ABSTRACT
African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa.
Subject(s)
Genetic Variation , Genetics, Population , Africa, Southern , Black People/genetics , Genetic Structures , Genetic Variation/genetics , HumansABSTRACT
Genetic studies in underrepresented populations identify disproportionate numbers of novel associations. However, most genetic studies use genotyping arrays and sequenced reference panels that best capture variation most common in European ancestry populations. To compare data generation strategies best suited for underrepresented populations, we sequenced the whole genomes of 91 individuals to high coverage as part of the Neuropsychiatric Genetics of African Population-Psychosis (NeuroGAP-Psychosis) study with participants from Ethiopia, Kenya, South Africa, and Uganda. We used a downsampling approach to evaluate the quality of two cost-effective data generation strategies, GWAS arrays versus low-coverage sequencing, by calculating the concordance of imputed variants from these technologies with those from deep whole-genome sequencing data. We show that low-coverage sequencing at a depth of ≥4× captures variants of all frequencies more accurately than all commonly used GWAS arrays investigated and at a comparable cost. Lower depths of sequencing (0.5-1×) performed comparably to commonly used low-density GWAS arrays. Low-coverage sequencing is also sensitive to novel variation; 4× sequencing detects 45% of singletons and 95% of common variants identified in high-coverage African whole genomes. Low-coverage sequencing approaches surmount the problems induced by the ascertainment of common genotyping arrays, effectively identify novel variation particularly in underrepresented populations, and present opportunities to enhance variant discovery at a cost similar to traditional approaches.
Subject(s)
DNA Mutational Analysis/economics , DNA Mutational Analysis/standards , Genetic Variation/genetics , Genetics, Population/economics , Africa , DNA Mutational Analysis/methods , Genetics, Population/methods , Genome, Human/genetics , Genome-Wide Association Study , Health Equity , Humans , Microbiota , Whole Genome Sequencing/economics , Whole Genome Sequencing/standardsABSTRACT
The mosquito midgut is the organ into which the blood meal passes and in which, within a peritrophic membrane secreted by the epithelium, the blood is retained during digestion and absorption. The mosquito midgut is lined with an actin filled microvilli that are exposed to the harsh environment of the gut lumen such as food particle abrasion, digestive hydrolases and attack by pathogens and parasites that are taken in by the blood meal. These microvilli are protected them these effects by the peritrophic matrix, the glycocalyx and the mucin proteins that line their epithelial surfaces. Immunization of BALB/c mice with AgMUC1/IL-12 cDNA has been shown to kill mosquitoes when fed on these mice. Mucin is one of the proteins produced in the mosquito midgut after a blood meal. The fine structure of the mosquito midgut epithelium interacting with immune factors such as antibodies or immune cells is of special significance for interpreting early events in the interaction between the mosquito midgut lining and the specific immune components present in the blood of AgMUC1/IL-12 cDNA immunized BALB/c mice. Following bright light microscopy, scanning electron and transmission electron microscopic observations of the features seen in mosquito midgut sections from An. gambiae mosquitoes fed on BALB/c mice immunized with AgMUC1/IL-12 cDNA, the most likely immune mechanisms responsible for mosquito killing could be cell mediated, most likely antibody dependent cellular cytotoxicity. Both necrotic and apoptotic processes that could be the cause of mosquito death were seen to take place in the cells lining the midgut epithelium.
El intestino medio es el órgano al cual pasa la sangre consumida por el mosquito y donde, mediante una membrana peritrófica secretada por el epitelio, esta sangre es mantenida durante la digestión y absorción. El intestino del mosquito está revestido por microvellosidades llenas de actina que son expuestas a las complejas condiciones en torno a la luz intestinal, tales como la abrasión producida por partículas de alimentos, hidrolasas digestivas y el ataque de patógenos y parásitos que son tomados en la sangre consumida. Estas microvellosidades se protegen de estos efectos mediante la matriz peritrófica, el glicocálix y las proteínas de mucina que revisten las superficies epiteliales. La inmunización con AgMUC1/IL-12 ADNc en ratones BALB/c ha demostrado ser útil para matar los mosquitos cuando se alimentan de estos ratones. La mucina es una de las proteínas producidas en el intestino medio del mosquito después de consumir sangre. La fina estructura del epitelio del intestino interactúa con factores inmunes tales como anticuerpos o células inmunes es de especial importancia para interpretar los eventos tempranos en la interacción entre el revestimiento del intestino medio y los componentes inmunológicos específicos presentes en la sangre de ratones BALB/c inmunizados con AgMUC1/IL-12 cDNA. Después de observar mediante microscopías de luz, electrónica de barrido y de transmisión las características de secciones del intestino medio del mosquito Anopheles gambiae alimentado de ratones BALB/c inmunizados con AgMUC1/IL-12 cDNA, mecanismos inmunes mediados por citotoxicidad celular dependiente de anticuerpos (ADCC) podrían ser los responsables de matar a los mosquitos. Los procesos necróticos y apoptóticos que pueden ser la causa de la muerte del mosquito tienen lugar en las células que recubren el epitelio del intestino medio.
