Baobab Index

Monoclonal antibodies hold significant promise for preventing HIV infection in infants and children. However, global access remains constrained by the high production costs and infrastructure requirements associated with complex mammalian cell manufacturing platforms. Alternative expression systems, including plant-based production, have been proposed as scalable and potentially lower-cost approaches for antibody manufacturing. Here, we evaluated the

Copy Number Variations (CNVs) play pivotal roles in complex disease etiology, often requiring large sample sizes to analyze disease associations. While genotyping arrays offer a cost-effective approach for CNV detection using Log R Ratio (LRR) and B Allele Frequency (BAF) signals, existing independent array-based callers suffer from high false positive rates and noise susceptibility, burdening manual validation. We present CNV-Finder, a deep learning pipeline employing Long Short-Term Memory (LSTM) networks for large-scale CNV identification within user-defined genomic regions. Trained on expert-annotated samples from the Global Parkinson's Genetics Program across four neurodegenerative disease-associated genes ( CNV-Finder is freely available at https://github.com/nvk23/CNV-Finder.

Chiari 1 malformation (CM1) is the most common congenital malformation of the human hindbrain. Although prior studies have implicated chromatin-remodeling genes in CM1, the de novo genetic architecture and underlying neurodevelopmental mechanisms remain incompletely defined. To investigate the molecular genetics of a novel familial form of CM1 linked with syringomyelia and tethered cord and determine whether rare, damaging de novo variants (DNVs) contribute to sporadic CM1 risk with gene- and pathway-level resolution, we performed whole-exome sequencing in an ultra-rare multigenerational family with CM1 and associated spinal pathology, and in the largest assembled trio-based cohort to date, comprising 1,585 proband-parent trios with sporadic, idiopathic CM1 (2017-2025). The comparison cohort included 1,798 unaffected control siblings. Clinical phenotyping was by systematic medical record review. Structural domain mapping, in silico modeling, and integration with single-cell transcriptomic data from developing human cerebellum was conducted to assess biological plausibility. A heterozygous loss-of-function variant in CHD3 segregated with CM1 and syringomyelia in a multigenerational family. In the trio-based cohort, rare protein-altering DNVs were significantly enriched across multiple chromodomain helicase DNA-binding (CHD) genes, including CHD1, CHD3, CHD4, and CHD8, exceeding gene-specific mutation expectations (protein-damaging variants: P = 1.3 × 10-9; predicted loss-of-function variants: P = 8.6 × 10-5). CHD1 contained two pathogenic DNVs (p.A999D and p.E984K). CHD4 (p.D744N, p.T1813P, and p.I1102T) and CHD8 (p.R1402X, p.R1472X, and p.R2035X) each contained three new DNVs. Variants clustered within conserved ATPase, helicase, and chromodomain regions essential for chromatin remodeling, and these patients frequently had comorbid developmental delay and related neurodevelopmental features. Single-cell transcriptomic analyses demonstrated enrichment in Purkinje cells and inhibitory neurons of midgestational cerebellum, where CHD gene products form a coherent chromatin-regulatory network. Rare, large-effect DNVs that disrupt chromatin-remodeling programs contribute to sporadic CM1, implicating genetically encoded dysregulation of cerebellar development as a central disease mechanism. Exome sequencing may complement surgical evaluation of children with sporadic CM1, particularly when accompanied by neurodevelopmental concerns, informing prognosis and family counseling.

Indigenous goats in Nigeria and neighbouring countries support livelihoods across forest-savanna-Sahel environments, yet genomic structure, connectivity history, and adaptive signals are rarely investigated in a single corridor-scale transboundary framework. We analysed three Nigerian populations (Sahel, Red Sokoto/Maradi, and West African Dwarf; WAD) and seven neighbouring populations from Burkina Faso, Mali, and Cameroon using 46,431 autosomal markers from 209 unrelated animals (with a South Asian outgroup where needed). We tested whether recurrent vernacular labels map onto shared genomic backgrounds across borders, reconstructed time-layered connectivity, quantified demographic contraction and inbreeding, and prioritised candidate adaptive regions using a structure-aware approach. Model-based ancestry and principal component analysis supported three transboundary genomic backgrounds: (i) a Sahel-Sudan background spanning Nigeria, Burkina Faso, and Mali; (ii) a southern Djallonké/WAD background spanning Nigeria, Burkina Faso, and Mali; and (iii) a distinct Cameroon dwarf lineage, with Guéra representing a drifted subgroup within the Sahel-Sudan background. Admixture-timing analysis, interpreted as approximate dates inferred from linkage-disequilibrium decay, suggested very recent cross-border involving Nigerian Sahel goats (~30-40 years under the assumed generation interval), superimposed on older Sahelian-dwarf exchange (~160-1,000 years). Effective population size declined from ~1,400-2,700 at ~960 generations ago to ~40-111 at 13 generations ago. Runs of homozygosity indicated low-to-moderate genomic inbreeding (0.004-0.040), with long segments (>8 Mb) most pronounced in Guéra and Red Sokoto/Maradi. A multi-statistic composite selection scan identified 53 candidate windows. Enrichment highlighted adhesion and translation quality-control themes in the Djallonké/WAD background background, neuronal/neuroendocrine terms in Guéra, and olfactory transduction in the Sahel-Sudan background. These results define transboundary genomic backgrounds rather than country-bounded "breeds" and provide background-specific hypotheses that can be validated in resilience-oriented breeding under ongoing mobility.

