The African Genome Variation Project shapes medical genetics in Africa.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa

Malaria protection due to sickle haemoglobin depends on parasite genotype.

Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2-4 PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations

Immunoglobulin G Antibodies to Merozoite Surface Antigens Are Associated with Recovery from Chloroquine-Resistant Plasmodium falciparum in Gambian Children

We examined the hypothesis that recovery from uncomplicated malaria in patients carrying drug-resistant Plasmodium falciparum is a measure of acquired functional immunity and may therefore be associated with humoral responses to candidate vaccine antigens. Gambian children with malaria were treated with chloroquine in 28-day trials, and recovery was defined primarily as the absence of severe clinical malaria at any time and absence of parasitemia with fever after 3 days. Plasma samples from these children were assayed by enzyme-linked immunosorbent assay for immunoglobulin G (IgG) to recombinant merozoite antigens: apical membrane antigen 1 (AMA-1) and the 19-kDa C-terminal region of merozoite surface protein 1 (MSP-1(19)), including antigenic variants of MSP-1(19) with double and triple substitutions. Antigen-specific IgG was more frequent in children who recovered, particularly that for MSP-1(19) (age-adjusted odds ratios: 0.32 [95% confidence interval, 0.05, 1.87; P = 0.168] for AMA-1, 0.19 [0.03, 1.11; P = 0.019] for recombinant MSP-1(19), 0.24 [0.04, 1.31; P = 0.032] for the recombinant MSP-1(19) double variant, and 0.18 [0.03, 0.97; P = 0.013] for the triple variant). IgG titers to MSP-1(19) and to the triple variant were higher in plasma samples taken 7 days after chloroquine treatment from children who carried resistant parasites but recovered and remained parasite free. Moreover, in children who were parasitemic on day 14 or day 28, there was an age-independent relationship between parasite density and IgG to both MSP-1(19) and the triple variant (coefficients of −0.550 and −0.590 and P values of 0.002 and 0.001, respectively). The results validate the use of this approach to identify antigens that are associated with protection from malaria

Effects of genetic variation at the CYP2C19/CYP2C9 locus on pharmacokinetics of chlorcycloguanil in adult Gambians.

AIMS: Antimalarial biguanides are metabolized by CYP2C19, thus genetic variation at the CYP2C locus might affect pharmacokinetics and so treatment outcome for malaria. MATERIALS & METHODS: Polymorphisms in CYP2C19 and CYP2C9 in 43 adult Gambians treated with chlorproguanil/dapsone for uncomplicated malaria were assessed. Chlorcycloguanil pharmacokinetics were measured and associations with CYP2C19 and CYP2C9 alleles and CYP2C19 metabolizer groups investigated. RESULTS: All CYP2C19/CYP2C9 alleles obeyed Hardy-Weinberg equilibrium. There were 15 CYP2C19/2C9 haplotypes with a common haplotype frequency of 0.23. Participants with the CYP2C19*17 allele had higher chlorcycloguanil area under the concentration versus curve at 24 h (AUC(0-24)) than those without (geometric means: 317 vs 216 ng.h/ml; ratio of geometric means: 1.46; 95% CI: 1.03 to 2.09; p = 0.0363) and higher C(max) (geometric mean ratio: 1.52; 95% CI: 1.13 to 2.05; p = 0.0071). CONCLUSION: CYP2C19*17 determines antimalarial biguanide metabolic profile at the CYP2C19/CYP2C9 locus

The African Genome Variation Project shapes medical genetics in Africa.

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa

Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya

This dataset contains summary statistics for association tests between human and Plasmodium falciparum malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya. These results underlie the analysis described in our paper: "Malaria protection due to sickle haemoglobin depends on parasite genotype

Imputation-based meta-analysis of severe malaria in three African populations.

Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP-based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles

A dataset of human and Plasmodium falciparum genotypes in severe malaria cases from The Gambia and Kenya

This data release accompanies the article “The protective effect of sickle cell haemoglobin depends on parasite genotype” which is currently under review and is available in preprint form at https://doi.org/10.1101/2021.03.30.437659. The release contains genotypes from human and Plasmodium falciparum genetic variants, genotyped using blood samples from 4,171 children ascertained with severe symptoms of malaria at the Royal Victoria Teaching Hospital (now the Edward Francis Small Teaching Hospital), The Gambia, and from the Kilifi District Hospital (now Kilifi County Hospital), Kenya in the period 1995-2009

Asiakastyytyväisyystutkimus : Simon Auto Oy

Opinnäytetyön tarkoituksena oli selvittää Pihtiputaan Simon Auto Oy:n asiakkaiden tyytyväisyyttä. Asiakkaiden tyytyväisyyttä selvitettiin myymälään ja kahvioon, sijaintiin sekä asiakaspalveluun. Tutkimuksessa selvitettiin samalla myös asiakkaiden taustatietoja sekä asiointitiheyttä. Opinnäytetyön teoriaosuudessa käsitellään palvelun laatua, markkinointia yleisellä tasolla, asiakastyytyväisyyttä sekä erilaisia tutkimustyyppejä. Lähteinä opinnäytetyössä käytettiin palvelua, markkinointia, asiakastyytyväisyyttä sekä tilastollista tutkimusta käsittelevää kirjallisuutta. Asiakastyytyväisyystutkimus suoritettiin kyselylomakkeella Pihtiputaan Simon Auto Oy:ssä. Vastauksia saatiin yhteensä 29 kappaletta. Tutkimuksen tulosten perusteella asiakaspalvelun laatuun sekä myymälään ja kahvioon oltiin pääosin tyytyväisiä.The purpose of this thesis was to study the satisfaction of the customers of Simon Auto Oy. The aim was to find out customers’ satisfaction with the store, cafeteria, location and customer service. This study also examined customers’ backgrounds and density of transactions. The theoretical part of this thesis deals with the quality of service, marketing at a general level, customer satisfaction and different research types. The sources of this thesis represented literature that covered service, marketing, customer satisfaction and statistical research. The customer satisfaction research was carried out by using questionnaire which took place at the store. The total number of answers was 29. Based on the research results, the customers were mainly contented with the quality of the customer service and with the store and the cafeteria