-cell RNA-sequencing (scRNA-seq) data from nasopharyngeal swabs collected from 67 adult participants during the Delta and Omicron waves with data from 45 participants collected during the original (Ancestral) wave in our prior study. By characterizing detailed cellular states during infection, we identified changes in epithelial and immune cells that are both unique and shared across variants and vaccination status. By defining SARS-CoV-2 RNA+ cells for each variant, we found that Delta samples had a marked increase in the abundance of viral RNA+ cells. Despite this dramatic increase in viral RNA+ cells in Delta cases, the nasal cellular compositions of Delta and Omicron exhibit greater similarity, driven partly by myeloid subsets, than the Ancestral landscapes associated with specialized epithelial subsets. We found that vaccination prior to infection was surprisingly associated with nasal macrophage recruitment and activation rather than adaptive immune cell signatures. While patients with severe disease caused by Ancestral or Delta variants had muted interferon responses, Omicron-infected patients had equivalent interferon responses regardless of disease severity. Our study defines the evolution of cellular targets and signatures of disease severity in the upper respiratory tract across SARS-CoV-2 variants, and suggests that intramuscular vaccines shape myeloid responses in the nasal mucosa upon SARS-CoV-2 infection.

immunology↗

bioRxiv2023

Small extracellular vesicles promote stiffness-mediated metastasis

Tissue stiffness is a critical prognostic factor in breast cancer and is associated with metastatic progression. Here we show an alternative and complementary hypothesis of tumor progression whereby physiological matrix stiffness affects the quantity and protein cargo of small EVs produced by cancer cells, which in turn drive their metastasis. Primary patient breast tissue produces significantly more EVs from stiff tumor tissue than soft tumor adjacent tissue. EVs released by cancer cells on matrices that model human breast tumors (25 kPa; stiff EVs) feature increased adhesion molecule presentation (ITG2{beta}1, ITG6{beta}4, ITG6{beta}1, CD44) compared to EVs from softer normal tissue (0.5 kPa; soft EVs), which facilitates their binding to extracellular matrix (ECM) protein collagen IV, and a 3-fold increase in homing ability to distant organs in mice. In a zebrafish xenograft model, stiff EVs aid cancer cell dissemination through enhanced chemotaxis. Moreover, normal, resident lung fibroblasts treated with stiff and soft EVs change their gene expression profiles to adopt a cancer associated fibroblast (CAF) phenotype. These findings show that EV quantity, cargo, and function depend heavily on the mechanical properties of the extracellular microenvironment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/545937v3_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1be1dbdorg.highwire.dtl.DTLVardef@928710org.highwire.dtl.DTLVardef@1e14e9borg.highwire.dtl.DTLVardef@efdb7f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection through aging

Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here, we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mt-genome in different tissues throughout aging. We used ultra-sensitive Duplex Sequencing to profile [~]2.5 million mt-genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloging [~]1.2 million mitochondrial somatic and ultra low frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the Light Strand Origin of Replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared to primates with a surfeit of reactive oxygen species-associated G>T/C>A mutations, and that somatic mutations in protein coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that "re-align" mito-nuclear ancestry within an organisms lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.

genomics↗

bioRxiv2022

Expanding the HDAC druggable landscape beyond enzymatic inhibition

Enzymatic pockets such as those of histone deacetylases (HDACs) are among the most favored targets for drug development. However, enzymatic inhibitors often exhibit low selectivity and high toxicity due to targeting multiple enzyme paralogs, which are often involved in distinct multisubunit complexes. Here, we report the discovery and characterization of a non-enzymatic small molecule inhibitor of HDAC transcriptional repression functions with comparable anti-tumor activity to the enzymatic HDAC inhibitor Vorinostat, and anti-psychedelic activity of an HDAC2 knockout in vivo. We highlight that these phenotypes are achieved while modulating the expression of 20- and 80-fold fewer genes than enzymatic and genetic inhibition in the respective models. Thus, by achieving the same biological outcomes as established therapeutics while impacting a dramatically smaller number of genes, inhibitors of protein-protein interactions can offer important advantages in improving the selectivity of epigenetic modulators. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/519454v2_ufig1.gif" ALT="Figure 1"> View larger version (96K): org.highwire.dtl.DTLVardef@3a4e68org.highwire.dtl.DTLVardef@1f1be2corg.highwire.dtl.DTLVardef@1fc5e94org.highwire.dtl.DTLVardef@1a54790_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Identification and characterization of the T cell receptor (TCR) repertoire of the Cynomolgus macaque (Macaca Fascicularis)