Flowering and maturity time in soybean are highly sensitive to photoperiod and influence adaptation and yield potential. In Ethiopia, soybean yield remains stagnant at about 2.4 t/ha. Precocious flowering and maturity induced by tropical short-day environments are the primary contributors to the low yields. This study dissects the genetic basis of flowering and maturity under Ethiopian conditions. A diverse panel of 323 accessions, from 13 U.S. maturity groups (MG 000 to X), was evaluated across four mid-altitude production environments. A multi-locus genome-wide association study was conducted using the mrMLM framework by integrating phenotypic data with 38,281 high-quality SNPs. Analysis of variance for the phenotypic traits revealed significant differences among the genotypes. Population structure analysis clustered the accessions into four groups, and linkage disequilibrium decayed at approximately 229 kb. Eight stable quantitative trait nucleotides (QTNs) with LOD > 3 were identified across five chromosomes; six co-localized with known loci and two were novel. Several candidate genes involved in controlling flowering and maturity act as regulators of phase transitions and circadian rhythms. For instance, Glyma.13g274900 encodes an SBP-type protein Glyma.13g274300 encodes a NAM domain, Glyma.13g273300 encodes a PHD-type domain, Glyma.12g009100, a cytochrome b5 domain, and Glyma.19g206100 encodes an auxin response factor. Allelic effect analysis demonstrated that homozygous alleles significantly delay flowering and extend maturity. The identified QTNs should be considered for advanced molecular breeding applications aimed at developing high-yielding soybean lines suited to Ethiopia's unique tropical mid-altitude environments. Future research should validate these candidate genes and their gene interactions. The online version contains supplementary material available at 10.1007/s11032-026-01695-0.

Returning individualized microbiome results in ways that are ethical, comprehensible, and useful remains under-explored in African settings. We nested a multi-site, mixed-methods study within the AWI-Gen Wave 2 gut microbiome sub-study of 1,801 women aged 42-86 years to engage participants and provide feedback. All (1,001) participants from Agincourt and Soweto (South Africa) and Nairobi (Kenya) were invited to feedback meetings: 496 from Agincourt, 87 from Soweto, and 195 from Nairobi responded. Engagement strategies were tailored by site (small-group and home-based sessions, visual metaphors, Foldscopes, and local-language delivery). Using semi-structured discussions and structured observations analyzed thematically in MAXQDA under COREQ, five cross-cutting themes emerged: (i) understanding of microbiome reports, (ii) emotional responses to feedback, (iii) perceived health relevance, (iv) trust in research institutions, and (v) suggestions for improving engagement. Culturally grounded explanations and local-language facilitation enhanced comprehension; English-heavy sessions were associated with more confusion. Most participants expressed satisfaction and described planned or enacted dietary and lifestyle changes, while frustration centered on delays between sampling and feedback. Trust increased with transparency and individualized return of results but was often conditional on minimizing burdensome procedures such as repeat blood sampling and ensuring timely feedback. Engagement was feasible and low cost (approximately USD 29-59 per participant) with site-specific resource needs. Limitations included constrained generalizability beyond the three study sites and the study population of women aged 42-86 years. Returning individualized microbiome findings in African community settings is acceptable, feasible, and can motivate health-promoting behaviors when delivered promptly and in culturally appropriate ways.IMPORTANCEMicrobiome studies rarely return individualized results in low-resource settings due to concerns about appropriate feedback and associated costs. This gap risks eroding trust and diminishing research impact. In three African communities, tailored feedback on gut microbiome profiles was provided to 778 women. By documenting a costed, multi-site engagement model and the themes influencing acceptance and actionability, this work offers a practical framework for ethically returning complex -omics results at scale in underrepresented populations-advancing scientific equity and strengthening community trust in microbiome research.

