Baobab Index

BACKGROUND: Congenital malformations, which are responsible for thousands of neonatal deaths every year, are prevalent in low-resource countries. Severe birth defects are mainly multifactorial but their occurrence may be exacerbated by low socioeconomic conditions and environmental factors, especially in mining areas. CASE PRESENTATION: A male neonate delivered, at term, by caesarean section from a 23-year-old woman presented multiple malformations (cardiac exstrophy, abdominal agenesis) and died 12 h after birth. The (non-consanguineous) father was an artisanal gold miner. No genetic or further morphological testing was done due to lack of resources. DISCUSSION AND CONCLUSION: The present case of severe congenital malformation in a gold mining area of the Democratic Republic of Congo, illustrates the challenges associated with the lack of specialized antenatal and neonatal care in a resource-poor country.

All cell lineages accumulate mutations over time, increasing the probability that some lineages eventually become malignant. Many of the processes responsible for generating mutations leave a characteristic footprint in the genome that allows their presence to be detected. However, the mutational pattern in a tumour is usually the combined result of multiple mutational processes being at work simultaneously, and the problem of disentangling the different footprints and their relative impact then becomes a deconvolution problem. Several algorithms have been developed for this purpose, most of them involving a factorisation of the mutation count matrix into two non-negative matrices, representing, respectively, the underlying mutational signatures and the relative exposure to these signatures. Here, we introduce the StarSignDNA algorithm for mutational signature analysis, which offers efficient re-fitting and

BackgroundGenomic research in dementia in Africa is of utmost importance based on recent reports from studies on African-Americans that the African ancestral gene is associated with a lower risk effect for developing AD. However, dementia-related genetic studies are still evolving in sub-Saharan Africa, with unique challenges influencing participant recruitment.ObjectiveThis study sought to identify key challenges of recruitment and retention how they were mitigated in the READD-ADSP Africa and 'Origins of AD in African ancestry' genetic studies.MethodsA qualitative narrative research design using in-depth interviews explored the challenges of recruiting participants and how these were managed by the nineteen stakeholders involved in the recruitment process from nine African countries participating in the African Dementia Consortium. An inductive thematic analysis was applied to code and analyze the data systematically.ResultsNineteen stakeholders from nine African countries, participating in READD-ADSP and 'Origins' studies were interviewed. Similar challenges were observed across most African countries, including the non-existing national dementia registry. Other challenges include language diversity, myths around blood collection, family dynamics, stigma, logistics, unmet expectations concerning incentives, fewer older controls and data privacy. Leveraging previous research programs, existing community engagement activities and client-doctor relationships were strategies used in addressing these challenges.ConclusionsThere are some unique challenges with recruiting and retaining participants in genetic studies in Africa. Strengthening community engagement and advocacy for genomic research, alongside a well-populated dementia registry in the African Dementia Consortium, could overcome these challenges and improve participant recruitment in genetic studies.

Integrin complexes facilitate cell communication, playing a role in ligament homeostasis.

Copy number variants (CNV) contribute significantly to the pathogenic variation associated with developmental disorders. CNV detection is often not included in standard exome sequencing (ES) analysis. Complementary methods such as chromosomal microarray are typically offered in diagnostic laboratories to diagnose pathogenic CNV. In this study, we aimed to develop an optimal approach for incorporating CNV detection within our ES analysis process for the Deciphering Developmental Disorders in Africa (DDD-Africa) cohort. We analyzed ES data from 505 probands with a developmental disorder, applying a CNV detection approach that assessed data generated using the tools CANOES and XHMM. When available, parental ES data was used to assess inheritance patterns. We confirmed a diagnosis in 42/505 (8,3%) patients with 44 pathogenic CNV identified in the probands. There were 31 deletions and 13 duplications. Among the 27 probands with parental data, all identified CNV were

Roots, Tubers, and Bananas (RTB), including banana and plantain, cassava, yam, sweetpotato, and potato crops, share several defining features that set them apart from cereals and legumes. They are essential for food and nutritional security for hundreds of millions of people, especially in developing countries. Despite their significance, RTB crop breeding has lagged due to the complexity of genetics and the use of vegetative propagation. Recent advancements in genomics-assisted breeding (GAB) offer opportunities to accelerate genetic gains. This review provides an updated synthesis of genomic tools and associated strategies applied in RTB breeding, with a focus on banana and plantain, cassava, and yam. It spans the recent development and application of genomic tools, from diversity studies and trait discovery to marker-assisted selection, genomic selection, pan-genomics, and gene editing. It also highlights the efforts to modernize RTB breeding through program optimization and digital tool integration. The review concludes by suggesting future directions for sustainable impact.

Exome sequencing (ES) is now widely accepted as an appropriate first-tier diagnostic test for developmental disorders (DD). International guidelines recommend that in diagnostic settings, ES findings be validated with an orthogonal method, such as Sanger sequencing, before reporting. However, more recent guidance recognizes that confirmatory testing for variants meeting strict quality criteria is redundant. Weighing up the cost to benefit ratio of this practice is crucial in settings where ES is not routinely implemented. The Deciphering Developmental Disorders in Africa (DDD-Africa) study aims to enable equitable implementation of genomic medicine in low-resourced settings, focusing on using ES in resolving DD in Africa. We performed confirmatory Sanger sequencing for the first 64 probands (70 variants) that underwent ES in which a variant of interest was identified. Strict quality parameters were key to diminishing the observation of false-positive variants. All high confidence variants identified by ES (n = 38) were confirmed using Sanger sequencing and low confidence variants (n = 32) were confirmed as false-positive. Confirming ES results with an orthogonal approach like Sanger sequencing is unnecessary in a resource-limited setting when robust, context-informed quality thresholds are applied. This recommendation removes significant barriers to the implementation of genomic medicine and allows for accelerated genomic access globally.

