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This study describes the roles of laboratory information management systems (LIMS) in multi-site genetics studies in Africa. We used the HiGeneS Africa project as a case study. The study participants were recruited in six African countries between 2019 to 2021. The Baobab LIMS, a server–client-based system (an African-led innovation) was used for the coordination of the biospecimen. The development phase of the LIMS showcased the team formation, data collection, biospecimen collection, and shipment strategies. The implementation phase showcased the biospecimen registration, processing, and quality control (QC) analytics. The sample QC was done using Nanodrop, Qubit, and PicoGreen/gDNATapestation assays. The results showed that a total of 3144 study participants were recruited from Cameroon, Ghana, Mali, Rwanda, Senegal, and South Africa. The biospecimen registration provided a comprehensive registry that included patient demographics, genetic information, and clinical and blood/saliva samples from the proband and family relatives. The QC analyzes identified 30 samples that failed QC, linked to overdue storage in the freezer before DNA extraction. The LIMS components implemented in this project formed a structure that can be upscaled to artificial intelligence-based LIMS. In conclusion, this study represents the largest and the most diverse collection of biospecimens for the genetic study of hearing impairment in Africa to date. A well-characterized LIMS should be recommended for multi-site molecular studies, particularly in Africa, to enhance African participation in global genomic medicine.

Founder mutations have been reported in BRCA1 and BCRA2 in different ethnic groups with inherited breast cancer. Testing of targeted mutations in specific populations is important for cancer prevention in mutation carriers. In Sub-Saharan Africa, only a few studies have reported specific founder mutations in inherited breast cancer. The pathogenic variant c.815_824dup of BRCA1 has been reported as the most frequent among African American populations with inherited breast cancer and was supposed to have a West African origin. Recent report from Senegal identified this variant in women with inherited breast cancer at the highest frequency ever reported. The variant was linked to a common haplotype confirming its founder effect in West Africa. In this article, we review the mutation history of c.815_824dup and discuss how it spread out of Africa through the transatlantic slave trade.

Abstract Background Pathogenic variants associated with hereditary breast cancer have been reported for BRCA1 and BRCA2 (BRCA1/2) genes in patients from multiple ethnicities, but limited information is available from sub-Saharan African populations. We report a BRCA2 pathogenic variant in a Senegalese family with hereditary breast cancer. Methods An index case from a consanguineous family and nineteen healthy female relatives were recruited after informed consent. Along with this family, 14 other index cases with family history of breast cancer were also recruited. For the control populations we recruited 48 healthy women with no cancer diagnosis and 48 women diagnosed with sporadic breast cancer without family history. Genomic DNA was extracted from peripheral blood. All BRCA2 exons were amplified by PCR and sequenced. Sequences were compared to the BRCA2 GenBank reference sequence (NM_000059.3) using Alamut Software. Results We identified a novel nonsense pathogenic variant c.5219 T > G; p.(Leu1740Ter) in exon 11 of BRCA2 in the index case. The pathogenic variant was also identified in three sisters and one daughter, but was absent in the controls and unrelated cases. Conclusions This is the first report of a novel BRCA2 pathogenic variant in a Senegalese family with hereditary breast cancer. This result confirms the diversity of hereditary breast cancer pathogenic variants across populations and extends our knowledge of genetic susceptibility to breast cancer in Africa.

This study aimed to investigate GJB2 (MIM: 121011) and GJB6 (MIM: 604418) variants associated with familial non-syndromic hearing impairment (HI) in Senegal. We investigated a total of 129 affected and 143 unaffected individuals from 44 multiplex families by segregating autosomal recessive non-syndromic HI, 9 sporadic HI cases of putative genetic origin, and 148 control individuals without personal or family history of HI. The DNA samples were screened for GJB2 coding-region variants and GJB6-D3S1830 deletions. The mean age at the medical diagnosis of the affected individuals was 2.93 ± 2.53 years [range: 1–15 years]. Consanguinity was present in 40 out of 53 families (75.47%). Variants in GJB2 explained HI in 34.1% (n = 15/44) of multiplex families. A bi-allelic pathogenic variant, GJB2: c.94C>T: p.(Arg32Cys) accounted for 25% (n = 11/44 families) of familial cases, of which 80% (n = 12/15) were consanguineous. Interestingly, the previously reported “Ghanaian” founder variant, GJB2: c.427C>T: p.(Arg143Trp), accounted for 4.5% (n = 2/44 families) of the families investigated. Among the normal controls, the allele frequency of GJB2: c.94C>T and GJB2: c.427C>T was estimated at 1% (2/148 ∗ 2) and 2% (4/148 ∗ 2), respectively. No GJB6-D3S1830 deletion was identified in any of the HI patients. This is the first report of a genetic investigation of HI in Senegal, and suggests that GJB2: c.94C>T: p.(Arg32Cys) and GJB2: c.427C>T: p.(Arg143Trp) should be tested in clinical practice for congenital HI in Senegal.

