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The fixation index Fst plays a central role in ecological and evolutionary genetic studies. The estimators of Wright (), Weir and Cockerham (), and Hudson et al. () are widely used to measure genetic differences among different populations, but all have limitations. We propose a minimum variance estimator using and . We tested in simulations and applied it to 120 unrelated East African individuals from Ethiopia and 11 subpopulations in HapMap 3 with 464,642 SNPs. Our simulation study showed that has smaller bias than for small sample sizes and smaller bias than for large sample sizes. Also, has smaller variance than for small Fst values and smaller variance than for large Fst values. We demonstrated that approximately 30 subpopulations and 30 individuals per subpopulation are required in order to accurately estimate Fst. [ABSTRACT FROM AUTHOR]

The recent feasibility of genome-wide studies of adaptation in human populations has provided novel insights into biological pathways that have been affected by adaptive pressures. However, only a few African populations have been investigated using these genome-wide approaches. Here, we performed a genome-wide analysis for evidence of recent positive selection in a sample of 120 individuals of Wolaita ethnicity belonging to Omotic-speaking people who have inhabited the mid- and high-land areas of southern Ethiopia for millennia. Using the 11 HapMap populations as the comparison group, we found Wolaita-specific signals of recent positive selection in several human leukocyte antigen (HLA) loci. Notably, the selected loci overlapped with HLA regions that we previously reported to be associated with podoconiosis-a geochemical lymphedema of the lower legs common in the Wolaita area. We found selection signals in PPARA, a gene involved in energy metabolism during prolonged food deficiency. This finding is consistent with the dietary use of enset, a crop with high-carbohydrate and low-fat and -protein contents domesticated in Ethiopia subsequent to food deprivation 10 000 years ago, and with metabolic adaptation to high-altitude hypoxia. We observed novel selection signals in CDKAL1 and NEGR1, well-known diabetes and obesity susceptibility genes. Finally, the SLC24A5 gene locus known to be associated with skin pigmentation was in the top selection signals in the Wolaita, and the alleles of single-nucleotide polymorphisms rs1426654 and rs1834640 (SLC24A5) associated with light skin pigmentation in Eurasian populations were of high frequency (47.9%) in this Omotic-speaking indigenous Ethiopian population. [ABSTRACT FROM AUTHOR]

Background: The first human mycobacterial susceptibility gene was identified amongst four children on the island of Malta in 1995. All affected children were homozygous for a nonsense mutation at position 395 of the interferon gamma receptor 1 (IFNGR1) gene, and all but one died of overwhelming mycobacterial infection. The population of Malta has high rates of infection with intracellular pathogens; leishmania, brucellosis and tuberculosis are all endemic, while leprosy, which was previously endemic, has only recently been eradicated. We hypothesised that heterozygous carriers of the IFNGR1 gene mutation, while resistant to infection with poorly pathogenic organisms, may have increased susceptibility to infection with more virulent pathogens. Methodology and Result: Screening patients with a past history of intracellular infection and healthy newborns for the presence of the IFNGR1 A->C395 mutation, using sequence specific primer PCR, did not identify any carriers of the mutation. Conclusion: These results suggest that the IFNGR1 mutation is unlikely to be of public health significance on Malta. [ABSTRACT FROM AUTHOR]

Progress in genomics and the associated technological, statistical and bioinformatics advances have facilitated the successful implementation of genome-wide association studies (GWAS) towards understanding the genetic basis of common diseases. Infectious diseases contribute significantly to the global burden of disease and there is robust epidemiological evidence that host genetic factors are important determinants of the outcome of interactions between host and pathogen. Indeed, infectious diseases have exerted profound selective pressure on human evolution. However, the application of GWAS to infectious diseases has been relatively limited compared with non-communicable diseases. Here we review GWAS findings for important infectious diseases, including malaria, tuberculosis and HIV. We highlight some of the pitfalls recognized more generally for GWAS, as well as issues specific to infection, including the role of the pathogen which also has a genome. We also discuss the challenges encountered when studying African populations which are genetically more ancient and more diverse that other populations and disproportionately bear the main global burden of serious infectious diseases. [ABSTRACT FROM AUTHOR]

