African Individuals Research Articles

Decreased diversity and connectivity of endophytic fungal assemblages within cultivated European olive trees compared to their native African counterpart

Host identity and location help shape fungal endophyte assemblages in plants. Hosts act as uptake filters from the environment and closely related hosts in the same location may harbour similar assemblages. We assessed the influence of host identity and geographic location on endophytic fungal assemblages within the native African olive and cultivated European olive in South Africa using high throughput sequencing. As hypothesised, the two hosts were found to share many endophytic species, but alpha diversity was lower within the European olive. The two hosts had significantly dissimilar endophyte assemblages. Distance between sites positively correlated with endophyte assemblage dissimilarities, demonstrating a strong effect of the surrounding environment on endophyte assemblages. African olive individuals had highly connected endophyte assemblages, unlike those within the European olive. Microbiome sharing and disconnected assemblages may have negative impacts on the health of the cultivated host.

The Influence of Hofstede's Cultural Dimensions on Job Satisfaction: A Study of African Expatriates in Turkey

This article investigates the influence of Hofstede's six cultural dimensions on job satisfaction among African expatriates working in Turkey. The study specifically focuses on the dimensions of Indulgence-Restraint, Individualism-Collectivism, Uncertainty Avoidance, Masculinity-Femininity, Power Distance, and Long-Short term orientation. A hierarchical regression model was employed to analyse the data collected through a survey questionnaire administered to legally employed African individuals from Ghana, Nigeria, South Africa, and Ethiopia. Results revealed that all five dimensions—Indulgence-Restraint, Individualism-Collectivism, Uncertainty Avoidance, Masculinity-Femininity, and Power Distance—displayed a significant relationship with job satisfaction. These dimensions exerted varying degrees of influence on job satisfaction, suggesting that cultural factors significantly influence the overall job satisfaction levels of African expatriates in Turkey. However, it is worth noting that no significant relationship was found between Long-Short term orientation and job satisfaction among the participants. This implies that this particular dimension may not play a prominent role in influencing job satisfaction among the surveyed African expatriates. The findings contribute to the existing body of knowledge on the intersection of cultural dimensions and job satisfaction, specifically within the context of African expatriates in Turkey. The results highlight the importance of understanding and considering cultural factors when examining job satisfaction levels among individuals from different cultural backgrounds.

CSMD1 rs10503253 increases schizophrenia risk in a Tunisian population-group

ObjectivesSchizophrenia is a complex and chronic neuropsychiatric disorder. Recent genome-wide association studies have identified several at risk genetic variants, including two single nucleotide polymorphisms, namely the rs10503253 and the rs1270942 respectively located in the CSMD1 and the CFB loci. The present case-control study was designed to assess potential associations between the two variants and the risk of developing schizophrenia and disease severity. Further we demonstrate the relationship between these variants and clinical characteristics in a population-group from Tunisia. Patients and methodsIn total, 216 patients diagnosed with schizophrenia along with176 healthy controls were included in this case–control study. The molecular analysis of the two polymorphisms was performed using tetra the Primer Amplification Refractory Mutation System–Polymerase Chain method. The statistical analysis was done using Compare V2.1 software, and correlations between genetic results and clinical characteristics were examined by Kruskal-Wallis testing. ResultsThe frequency of the rs10503253A allele was found significantly higher among patients with schizophrenia as compared to healthy controls and associated with high negative PANSS scores. While no association was found concerning the implication of the rs1270942 variant in schizophrenia risk, a positive correlation with high positive PANSS scores was further observed. ConclusionThe present finding confirms the previously reported association between the Cub and Sushi multiple Domain 1 rs10503253A allele and the risk to develop schizophrenia and identified the rs1270942 variant as a potential disease risk modifier. Such observations may be important for the definition of the susceptible immunogenetic background in North African individuals at risk to develop mental disorders.

Comparing Cardiovascular Outcomes and Costs of Perindopril-, Enalapril- or Losartan-Based Antihypertensive Regimens in South Africa: Real-World Medical Claims Database Analysis.

Differences in class or molecule-specific effects between renin-angiotensin-aldosterone system (RAAS) inhibitors have not been conclusively demonstrated. This study used South African data to assess clinical and cost outcomes of antihypertensive therapy with the three most common RAAS inhibitors: perindopril, losartan and enalapril. Using a large, South African private health insurance claims database, we identified patients with a hypertension diagnosis in January 2015 receiving standard doses of perindopril, enalapril or losartan, alone or in combination with other agents. From claims over the subsequent 5years, we calculated the risk-adjusted rate of the composite primary outcome of myocardial infarction, ischaemic heart disease, heart failure or stroke; rate of all-cause mortality; and costs per life per month (PLPM), with adjustments based on demographic characteristics, healthcare plan and comorbidity. Overall, 32,857 individuals received perindopril, 16,693 losartan and 13,939 enalapril. Perindopril-based regimens were associated with a significantly lower primary outcome rate (205 per 1000 patients over 5years) versus losartan (221; P<0.0001) or enalapril (223; P<0.0001). The risk-adjusted all-cause mortality rate was lower with perindopril than enalapril (100 vs. 139 deaths per 1000 patients over 5years; P=0.007), but not losartan (100 vs. 94; P=0.650). Mean (95% confidence interval) overall risk-adjusted cost PLPM was Rands (ZAR) 1342 (87-8973) for perindopril, ZAR 1466 (104-9365) for losartan (P=0.0044) and ZAR 1540 (77-10,546) for enalapril (P=0.0003). In South African individuals with private health insurance, a perindopril-based antihypertensive regimen provided better clinical and cost outcomes compared with other regimens.