BackgroundNon-human primates (NHP) are desirable as animal models of human disease because they share behavioral, physiological, and genomic traits with people. Hence, NHP recapitulate manifestations of disease not observed in other animal species. The Macaca fascicularis (i.e., Cynomolgus macaque) is an NHP species extensively used for biomedical research, but the TCR repertoire hasnt been characterized yet. ResultWe used the genomic sequences to design primers to identify the expressed TCR repertoire by single cell RNAseq. The data analysis from 22 unique samples were used to assign a functional status to each TCR genes. We identified and analyzed the TRA/D, TRB and TRG loci of the Cynomolgus macaque. ConclusionThe genomic organization of the Cynomolgus macaque has great similarity with Macaca mulatta (i.e., Rhesus macaque) and they shared >90% sequence similarity with the human TCR repertoire. These data will facilitate the analysis of T cell immunity in Cynomolgus macaques.

immunology↗

bioRxiv2022

Curcumin and NCLX Inhibitors Share Anti-Tumoral Mechanisms in Microsatellite-Instability-Driven Colorectal Cancer

Colorectal cancer (CRC) is associated with high mortality worldwide and new targets are needed to overcome treatment resistance. Recent evidences highlight a role of the mitochondria calcium homeostasis in the development of CRC. In this context, we aimed to evaluate the role of the mitochondrial sodium-calcium-lithium exchanger (NCLX) and its targeting in CRC. We also identified curcumin as a new potential inhibitor of NCLX. In vitro, curcumin exerted strong anti-tumoral activity through its action on NCLX with mtCa2+ and reactive oxygen species overload associated with a mitochondrial membrane depolarization, leading to reduced ATP production and apoptosis through mitochondrial permeability transition pore opening concomitant with G2/M cell cycle arrest. NCLX inhibition with either CGP37157 (a benzodiazepine derivative), small interfering RNA-mediated knock-down or knockout approaches reproduced the effects of curcumin. Altered mitochondrial respiration, cellular aerobic glycolysis and endoplasmic reticulum-mitochondria membrane perturbations participated in these mechanisms. In a xenograft mouse model, NCLX inhibitors decreased CRC tumor growth. Both transcriptomic analysis of The Cancer Genome Atlas dataset and immunohistochemical analysis of tissue microarrays from 381 patients with microsatellite instability (MSI)-driven CRC demonstrated that higher NCLX expression was associated with MSI status and for the first time NCLX expression was significantly associated with recurrence-free survival in MSI CRC patients. Our findings provide strong evidence that blocking NCLX inhibits CRC in vitro and in vivo. We highlight a novel anti-tumoral mechanism of curcumin through its action on NCLX and mitochondria calcium overload that could benefit for therapeutic treatment of patients with MSI CRC.

cancer biology↗

bioRxiv2021

North and East African mitochondrial genetic variation needs further characterization towards precision medicine

IntroductionMitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. ObjectivesTo address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial dataset to date and use it for characterizing mitochondrial genetic variation in this region. MethodsWe compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n=2,504) and the Human Genome Diversity Project (n=828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. ResultsUsing a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. ConclusionOur findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.

genetics↗

bioRxiv2021

High-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice provides novel insight on the impact of host genetics

Determining the forces that shape diversity in host-associated bacterial communities is critical to understanding the evolution and maintenance of metaorganisms. To gain deeper understanding of the role of host genetics in shaping gut microbial traits, we employed a powerful genetic mapping approach using inbred lines derived from the hybrid zone of two incipient house mouse species. Further, we uniquely performed our analysis on microbial traits measured at the gut mucosal interface, which is in more direct contact with host cells and the immune system. A high number of mucosa-associated bacterial taxa have significant heritability estimates; heritabilities are greater for 16S rRNA transcript-compared to gene copy-based traits, and interestingly, are positively correlated with cospeciation rate estimates. Genomewide association mapping identifies 443 loci influencing 123 taxa, with narrow genomic intervals pinpointing promising candidate genes and pathways. Importantly, we identified an enrichment of candidate genes associated with several human diseases, including inflammatory bowel disease, and functional categories including innate immunity and G-protein-coupled receptors. These results highlight key features of the genetic architecture of mammalian host-microbe interactions and how they diverge as new species form.

genetics↗

bioRxiv2021

Species ecology explains the various spatial components of genetic diversity in tropical reef fishes

Intraspecific genetic diversity should be dependent on species ecology, but the influence of ecological traits on interspecific differences in genetic variation is yet to be explored. Generating sequenced data for 20 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the , {beta} and{gamma} components of genetic diversity, which we subsequently link to six ecological traits. In contrast to what is expected by the neutral theory of molecular evolution, we find that the and{gamma} components of genetic diversity are negatively associated with species abundance, which can be explained by larger variance in reproductive success in large populations and/or higher introgression in less frequent species. Pelagic larval duration, an important dispersal trait in marine fishes, is found to be negatively related to genetic {beta} diversity, as expected by theory. We conclude that the neutral theory of molecular evolution may not be sufficient to explain genetic diversity in tropical reef fishes and that additional processes influence those relationships.