During the COVID-19 pandemic, international border restrictions, along with traveler screening and quarantine, were implemented to limit virus spread. This study analyzes the epidemiological and genomic profiles of SARS-CoV-2 infections imported into Kinshasa (DRC) during the restrictions period in 2021. As part of the national response to the pandemic, self-reported demographic and clinical data were collected from travelers entering the DRC via N'djili-Kinshasa International Airport. SARS-CoV-2 infection was diagnosed using RT-PCR, and positive samples were subjected to whole genome sequencing (WGS) to determine variant types and viral lineages. The impact of the virus's genomic profile on the clinical presentation of travelers and on the COVID-19 epidemiology in the DRC was then assessed. Of 102,810 included travelers, 1037 (1.0%) tested positive for SARS-CoV-2 and reported significantly more nausea, diarrhea, and weight loss than uninfected travelers (p < 0.001). SARS-Cov-2-infected travelers were predominantly under 43 years old (p < 0.001) and primarily from France (24.8%) and Belgium (19.5%). Of the 105 WGS analyzed, 86 (81.9%) were variants of concern (VOCs), 14 (13.3%) were variants under monitoring (VUM), and the main genomic lineages identified were Delta-B.1.617.2 (24.8%), Alpha-B.1.1.7 (10.5%), Delta-AY.122 (7.6%), and B.1.620 (5.7%). The Delta-VOC was the most prevalent among positive travelers (61/86) and appeared to cause more symptomatic infections than non-Delta variants, although one-third of positive travelers reported no symptoms. SARS-CoV-2 importation into Kinshasa (DRC) mirrored global variant circulation patterns at the study's time. This genomic landscape was consistent with in-country clinical observations, emphasizing the importance of robust border surveillance and adaptive public health strategies during pandemics.

Cross-border parasite movement drives resistance emergence in endemic regions. In Uganda, Plasmodium falciparum with artemisinin partial resistance emerged early and spread rapidly, making it a focal point for surveillance. In northeastern Democratic Republic of Congo (DRC), a key trade corridor bordering Uganda, we investigated molecular markers of artemisinin partial resistance and resistance to partner drugs used in artemisinin-based combination therapies (ACTs). Monitoring these resistance markers in DRC is essential for guiding regional containment efforts. From May to June 2023, we conducted active and passive malaria case detection in 20 villages and a central hospital, respectively. Molecular analyses included copy number variation (CNV) in pfmdr1 and pfpm2/3, and genotyping of pfkelch13, pfmdr1, and pfcrt. For pfmdr1 CNV determination, we adopted a quantitative real-time PCR threshold of 1.4, recently proposed for parasite populations with frequent multiclonal infections. Whole-genome sequencing (WGS) was performed on hospital-derived samples to assess parasite relatedness and trace resistance spread. Among the 536 individuals sampled from the villages, 49.8% tested positive for P. falciparum by PCR. The pfmdr1 N86 allele was fixed, and 50.3% of samples carried the NFD haplotype (amino acid positions 86, 184, and 1246), a marker associated with reduced lumefantrine susceptibility in Africa. Pfmdr1 CNV was detected in 4.4% of samples using the conventional threshold (≥ 1.5), increasing to 11.7% with the 1.4 threshold. Pfpm2/3 CNVs, which may influence piperaquine susceptibility, were identified in 7.0% of samples. The validated pfkelch13 mutations A675V and C469Y, associated with artemisinin partial resistance, were detected in 4.3% and 1.3% of village samples, respectively. Principal component analysis of WGS data showed that DRC parasites carrying A675V or C469Y clustered closely with Ugandan strains, supporting cross-border spread of resistant parasites between DRC and Uganda. Our findings identified the presence of molecular markers associated with artemisinin partial resistance and reduced susceptibility to lumefantrine in northeastern DRC, along with evidence of cross-border parasite migration from Uganda. Given opposing selection pressures of lumefantrine and amodiaquine on pfmdr1 and pfcrt, alternative ACTs such as artesunate-amodiaquine may merit further evaluation. To sustain ACT efficacy, integrated genomic surveillance, clinical monitoring, and coordinated regional policy responses are essential.

Monopisthocotylan parasites have been proposed as tags for studying host population structure due to their direct life cycles and short generation times. However, their effectiveness in reflecting host population connectivity remains under scrutiny. The poorly-understood connectivity of fisheries stocks in Lake Tanganyika, the second deepest lake in the world with a permanently stratified, relatively species-poor and well-delimited pelagic zone, serves as a case-study to test utility of parasites for fish stock identification. This study investigates the population structure of two Kapentagyrus species parasitizing dorosomatid fish in Lake Tanganyika, by analyzing variation in mitochondrial protein-coding genes across a geographic gradient. The study comprised 12 population genomic datasets from the central and southern subbasins of the lake sampled within the same week to account for host migration. We observed differences in geographic population structure of the two parasite species, with restricted gene flow in Kapentagyrus limnotrissae infecting a single dorosomatid species and smaller hosts preferring the littoral zone. Conversely, K. tanganicanus exhibited no geographical structure, reflecting its broader host range and preference for larger hosts preferring the pelagic zone. The results also highlight that other mitochondrial genes such as those from the dehydrogenase family or atp6 provide higher resolution for population genetic studies in these parasites than the frequently used cox1. The study also compared two sequencing strategies-individual versus pooled sequencing (PoolSeq)-for assessing population structure of monopisthocotylan parasites, and found that PoolSeq yielded similar results with lower demands on individual DNA quantity and sequencing costs. This work supports the use of host-specific, directly transmitted parasites as ecosystem tags and provides valuable insights into the role of host ecology and parasite life-history traits in shaping population dynamics.