Factors Associated with Large Cup-to-Disc Ratio and Blindness in the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study.

Primary open-angle glaucoma (POAG) disproportionately affects individuals of African ancestry. In these patients' eyes, a large cup-to-disc ratio (LCDR > 0.90) suggests greater retinal ganglion cell loss, though these patients often display varied visual ability. This study investigated the prevalence and risk factors associated with LCDR in African ancestry individuals with POAG and explored the differences between blind (>20/200) and not blind (≤20/200) LCDR eyes. A case-control methodology was used to investigate the demographic, optic disc, and genetic risk factors of subjects in the Primary Open-Angle African American Glaucoma Genetics Study. Risk factors were analyzed using univariable and multivariable logistic regression models with inter-eye correlation adjusted using generalized estimating equations. Out of 5605 eyes with POAG, 1440 eyes (25.7%) had LCDR. In the multivariable analysis, LCDR was associated with previous glaucoma surgery (OR = 1.72), increased intraocular pressure (OR = 1.04), decreased mean deviation (OR = 1.08), increased pattern standard deviation (OR = 1.06), thinner retinal nerve fiber layer (OR = 1.05), nasalization of vessels (OR = 2.67), bayonetting of vessels (OR = 1.98), visible pores in the lamina cribrosa (OR = 1.68), and a bean-shaped cup (OR = 2.11). Of LCDR eyes, 30.1% were classified as blind (≤20/200). In the multivariable analysis, the statistically significant risk factors of blindness in LCDR eyes were previous glaucoma surgery (OR = 1.72), increased intraocular pressure (OR = 1.05), decreased mean deviation (OR = 1.04), and decreased pattern standard deviation (OR = 0.90). These findings underscore the importance of close monitoring of intraocular pressure and visual function in African ancestry POAG patients, particularly those with LCDR, to preserve visual function.

Polymorphisms within the SARS-CoV-2 Human Receptor Genes Associate with Variable Disease Outcomes across Ethnicities.

The contribution of human genes to the variability of disease outcomes has been shown to be important across infectious diseases. Studies have shown mutations within specific human genes are associated with variable COVID-19 outcomes. We focused on the SARS-CoV-2 receptors/co-receptors to identify the role of specific polymorphisms within ACE2, TMPRSS2, NRP1 and CD147. Polymorphisms within ACE2 (rs2285666), TMPRSS2 (rs12329760), CD147 (rs8259) and NRP1 (rs10080) have been shown to associate with COVID-19 severity. Using cryopreserved samples from COVID-19-positive African, European and South Asian individuals within South Africa, we determined genotype frequencies. The genetic variant rs2285666 was associated with COVID-19 severity with an ethnic bias. African individuals with a CC genotype demonstrate more severe COVID-19 outcomes (OR = 7.5; 95% CI 1.164-80.89; p = 0.024) compared with those with a TT genotype. The expressions of ACE2 and SARS-CoV-2 viral load were measured using droplet digital PCR. Our results demonstrate rs2285666 and rs10080 were significantly associated with increased SARS-CoV-2 viral load and worse outcomes in certain ethnicities. This study demonstrates two important findings. Firstly, SARS-CoV-2 viral load is significantly lower in Africans compared with individuals of European and South Asian descent (p = 0.0002 and p < 0.0001). Secondly, SARS-CoV-2 viral load associates with specific SARS-CoV-2 receptor variants. A limited number of studies have examined the receptor/co-receptor genes within Africa. This study investigated genetic variants within the SARS-CoV-2 receptor/co-receptor genes and their association with COVID-19 severity and SARS-CoV-2 viral load across different ethnicities. We provide a genetic basis for differences in COVID-19 severity across ethnic groups in South Africa, further highlighting the importance of further investigation to determine potential therapeutic targets and to guide vaccination strategies that may prioritize specific genotypes.

