Evaluating the Accuracy of Imputation Methods in a Five-Way Admixed Population

Genotype imputation is a powerful tool for increasing statistical power in an association analysis. Meta-analysis of multiple study datasets also requires a substantial overlap of SNPs for a successful association analysis, which can be achieved by imputation. Quality of imputed datasets is largely dependent on the software used, as well as the reference populations chosen. The accuracy of imputation of available reference populations has not been tested for the five-way admixed South African Colored (SAC) population. In this study, imputation results obtained using three freely-accessible methods were evaluated for accuracy and quality. We show that the African Genome Resource is the best reference panel for imputation of missing genotypes in samples from the SAC population, implemented via the freely accessible Sanger Imputation Server

A Sex-Stratified Genome-Wide Association Study of Tuberculosis Using a Multi-Ethnic Genotyping Array

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males than in females. While socio-economic status, behavior and sex hormones influence the male bias they do not fully account for it. Males have only one copy of the X chromosome, while diploid females are subject to X chromosome inactivation. In addition, the X chromosome codes for many immune-related genes, supporting the hypothesis that X-linked genes could contribute to TB susceptibility in a sex-biased manner. We report the first TB susceptibility genome-wide association study (GWAS) with a specific focus on sex-stratified autosomal analysis and the X chromosome. A total of 810 individuals (410 cases and 405 controls) from an admixed South African population were genotyped using the Illumina Multi Ethnic Genotyping Array, specifically designed as a suitable platform for diverse and admixed populations. Association testing was done on the autosome (8,27,386 variants) and X chromosome (20,939 variants) in a sex stratified and combined manner. SNP association testing was not statistically significant using a stringent cut-off for significance but revealed likely candidate genes that warrant further investigation. A genome wide interaction analysis detected 16 significant interactions. Finally, the results highlight the importance of sex-stratified analysis as strong sex-specific effects were identified on both the autosome and X chromosome

African wild dogs (Lycaon pictus) from the Kruger National Park, South Africa are currently not inbred but have low genomic diversity

African wild dogs (Lycaon pictus) have undergone severe population reductions and are listed as endangered on the International Union for Conservation of Nature Red List. Small, isolated populations have the potential to suffer from threats to their genetic diversity that may impact species viability and future survival. This study provides the first set of population-wide genomic data to address conservation concerns for this endangered species. Whole genome sequencing data were generated for 71 free-ranging African wild dogs from the Kruger National Park (KNP), South Africa, and used to estimate important population genomic parameters. Genomic diversity metrics revealed that variation levels were low; however, this African wild dog population showed low levels of inbreeding. Very few first- and second-order relationships were observed in this cohort, with most relationships falling into the third-order or distant category. Patterns of homozygosity could have resulted from historical inbreeding or a loss in genome variation due to a population bottleneck. Although the results suggest that this stronghold African wild dog population maintains low levels of inbreeding, likely due to their cooperative breeding system, it may lead to a continuous population decline when a reduced number of suitable mates are available. Consequently, the low genomic variation may influence species viability over time. This study highlights the importance of assessing population genomic parameters to set conservation priorities. Future studies should include the investigation of the potential of this endangered species.https://www.nature.com/srepdm2022Veterinary Tropical Disease

Sex-bias and tuberculosis susceptibility: Bioinformatic and Biostatistical evaluation of trans-ethnic genomic datasets