To determine whether variation in two interleukin 1 family genes (IL1B and interleukin 1 receptor antagonist, IL1RN) is associated with pulmonary tuberculosis (TB), two published polymorphisms at nucleotide positions —511 and +3953 in IL1B and one in the IL1RN 86 bp VNTR were genotyped in 335 smear positive Gambian TB patients, and 298 ethnically matched controls. All individuals were HIV negative. Decreased risk of pulmonary TB was associated with both heterozygosity and homozygosity for the IL1B—511-C allele (OR 0.66, P = 0.027, and OR 0.58, P = 0.015, respectively). Nonetheless, the C allele was present at a frequency of 0.66 in TB cases suggesting that whilst IL-1β contributes to disease susceptibility, it is not the major factor. There was no association between the IL1B+3953-T/C polymorphism or the 86 bp IL1RN pentallelic repeat and TB in this population. Using an ex-vivo whole blood assay, healthy Gambian individuals who are homozygous for the IL1B—511-T allele failed to exhibit a significant increase in IL-1β production in response to LPS after IFN-ypriming. [ABSTRACT FROM PUBLISHER]

1 Here we describe the research capacity building partnership developedbetweentheMycetomaResearchCentreinKhartoum, Sudan, and the Centre for Global Health Research at Brighton & Sussex Medical School (BSMS), Brighton, UK. 3 With the Mycetoma Research Centre already strongly equipped to carry out clinical and laboratory research, 4 our partnership has deployed approaches less frequently used in Sudan, including geospatial analysis, health economics and medical anthropology. Mycetoma in the Sudan: an update from the Mycetoma Research Centre, University of Khartoum, Sudan.PLoSNeglTropDis.2015;9(3):e0003679. [Extracted from the article]

Background: Genetic differences in immune responses may affect susceptibility to mycobacterial infection, but no specific genes have been implicated in humans. We studied four children who had an unexplained genetic susceptibility to mycobacterial infection and who appeared to have inherited the same recessive mutation from a common ancestor. Methods: We used microsatellite analysis, immunofluorescence studies, and sequence analysis to study the affected patients, unaffected family members, and normal controls. Results: A genome search using microsatellite markers identified a region on chromosome 6q in which the affected children were all homozygous for eight markers. The gene for interferon-γ receptor 1 maps to this region. Immunofluorescence studies showed that the receptor was absent on leukocytes from the affected children. Sequence analysis of complementary DNA for the gene for interferon- γ receptor 1 revealed a point mutation at nucleotide 395 that introduces a stop codon and results in a truncated protein that lacks the transmembrane and cytoplasmic domains. Conclusions: Four children with severe mycobacterial infections had a mutation in the gene for interferon-γ receptor 1 that leads to the absence of receptors on cell surfaces and a functional defect in the up-regulation of tumor necrosis factor α by macrophages in response to interferon-γ. The interferon-γ pathway is important in the response to intracellular pathogens such as mycobacteria. (N Engl J Med 1996;335:1941-9.) [ABSTRACT FROM AUTHOR]