genetics↗

bioRxiv2021

12-Lipoxygenase Governs the Innate Immune Pathogenesis of Islet Inflammation and Autoimmune Diabetes

Macrophages and related myeloid cells are innate immune cells that participate in the early islet inflammation of type 1 diabetes (T1D). The inflammatory signals and antigen presentation by these cells may be inducers of the adaptive immune response that is the hallmark of T1D. The enzyme 12-lipoxygenase (12-LOX) catalyzes the formation of pro-inflammatory eicosanoids from membrane-derived phospholipids, but its role and mechanisms in the pathogenesis of islet inflammation have not been elucidated. Leveraging a model of T1D-like islet inflammation in zebrafish, we show here that macrophages contribute significantly to the loss of {beta}-cells and the subsequent development of hyperglycemia. Depletion or inhibition of 12-LOX in this model resulted in significantly reduced macrophage infiltration into islets with preservation of {beta}-cell mass. In mice, we deleted the gene encoding 12-LOX (Alox15) in the myeloid lineage in the non-obese diabetic (NOD) model of T1D. Myeloid cell-specific Alox15 knockout NOD mice demonstrated reduced insulitis and T-cell responses, preserved {beta} cell mass, and almost complete protection from the development of T1D. A critical effect of 12-LOX depletion appeared secondary to a defect in myeloid cell migration, a function required for immune surveillance and tissue injury responses. This effect on migration appeared to be secondary to the loss of the chemokine receptor CXCR3. Transgenic expression of the gene encoding CXCR3 rescued the migrator defect in zebrafish 12-LOX morphants. Taken together, our results reveal a formative role for innate immune myeloid cells in the early pathogenesis of T1D and identify 12-LOX as a necessary enzyme to promote their pro-diabetogenic phenotype in the context of autoimmunity.

immunology↗

bioRxiv2020

Loss of p32 triggers energy deficiency and impairs goblet cell differentiation in ulcerative colitis

Cell differentiation in the colonic crypt is driven by a metabolic switch from glycolysis to mitochondrial oxidation. Mitochondrial and goblet cell (GC) dysfunction have been attributed to the pathology of ulcerative colitis (UC). We hypothesized that p32/gC1qR/HABP1, which critically maintains oxidative phosphorylation, is involved in GC differentiation and hence in the pathogenesis of UC. In UC patients in remission, colonic GC differentiation was significantly decreased compared to controls in a p32-dependent manner. Plasma/serum lactate and colonic pAMPK level were increased, pointing at high glycolytic activity and energy deficiency. Consistently, p32 silencing in mucus-secreting HT29-MTX cells abolished butyrate-induced differentiation and induced a shift towards glycolysis. In mitochondrial respiratory chain complex V-deficient mice, colonic p32 expression correlated with loss of differentiated GCs, resulting in a thinner mucus layer. Conversely, feeding mice an isocaloric glucose-free, high-protein diet increased mucosal energy supply that promoted colonic p32 level, GC differentiation and mucus production. We here describe a new molecular mechanism linking mucosal energy deficiency in UC to impaired p32-dependent GC differentiation that may be therapeutically prevented by nutritional intervention.

molecular biology↗

bioRxiv2019

A personal and population-based Egyptian genome reference

The human genome is composed of chromosomal DNA sequences consisting of bases A, C, G and T - the blueprint to implement the molecular functions that are the basis of every individuals life. Deciphering the first human genome was a consortium effort that took more than a decade and considerable cost. With the latest technological advances, determining an individuals entire personal genome with manageable cost and effort has come within reach. Although the benefits of the all-encompassing genetic information that entire genomes provide are manifold, only a small number of de novo assembled human genomes have been reported to date 1-3, and few have been complemented with population-based genetic variation 4, which is particularly important for North Africans who are not represented in current genome-wide data sets 5-7. Here, we combine long- and short-read whole-genome next-generation sequencing data with recent assembly approaches into the first de novo assembly of the genome of an Egyptian individual. The resulting assembly demonstrates well-balanced quality metrics and is complemented with high-quality variant phasing via linked reads into haploblocks, which we can associate with gene expression changes in blood. To construct an Egyptian genome reference, we further assayed genome-wide genetic variation occurring in the Egyptian population within a representative cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genetic studies and corresponding genome references. The Egyptian genome reference represents a comprehensive population data set based on a high-quality personal genome. It is a proof of concept to be considered by the many national and international genome initiatives underway. More importantly, we anticipate that the Egyptian genome reference will be a valuable resource for precision medicine targeting the Egyptian population and beyond.

genetics↗