Thesis (PhD)--Stellenbosch University, 2018.ENGLISH ABSTRACT: Approximately 25% of the world’s population is infected with Mycobacterium tuberculosis (M.tuberculosis). Progression to active tuberculosis (TB) is influenced by the infecting strain of M.tuberculosis, the environment and the genetic makeup of the host. Globally, the incidence rate for TB in males is nearly twice as high compared to females, indicating that biological sex of an individual also contributes to TB susceptibility. While environmental factors and sex hormones influence the immune system and affect the male bias, they do not fully account for it. This suggests that the X chromosome and the unique biology regulating X-linked gene expression in females could significantly influence progression to active TB. The X chromosome contains nearly 200 genes that are involved in the immune system. This clearly links the X chromosome to both the innate and humoral immune response and could explain why females have a more robust immune response against infections. X-linked genes have also been implicated in TB susceptibility, but these have not been conclusively linked to disease. Population specific effects could further contribute to the impact of the X chromosome on disease progression especially for populations that experienced sex-biased admixture. Here we investigated the five way admixed South African Coloured (SAC) population that has sexspecific genetic contributions from Bantu-speaking African, European, KhoeSan and South and East Asian populations. We showed that global ancestry inference could be used to detect the presence of sex-biased admixture and that this correlates with previous results indicating a KhoeSan female bias and a European and Bantu-speaking African male bias. We used SAC genome-wide association (GWAS) data and analysed the autosomes and X chromosome in a sex-stratified and combined manner, revealing sex-specific effects on both the autosome and X chromosome. A genome-wide interaction analysis also revealed significant interactions highlighting the need for epistatic and sex-stratified analysis in complex diseases. X chromosome data from the International Tuberculosis Host Genetic Consortium (ITHGC) was available to conduct a large trans-ethnic X-linked meta-analysis of TB susceptibility. The metaanalysis included imputed GWAS data from two Chinese, one Russian, a Ghanaian and Gambian and two SAC cohorts (23229 samples). We optimised imputation in our SAC data and showed that even diverse African populations can be imputed with great accuracy. The meta-analysis revealed novel X-linked genes associated with TB susceptibility. These genes were located in genomic regions on the X chromosome previously associated with TB susceptibility. Results from the meta-analysis also further confirmed the presence of both sex-specific and population specific effects. Our work highlights the importance of not only conducting sex-stratified analysis to elucidate sexspecific effects, but also to plan the study accordingly. Due to the strong impact of population specific effects, extremely large meta-analysis will be needed to fully elucidate global and population specific susceptibility variants. While the X chromosome has been mostly neglected in the past, tools for its analysis are now readily available. Our findings support the mandatory inclusion of the X chromosome in large-scale genetic studies.AFRIKAANSE OPSOMMING: Ongeveer 25% van die wêreld se bevolking is geïnfekteer met Mikobacterium tuberculosis. Die ontwikkeling van aktiewe tuberkulose (TB) word beïnvloed deur die bakterium, die omgewing en die genetiese komponent van die gasheer. Die siekte tas twee keer soveel mans as vroue aan, wat aandui dat biologiese geslag ook bydra tot TB vatbaarheid. Alhoewel beide omgewingsfaktore en geslagshormone die immuunstelsel sowel as die TB geslagsvooroordeel beïnvloed, is dit nie ten volle daarvoor verantwoordelik nie. Dit dui daarop dat die X-chromosoom en die unieke biologie wat Xgekoppelde geenuitdrukking in vroue reguleer aansienlik kan bydra tot die ontwikkeling van aktiewe TB. Die X-chromosoom bevat byna 200 gene wat by die immuunstelsel betrokke is. Hierdie gene verbind die X-chromosoom aan beide die aangebore en humorale immuunrespons en kan verduidelik waarom vroue 'n sterker immuunrespons teen infeksies het. X-gekoppelde gene is ook betrek by TB vatbaarheid, maar dit is nie voldoende verbind aan die siekte nie. Bevolkingspesifieke effekte kan verder bydra tot die impak van die X-chromosoom op die ontwikkeling van die siekte, veral vir bevolkings waar genetiese vermenging met geslagsvooroordeel plaas gevind het. Hierdie tesis ondersoek Suid-Afrikaanse individue (SAC) wat geslags-spesifieke genetiese vermenging het van Bantoe-sprekende Afrikane-, Europese, KhoeSan- en Suid- en Oos-Asiatiese bevolkings. Ons wys dat globale vermenging inferensie gebruik kan word om die teenwoordigheid van geslagsvooroordeel te bepaal en dat dit korreleer met vorige resultate wat dui op 'n vroulike KhoeSan vooroordeel en 'n manlike Europese en Bantoe-sprekende Afrika vooroordeel. Ons gebruik SAC genoom-wye assosiasie (GWAS) data en ontleed die outosoom- en X-chromosoom op 'n geslags-gestratifiseerde en gekombineerde wyse, wat geslags-spesifieke effekte op beide die autosome en X-chromosoom openbaar. 'n Genoom-wye interaksie-analise het ook betekenisvolle interaksies aangedui wat die nut van epistatiese en geslags-gestratifiseerde analise in komplekse siektes beklemtoon. X chromosoom data van die Internasionale Tuberkulose gasheer genetiese konsortium (ITHGC) was beskikbaar om 'n groot transetniese X-gekoppelde meta-analise van TB-vatbaarheid uit te voer. Die meta-analise het toegepaste GWAS data van twee Chinese, een Russiese, 'n Ghanese en Gambiese en twee SAC versamelings (23229 monsters) ingesluit. Ons het toerekening in ons SAC-data optimiseer en toon dat selfs diverse Afrika-bevolkings met groot akkuraatheid toegereken kan word. Die meta-analise onthul nuwe X-gekoppelde gene wat verband hou met TB-vatbaarheid. Hierdie gene word gevind in genomiese streke op die X-chromosoom wat voorheen geassosieer is met TBvatbaarheid. Resultate van die meta-analise bevestig verder die teenwoordigheid van beide gespesifiseerde en populasie spesifieke effekte.Doctora

IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing.