Introduction: Comorbid non-communicable diseases (NCDs) like diabetes, cardiovascular diseases (CVD), kidney diseases, and hypertension, could have implications for tuberculosis (TB) treatment management and increase the disease burden amongst active TB patients., Methods: This cross-sectional study aimed at profiling comorbidities amongst sputum-positive TB patients in the South West and Littoral regions of Cameroon and was relevant for improving disease management and public health interventions. Diabetes was defined by elevated blood glucose, body mass index (underweight: <18.5 kg/m 2 , normal: 18.5-<25.0 kg/m 2 , overweight: 25-<30 kg/m 2 and obese: ≥30.0 kg/m 2 ) and hypertension by elevated blood pressure levels (i.e., systolic ≥130 mmHg or diastolic ≥80 mmHg). Socio-demographic and clinical data were collected using case report forms. Descriptive analysis was performed, bivariate logistic regression analysis was computed with at least one comorbidity as the dependent variable (global model) and a multivariable logistic regression analysis was done to provide adjusted odds ratios (final model). The covariate with the highest p -value was removed until p < 0.25 cut-off, using R software version 4.3.1. p -value <0.05 at 95% confidence interval was considered statistically significant., Results: Five hundred and forty-nine sputum-positive microscopically confirmed active TB patients were enrolled into this study. Two-thirds (65.8%) of the total patients were male. Overall, 56 sputum-positive TB patients had at least one non-communicable disease, thus a prevalence of 10.2% (95% CI = 7.9-13.0). The most frequently recorded NCD was diabetes 4.4% (95% CI = 3.1-6.7) followed by kidney disease 2% (95% CI = 1.1-3.6), hypertension 0.9% (95% CI = 0.4-2.2), and CVD 0.91% (95% CI = 0.4-2.2). Three TB patients (0.6%) had all four comorbidities examined. Age group ( p < 0.001), and level of education ( p = 0.049) were factors significantly associated with having at least one comorbidity., Discussion: Our findings showed that diabetes was significantly the most prevalent comorbid NCD amongst sputum-positive TB patients ( p < 0.001). HIV status, occupation, body mass index (BMI), and alcohol intake were not significantly associated with having at least one comorbidity. Implementing public health intervention programmes such as systematic screening of TB patients for NCDs especially diabetes is highly recommended for better control of these diseases., Competing Interests: Conflict of interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Intravesical Bacillus Calmette-Guérin (BCG) immunotherapy preserves the bladder after resection of high-risk non-muscle-invasive bladder cancer (NMIBC). About 30% of patients experience treatment failure, which cannot be predicted a priori and carries a high risk of disease progression. We examined the in vitro tuberculin responsiveness of CD4 + T cells before BCG immunotherapy in 42 patients with high-risk NMIBC. The frequencies and functionalities of cytokine-expressing CD4 + T cells immediately before and after BCG immunotherapy induction were assessed by flow cytometry after overnight tuberculin stimulation. Tuberculin-induced secreted mediators were measured by electrochemiluminescence. We correlated the results with recurrence-free patient survival 6 months after induction. A tuberculin-induced, secreted, IL2 concentration > 250 pg/mL was the best predictor of recurrence-free survival, providing 79% sensitivity, 86% specificity (AUC = 0.852, P = 0.000), and overall correct classification in 78.6% of cases. In 50% of patients later experiencing recurrence, but not in any of the recurrence-free survivors, IL2 secretion was < 120 pg/mL. Other parameters predicting recurrence-free survival included secreted IFNγ (AUC = 0.796, P = 0.002) and the frequencies of TNF-producing (TNF + ) CD4 + T cells (AUC = 0.745, P = 0.010). "Polyfunctional" CD4 + T cells (IFNγ + /IL2 + /TNF + ) were significantly associated with recurrence-free survival (AUC = 0.801, P = 0.002). Thus, the amount of IL2 secretion from CD4 + T cells after overnight in vitro incubation with tuberculin predicted the outcome of BCG immunotherapy. As many as half of potential BCG failures could be identified before induction therapy is begun, enabling better choices regarding treatment. Cancer Immunol Res; 6(10); 1212-9. ©2018 AACR ., (©2018 American Association for Cancer Research.)

Background: The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences., Results: Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (p<2.2e-16) than HK gene promoters. The entropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes., Conclusion: Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Africa is home to genetically diverse human populations. We compared the genetic structure of the Wolaita ethnic population from Southern Ethiopia (WETH, n=120) with HapMap populations using genome-wide variants. We investigated allele frequencies of 443 clinically and pharmacogenomically relevant genetic variants in WETH compared with HapMap populations. We found that WETH were genetically most similar to the Kenya Maasai and least similar to the Japanese in HapMap. Variant alleles associated with increased risk of adverse reactions to drugs used for treating tuberculosis (rs1799929 and rs1495741 in NAT2), thromboembolism (rs7294, rs9923231 and rs9934438 in VKORC1), and HIV/AIDS and solid tumors (rs2242046 in SLC28A1) had significantly higher frequencies in WETH compared with African ancestry HapMap populations. Our results illustrate that clinically relevant pharmacogenomic loci display allele frequency differences among African populations. We conclude that drug dosage guidelines for important global health diseases should be validated in genetically diverse African populations.

Aim: Calcineurin inhibitors are substrates for P-glycoprotein (P-gp), the expression of which is associated with ABCB1 C3435T polymorphism. Individual P-gp response to calcineurin inhibitor may be linked to nephrotoxicity or rejection. Tc-2-Methoxyisobutylisonitrile (Tc-MIBI) is also a P-gp substrate. The aim of this study, therefore, was to determine Tc-MIBI organ kinetics and compare them with ABCB1 genotype with a view to replacing Tc-mercaptoacetyltriglycine (Tc-MAG3) with Tc-MIBI in renal transplant care., Methods: Thirty prospective donors (13 male) were imaged for 20 min after administration of Tc-MIBI (400 MBq) intravenously. Posterior images of the abdomen were acquired at 30 and 120 min. Organ 30 min/peak count rate ratios and exponential two-point (30-120 min) rate constants (k, min) were calculated. Nineteen donors were genotyped for C3435T (exon 26), G2677T (exon 21), C1236T (exon 12), and G1199A (exon 11) ABCB1 polymorphisms using a PCR-based technique., Results: Tc-MIBI and Tc-MAG3 gave similar perfusion images. Although their patterns of renal elimination were different, differential renal function was not significantly different. There was a negative trend between the hepatic 30 min/peak ratio and C3435T genotype (CC: 0.8374 ± 0.0502; TC: 0.6806 ± 0.1300; TT: 0.6919 ± 0.1506; P=0.083). Renal k showed a negative trend with C3435T (CC: 0.0021 ± 0.0020; TC: 0.0037 ± 0.0013; TT: 0.0040 ± 0.0012 min; P=0.087) but with no other genotypes. There were no significant sex-related differences in Tc-MIBI kinetics., Conclusion: Tc-MIBI can replace Tc-MAG3 for pretransplant workup. The ABCB1 C3435T polymorphism may influence Tc-MIBI kinetics and thus have a role in renal transplant care. Further prospective trials are required to establish the full potential of Tc-MIBI in renal transplant management.