Abstract Background The intake of nutrient-rich foods from diverse diets ensures adequate nutrition for women. This study aims to determine dietary diversity among women of reproductive age (WRA) using the MDD-W indicator and how it relates to their socio-economic characteristics in the city of Nouakchott, Mauritania. Methods A community-based cross-sectional study was conducted on 240 women of reproductive age, aged 15–49 years. Food consumption data were obtained through unquantified 24 h recall which is designed to identify all foods consumed by the women during this period. We computed MDD-W as the consumption of at least five out of ten predefined food groups according to the guideline of the Food and Agriculture Organization (FAO) of the United Nations. In order to determine which factors had a statistically significant influence on dietary diversity among women, we used a value of P

Rice plays a paramount role in food and nutrition security in many West African countries. Despite the doubling of production during the last decade, rice consumption has grown faster, creating a deficit between the demand and supply. Although the West African sub-region remains the main rice-producing centre on the continent, production is severely hampered by biotic and abiotic stresses. Drought is one of the factors that most severely reduce grain yields of rice. Systems of production need to be established in order to mitigate yield loss as a result of drought. This review discusses the effects of drought on rice production in West Africa and its mitigation with an emphasis on the improvement of tolerance to drought stress. Yield stability can be achieved by developing drought-tolerant varieties through several processes encompassing profiling of known QTLs and identification of new ones, marker-assisted selection, genomic selection, and extensive multi-locational yield trials. We suggest a comprehensive strategy for breeding drought-tolerant rice varieties in West Africa.

This article reviews some current trends that can be observed in the development of neutron scattering instrument technologies. While the number of neutron scattering facilities worldwide and the number of beam days they offer are largely stable, their scientific impact is increasing through improving instrumental capabilities, new and more versatile instruments, and more efficient data collection protocols. Neutron beams are becoming smaller but more intense, and instruments are being designed to utilize more ‘useful’ neutrons in unit time. This article picks and discusses a few recent developments in the areas of integrated source and instrument design, use of computational tools, new detectors, and experiment automation.

Objective To evaluate the added value of the use of upper arm length (UAL) along with mid-upper arm circumference (MUAC) to diagnose and estimate the prevalence of wasting in comparison to current WHO standard and other MUAC-based methods.Design UAL and usual anthropometric measurements were collected during a national cross-sectional nutritional survey. Children were classified into three upper arm length groups (UALGs): UALG1, UALG2 and UALG3 according to the following UAL limits: ≤150, 151–180 and ≥181 mm, respectively. Receiver operating characteristic curves were used to determine the best MUAC cut-off for each group using weight-for-height Z-score (WHZ) as a reference standard. Wasting prevalence, sensitivity and specificity of all diagnostic methods were compared.Setting This study was conducted in Mauritania.Participants National representative sample of children from 6 to 59 months old.Results In total, 12 590 children were included in the study. Wasting prevalence was 16.1%, 5.0% and 12.5% when diagnosed by WHZ

The West African Sahel Cropland map (WASC30) is a new 30-m cropland extent product for the nominal year of 2015. We used the computing resources provided by Google Earth Engine (GEE) to fit and apply Random Forest models for cropland detection in each of 189 grid cells (composed of 100 km2, hence a total of ~1.9 × 106 km2) across five countries of the West African Sahel (Burkina Faso, Mauritania, Mali, Niger, and Senegal). Landsat-8 surface reflectance (Bands 2–7) and vegetation indices (NDVI, EVI, SAVI, and MSAVI), organized to include dry-season and growing-season band reflectances and vegetation indices for the years 2013–2015, were used as predictors. Training data were derived from an independent, high-resolution, visually interpreted sample dataset that classifies sample points across West Africa using a 2-km grid (~380,000 points were used in this study, with 50% used for model training and 50% used for model validation). Analysis of the new cropland dataset indicates a summed cropland area of ~316 × 103 km2 across the 5 countries, primarily in rainfed cropland (309 × 103 km2), with irrigated cropland area (7 × 103 km2) representing 2% of the total cropland area. At regional scale, the cropland dataset has an overall accuracy of 90.1% and a cropland class (rainfed and irrigated) user’s accuracy of 79%. At bioclimatic zones scale, results show that land proportion occupied by rainfed agriculture increases with annual precipitation up to 1000 mm. The Sudanian zone (600–1200 mm) has the highest proportion of land in agriculture (24%), followed by the Sahelian (200–600 mm) and the Guinean (1200 +) zones for 15% and 4%, respectively. The new West African Sahel dataset is made freely available for applications requiring improved cropland area information for agricultural monitoring and food security applications.

Accurate estimates of cultivated area and crop yield are critical to our understanding of agricultural production and food security, particularly for semi-arid regions like the Sahel of West Africa, where crop production is mainly rain-fed and food security is closely correlated with the inter-annual variations in rainfall. Several global and regional land cover products, based on satellite remotely-sensed data, provide estimates of the agricultural land use intensity, but the initial comparisons indicate considerable differences among them, relating to differences in the satellite data quality, classification approaches, and spatial and temporal resolutions. Here, we quantify the accuracy of available cropland products across Sahelian West Africa using an independent, high-resolution, visually interpreted sample dataset that classifies all points across West Africa using a 2-km sample grid (~500,000 points for the study area). We estimate the “quantity” and “allocation” disagreements for the cropland class of eight land cover products in five Western Sahel countries (Burkina Faso, Mali, Mauritania, Niger, and Senegal). The results confirm that coarse spatial resolution (300 m, 500 m, and 1000 m) land cover products have higher disagreements in mapping the fragmented agricultural landscape of the Western Sahel. Earlier products (e.g., GLC2000) are less accurate than recent products (e.g., ESA CCI 2013, MODIS 2013 and GlobCover 2009). We also show that two of the finer spatial resolution maps (GFSAD30, and GlobeLand30) using advanced classification approaches (random forest, decision trees, and pixel-object combined) are currently the best available products for cropland identification. However, none of the eight land cover databases examined is consistent in reaching the targeted 75% accuracy threshold in the five Sahelian countries. The majority of currently available land cover products overestimate cultivated areas by an average of 170% relative to the cropland area in the reference data.