We introduce IMPUTOR, software for phylogenetically aware imputation of missing haploid nonrecombining genomic data. Targeted for next-generation sequencing data, IMPUTOR uses the principle of parsimony to impute data marked as missing due to low coverage. Along with efficiently imputing missing variant genotypes, IMPUTOR is capable of reliably and accurately correcting many nonmissing sites that represent spurious sequencing errors. Tests on simulated data show that IMPUTOR is capable of detecting many induced mutations without making erroneous imputations/corrections, with as many as 95% of missing sites imputed and 81% of errors corrected under optimal conditions. We tested IMPUTOR with human Y-chromosomes from pairs of close relatives and demonstrate IMPUTOR's efficacy in imputing missing and correcting erroneous calls

TLR1, 2, 4, 6 and 9 variants associated with tuberculosis susceptibility: a systematic review and meta-analysis

CITATION: Schurz, H., et al. 2015. TLR1, 2, 4, 6 and 9 variants associated with tuberculosis susceptibility: a systematic review and meta-analysis. PLoS ONE, 10(10):1-24, doi:10.1371/journal.pone.0139711.The original publication is available at http://journals.plos.org/plosoneBackground: Studies investigating the influence of toll-like receptor (TLR) polymorphisms and tuberculosis susceptibility have yielded varying and often contradictory results in different ethnic groups. A meta-analysis was conducted to investigate the relationship between TLR variants and susceptibility to tuberculosis, both across and within specific ethnic groups. Methods: An extensive database search was performed for studies investigating the relationship between TLR and tuberculosis (TB) susceptibility. Data was subsequently extracted from included studies and statistically analysed. Results: 32 articles involving 18907 individuals were included in this meta-analysis, and data was extracted for 14 TLR polymorphisms. Various genetic models were employed. An increased risk of TB was found for individuals with the TLR2 rs3804100 CC and the TLR9 rs352139 GA and GG genotypes, while decreased risk was identified for those with the AG genotype of TLR1 rs4833095. The T allele of TLR6 rs5743810 conferred protection across all ethnic groups. TLR2 rs5743708 subgroup analysis identified the A allele to increase susceptibility to TB in the Asian ethnic group, while conferring protection in the Hispanic group. The T allele of TLR4 rs4986791 was also found to increase the risk of TB in the Asian subgroup. All other TLR gene variants investigated were not found to be associated with TB in this meta-analysis. Discussion: Although general associations were identified, most TLR variants showed no significant association with TB, indicating that additional studies investigating a wider range of pattern recognition receptors is required to gain a better understanding of this complex diseasehttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139711Publisher's versio

Table_2_Persistence of Mycobacterium tuberculosis in response to infection burden and host-induced stressors.docx

IntroductionAs infection with Mycobacterium tuberculosis progresses, the bacilli experience various degrees of host stressors in the macrophage phagosome such as low pH, nutrient deprivation, or exposure to toxic agents, which promotes cell-to-cell phenotypic variation. This includes a physiologically viable but non- or slowly replicating persister subpopulation, which is characterised by a loss of growth on solid media, while remaining metabolically active. Persisters additionally evade the host immune response and macrophage antimicrobial processes by adapting their metabolic pathways to maintain survival and persistence in the host.MethodsA flow cytometry-based dual-fluorescent replication reporter assay, termed fluorescence dilution, provided a culture-independent method to characterize the single-cell replication dynamics of M. tuberculosis persisters following macrophage infection. Fluorescence dilution in combination with reference counting beads and a metabolic esterase reactive probe, calcein violet AM, provided an effective approach to enumerate and characterize the phenotypic heterogeneity within M. tuberculosis following macrophage infection.ResultsPersister formation appeared dependent on the initial infection burden and intracellular bacterial burden. However, inhibition of phagocytosis by cytochalasin D treatment resulted in a significantly higher median percentage of persisters compared to inhibition of phagosome acidification by bafilomycin A1 treatment.DiscussionOur results suggest that different host factors differentially impact the intracellular bacterial burden, adaptive mechanisms and entry into persistence in macrophages.</p

The X chromosome and sex-specific effects in infectious disease susceptibility

CITATION: Schurz, H., et al. 2019. The X chromosome and sex-specific effects in infectious disease susceptibility. Human Genomics, 13:2, doi:10.1186/s40246-018-0185-z.The original publication is available at https://humgenomics.biomedcentral.comENGLISH ABSTRACT: The X chromosome and X-linked variants have largely been ignored in genome-wide and candidate association studies of infectious diseases due to the complexity of statistical analysis of the X chromosome. This exclusion is significant, since the X chromosome contains a high density of immune-related genes and regulatory elements that are extensively involved in both the innate and adaptive immune responses. Many diseases present with a clear sex bias, and apart from the influence of sex hormones and socioeconomic and behavioural factors, the X chromosome, X-linked genes and X chromosome inactivation mechanisms contribute to this difference. Females are functional mosaics for X-linked genes due to X chromosome inactivation and this, combined with other X chromosome inactivation mechanisms such as genes that escape silencing and skewed inactivation, could contribute to an immunological advantage for females in many infections. In this review, we discuss the involvement of the X chromosome and X inactivation in immunity and address its role in sexual dimorphism of infectious diseases using tuberculosis susceptibility as an example, in which male sex bias is clear, yet not fully explored.https://humgenomics.biomedcentral.com/articles/10.1186/s40246-018-0185-zPublisher's versio