Background: Despite the importance of the human leukocyte antigen (HLA) gene locus in research and clinical practice, direct HLA typing is laborious and expensive. Furthermore, the analysis requires specialized software and expertise which are unavailable in most developing country settings. Recently, in silico methods have been developed for predicting HLA alleles using single nucleotide polymorphisms (SNPs). However, the utility of these methods in African populations has not been systematically evaluated., Methodology/principal Findings: In the present study, we investigate prediction of HLA class II (HLA-DRB1 and HLA-DQB1) alleles using SNPs in the Wolaita population, southern Ethiopia. The subjects comprised 297 Ethiopians with genome-wide SNP data, of whom 188 had also been HLA typed and were used for training and testing the model. The 109 subjects with SNP data alone were used for empirical prediction using the multi-allelic gene prediction method. We evaluated accuracy of the prediction, agreement between predicted and HLA typed alleles, and discriminative ability of the prediction probability supplied by the model. We found that the model predicted intermediate (two-digit) resolution for HLA-DRB1 and HLA-DQB1 alleles at accuracy levels of 96% and 87%, respectively. All measures of performance showed high accuracy and reliability for prediction. The distribution of the majority of HLA alleles in the study was similar to that previously reported for the Oromo and Amhara ethnic groups from Ethiopia., Conclusions/significance: We demonstrate that HLA class II alleles can be predicted from SNP genotype data with a high level of accuracy at intermediate (two-digit) resolution in an African population. This finding offers new opportunities for HLA studies of disease epidemiology and population genetics in developing countries.

Background: BCG vaccination of infants is thought to provide good protection in all settings. This study investigated whether Malawian infants made weaker responses across a cytokine panel after BCG vaccination, compared with UK infants., Methods: Diluted whole-blood samples were cultured with Mycobacterium tuberculosis purified protein derivative for 6 days from BCG-vaccinated infants 3 months (n = 40 Malawi, 28 UK) and 12 months (n = 34 Malawi, 26 UK) after vaccination, and also from UK unvaccinated infants (n = 9 at 3 months, n = 10 at 12 months). Forty-two cytokines were measured in supernatants using a multiplex bead array assay. Principal component analysis was used to summarize the overall patterns in cytokine responses., Results: We found differences in median responses in 27 of the 42 cytokines: 7 higher in the UK and 20 higher in Malawi. The cytokines with higher responses in the UK were all T helper 1 related. The cytokines with higher responses in Malawi included innate proinflammatory cytokines, regulatory cytokines, interleukin 17, T helper 2 cytokines, chemokines, and growth factors. Principal component analysis separated the BCG-vaccinated infants from Malawi from the UK vaccinated infants and from the unvaccinated infants., Conclusions: Malawian infants make cytokine responses following BCG vaccination, but the cytokine profile is different from that in the UK. The different biosignatures following BCG vaccination in the 2 settings may indicate variability in the protective efficacy of infant BCG vaccination.

Bacille Calmette-Guérin (BCG) vaccination induces a marked increase in the interferon (IFN)-gamma response to Mycobacterium tuberculosis purified protein derivative (Mtb PPD) in UK adolescents, but not in Malawian adolescents. We hypothesized that Mtb PPD-induced IFN-gamma after BCG vaccination would be similar in infants from these 2 countries. Infants were vaccinated with BCG during the first 3-13 weeks of life. Three months after BCG vaccination, 51 (100%) of 51 UK infants had an IFN-gamma response to Mtb PPD, compared to 41 (53%) of 78 of Malawian infants, in whom responses varied according to their season of birth. We conclude that population differences in immune responses after BCG vaccination are observed among infants, as well as among young adults.