Africa is entering a new era of cancer research, driven by renewed commitments to genomic innovation, data equity, and strengthened cancer registry systems. The "Harnessing Functional Genomics in Cancer Research: Opportunities for Diagnosis and Treatment" conference, held in Windhoek, Namibia, from 23 to 26 September 2025, convened leading experts to evaluate current progress and identify priorities for advancing cancer genomics and precision oncology across the continent. This conference synthesis report and narrative review drew on four days of expert-led presentations, interactive panel discussions, and structured delegate engagement sessions. Conference proceedings were documented through session minutes, presenter slide decks, recorded discussions, and post-conference feedback. Perspectives from more than 160 participants representing 21 countries were synthesized into priority thematic areas through an iterative drafting and multi-author review process. Conference findings were integrated with supporting peer-reviewed and grey literature to identify opportunities, challenges, and strategic priorities for advancing precision oncology in Africa. Discussions highlighted Africa's unparalleled human genomic diversity and its continued underrepresentation in global genomic datasets, emphasizing the need for African-led genomic discovery and precision oncology strategies. Key priorities included strengthening cancer registries and surveillance systems, expanding genomic infrastructure and workforce capacity, establishing ethical and sovereign data-governance frameworks, and improving the translation of genomic discoveries into clinical practice. Next-generation sequencing, multi-omics approaches, artificial intelligence, and collaborative research networks were identified as important enablers of equitable and sustainable precision oncology implementation across Africa. Africa's genetic diversity represents a critical resource for advancing precision oncology. Conference insights, supported by the literature, underscore the need for coordinated investments in genomic infrastructure, cancer surveillance systems, workforce development, ethical data governance, and translational implementation. Advancing these priorities will strengthen genomics-informed cancer prevention, diagnosis, and treatment while positioning Africa as an increasingly important contributor to global oncology innovation.

Genome-wide association studies (GWAS) have identified 80+ genetic loci associated with Alzheimer's disease (AD), enabling the development of polygenic risk scores (PRS). However, the predictive accuracy of PRS in diverse populations remains low. Here, we evaluated the predictive accuracy of single-, multi-, and cross-ancestry AD-PRS models across multi-ancestral populations. We used AD GWAS summary statistics from European, African, Admixed American, and East Asian populations to construct AD-PRS for each target population. Model performance was assessed by estimating odds ratios, R The cross-ancestry Bayesian PRS model demonstrated the highest predictive performance in non-European populations. It was significantly associated with poorer cognitive function, lower Aβ Inclusive genetic datasets and cross-ancestry PRS models are needed to enhance the transportability of AD-PRS across multi-ancestral populations.

Indigenous chickens in Eritrea are raised mainly in low-input village systems and show marked variation in body size, including reduced body size phenotype, a trait associated with reduced feed consumption, thermotolerance, disease resistance, and adaptability to resource-limited environments. This study aimed to identify genomic regions associated with reduced body size using a genome-wide association study (GWAS) in Eritrean chicken ecotypes. Blood samples from 384 ICs across 16 ecotypes (21 to 24 birds per ecotype) were genotyped using DArTseq technology. Three putative short-bodied ecotypes, Barentu (BAR), Foro (FORO), and Gogne (GOG), were compared with five heavier control ecotypes: Fshe-Mrara (FM), Adi-Tekeliezan (ADTEK), Emni-Haili (HAYL), Dekemhare (DEKE), and Adikeyh (KEIH). After filtering for individual missingness, marker call rate, and minor allele frequency, 141 birds and 42,356 SNP remained. Population structure was evaluated by principal component analysis and ADMIXTURE. Exploratory case-control GWAS were conducted for each putative reduced-body-size ecotype and for the 3 ecotypes combined. Complementary quantitative-trait GWAS used body weight, body length, back length, and shank length was carried out. Linear mixed models implemented in GEMMA included sex as a fixed effect and genomic kinship as a random effect. The first 2 principal components showed extensive ancestry sharing, although GOG was more differentiated. Ecotype-specific analyses identified significant regions near CDK6, BDNF, FOXP1, TNS3, and LGR4 in FORO; EIF2AK2, NANP, MDH1, UGP2 and FGF13 in GOG; and HMGA2, IGF2, BRSK1 and SUCNR1 in BAR. The combined analysis showed no genome-wide significant variants but revealed suggestive signals near ASAP1, EIF2AK2, and FOXP1, indicating a polygenic and ecotype-specific architecture. Overlapping candidate genes across analyses included TH (common to all) and EIF2AK2 (present in all ecotypes except FORO). Quantitative-trait analyses detected a single significant SNP within CACNB4 for back length, but none for the other traits. Overall, reduced body size in Eritrean IC appears to be a complex trait controlled by multiple loci, involving both conserved growth regulators and genes related to metabolic efficiency and environmental adaptation. These findings provide a genomic basis for future breeding strategies to improve productivity, resilience and sustainability of village poultry production systems in resource-limited regions of Eritrea.