Africa is the ultimate source of modern humans and as such harbors more genetic variation than any other continent. For this reason, studies of the patterns of genetic variation in African populations are crucial to understanding how genes affect phenotypic variation, including disease predisposition. In addition, the patterns of extant genetic variation in Africa are important for understanding how genetic variation affects infectious diseases that are a major problem in Africa, such as malaria, tuberculosis, schistosomiasis, and HIV/AIDS. Therefore, elucidating the role that genetic susceptibility to infectious diseases plays is critical to improving the health of people in Africa. It is also of note that recent and ongoing social and cultural changes in sub-Saharan Africa have increased the prevalence of non-communicable diseases that will also require genetic analyses to improve disease prevention and treatment. In this review we give special attention to many of the past and ongoing studies, emphasizing those in Sub-Saharan Africans that address the role of genetic variation in human disease.

The in vitro IFN-gamma response to tuberculin was recently proposed as a correlate of vaccine-induced immunity to tuberculosis. IFN-gamma also plays a central role in the tuberculin skin test (TST), commonly used as a marker of mycobacterial infection. However, the use of TST as a marker of immunity to tuberculosis is limited for reasons ascribed mainly to interference by environmental mycobacteria. We prospectively investigated the relationship between the TST and cytokine responses to BCG in early infancy, a cohort with relatively low exposure to environmental mycobacteria. Neonatal BCG vaccination induced positive TST responses and predominant IFN-gamma responses to tuberculin in most newborns. However, the production of IFN-gamma, IL-5 and IL-13 was similar in TST responders and non-responders, and there was no significant correlation between the size of TST response and cytokine production. These results indicate that the IFN-gamma assay provides different information than TST in BCG-vaccinated newborns and could be a better marker of vaccine-induced immunity.

The clinical syndrome of oedema with proteinuria is an important cause of paediatric morbidity in sub-Saharan Africa. The aim of this study was to assess its prevalence, clinical presentation and outcome in The Gambia, where the syndrome is perceived to be common but has not previously been studied. All children admitted with oedema and proteinuria to three hospitals in the Western region of The Gambia between January 1995 and June 1998 were identified retrospectively. Hospital records were retrieved to assess admission characteristics. All traceable children were clinically reviewed, and urinalysis was performed between 3 months and 4 years after admission. Two hundred and two children who presented with proteinuria and oedema were identified, accounting for 1.2% of paediatric hospital admissions in The Gambia. Haematuria on dipstick testing was common (76.5%). Of 39 children who were traced, four (10.3%) were dead. Eighteen of the remaining 35 (51.4%) had proteinuria at follow up. Older age at first presentation was significantly associated with increased long-term morbidity. These preliminary data suggest that oedema with proteinuria may be common and could cause long-term morbidity and mortality in Gambian children. Further studies on its aetiology and treatment are warranted.

To determine whether variation in two interleukin 1 family genes (IL1B and interleukin 1 receptor antagonist, IL1RN) is associated with pulmonary tuberculosis (TB), two published polymorphisms at nucleotide positions -511 and +3953 in IL1B and one in the IL1RN 86 bp VNTR were genotyped in 335 smear positive Gambian TB patients, and 298 ethnically matched controls. All individuals were HIV negative. Decreased risk of pulmonary TB was associated with both heterozygosity and homozygosity for the IL1B-511-C allele (OR 0.66, P = 0.027, and OR 0.58, P = 0.015, respectively). Nonetheless, the C allele was present at a frequency of 0.66 in TB cases suggesting that whilst IL-1beta contributes to disease susceptibility, it is not the major factor. There was no association between the IL1B+3953-T/C polymorphism or the 86 bp IL1RN pentallelic repeat and TB in this population. Using an ex-vivo whole blood assay, healthy Gambian individuals who are homozygous for the IL1B-511-T allele failed to exhibit a significant increase in IL-1beta production in response to LPS after IFN-gamma priming.

Host genetic factors are major determinants of susceptibility to tuberculosis, and an understanding of the molecular basis of this observation has major implications for the development of novel therapies and vaccines. Slc11a1 (formerly Nramp1), the first murine infection susceptibility locus identified, regulates early innate responses to intracellular pathogens. Variation in the human homologue SLC11A1 is associated with and linked to tuberculosis in genetically different populations. In a case-control study of 329 tuberculosis case patients and 324 control subjects, the association between allele 2 of a functional SLC11A1 polymorphism and tuberculosis has been reproduced. This variant is associated with higher lipopolysaccharide-induced production of the macrophage-deactivating cytokine interleukin-10. Furthermore, monocytes from persons who develop tuberculosis innately produce more interleukin-10 than do monocytes from healthy control subjects. These data therefore confirm the importance of SLC11A1 in tuberculosis susceptibility in humans and suggest that SLC11A1 influences tuberculosis susceptibility by regulation of interleukin-10.