Poster (Clinical/Best Practice Implementation) ID 1969155

Background This study examined the influence of race/ethnicity on the individuals’ survival and neurological recovery within the first year after tSCI. Methods This retrospective cohort study included all 306 cases enrolled in the NASCIS-1, who were grouped into (a) African Americans (n=84), (b) non-Hispanic whites (n=159), and (c) other races/ethnicities that included Hispanics (n=60) and Asians (n=3). Outcome measures included survival and neurological recovery (as assessed using the NASCIS motor, and pinprick and light-touch sensory scores) within the first year post-tSCI. Data analyses of neurological recovery were adjusted for major potential confounders. Results There were 39 females and 267 males with a mean age of 31 years who mostly sustained cervical severe tSCI after vehicular accidents or falls. The three groups were comparable regarding sex distribution, level and severity of tSCI, level of consciousness at admission, and total received dose of methylprednisolone. However, African Americans were significantly older than non-Hispanic white individuals (P=0.0238). African Americans and individuals of other races/ethnicities had tSCI with open wounds caused by missile and water-related accidents more often than non-Hispanic white individuals (P&amp;lt;0.0001). However, survival rates within the first year post-tSCI were statistically comparable among the three groups (P=0.3191). Among the survivors, there was no statistically significant difference among the three groups regarding motor, and pinprick and light-touch sensory recovery (P&amp;gt;0.0500). Conclusions The results of this study suggest that the epidemiology of tSCI might vary depending upon the individual’s race/ethnicity. Nevertheless, race/ethnicity did not influence survival rate or neurological recovery within first year post-tSCI.

Reliability and Validity of Self-Reported Vascular Risk Factors: Hypertension, Diabetes, and Heart Disease, in a Multi-Ethnic Community Based Study of Aging and Dementia.

Queries for the presence of cardiovascular and cerebrovascular risk factors are typically assessed through self-report. However, the reliability and validity of self-reported cardiovascular and cerebrovascular risk factors remain inconsistent in aging research. To determine the reliability and validity of the most frequently self-reported vascular risk factors: hypertension, diabetes, and heart disease. 1,870 individuals aged 65 years or older among African Americans, Caribbean Hispanics, and white non-Hispanic individuals were recruited as part of a community study of aging and dementia. We assessed the reliability, validity, sensitivity, specificity, and percent agreement of self-reported hypertension, diabetes, and heart disease, in comparison with direct measures of blood pressure, hemoglobin A1c (HbA1c), and medication use. The analyses were subsequently stratified by age, sex, education, and ethnic group. Reliability of self-reported hypertension, diabetes, and heart disease was excellent. Agreement between self-reports and clinical measures was moderate for hypertension (kappa: 0.58), good for diabetes (kappa: 0.76-0.79), and moderate for heart disease (kappa: 0.45) differing slightly by age, sex, education, and ethnic group. Sensitivity and specificity for hypertension was 88.6% -78.1%, for diabetes was 87.7% -92.0% (HbA1c ≥6.5%) or 92.7% -92.8% (HbA1c ≥7%), and for heart disease was 85.8% -75.5%. Percent agreement of self-reported was 87.0% for hypertension, 91.6% -92.6% for diabetes, and 77.4% for heart disease. Ascertainment of self-reported histories of hypertension, diabetes, and heart disease are reliable and valid compared to direct measurements or medication use.

Identification of genetic risk loci and causal insights associated with Parkinson's disease in African and African admixed populations: a genome-wide association study

An understanding of the genetic mechanisms underlying diseases in ancestrally diverse populations is an important step towards development of targeted treatments. Research in African and African admixed populations can enable mapping of complex traits, because of their genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns. We aimed to do a comprehensive genome-wide assessment in African and African admixed individuals to better understand the genetic architecture of Parkinson's disease in these underserved populations. We performed a genome-wide association study (GWAS) in people of African and African admixed ancestry with and without Parkinson's disease. Individuals were included from several cohorts that were available as a part of the Global Parkinson's Genetics Program, the International Parkinson's Disease Genomics Consortium Africa, and 23andMe. A diagnosis of Parkinson's disease was confirmed clinically by a movement disorder specialist for every individual in each cohort, except for 23andMe, in which it was self-reported based on clinical diagnosis. We characterised ancestry-specific risk, differential haplotype structure and admixture, coding and structural genetic variation, and enzymatic activity. We included 197 918 individuals (1488 cases and 196 430 controls) in our genome-wide analysis. We identified a novel common risk factor for Parkinson's disease (overall meta-analysis odds ratio for risk of Parkinson's disease 1·58 [95% CI 1·37-1·80], p=2·397 × 10-14) and age at onset at the GBA1 locus, rs3115534-G (age at onset β=-2·00 [SE=0·57], p=0·0005, for African ancestry; and β=-4·15 [0·58], p=0·015, for African admixed ancestry), which was rare in non-African or non-African admixed populations. Downstream short-read and long-read whole-genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. The identified signal seems to be associated with decreased glucocerebrosidase activity. Our study identified a novel genetic risk factor in GBA1 in people of African ancestry, which has not been seen in European populations, and it could be a major mechanistic basis of Parkinson's disease in African populations. This population-specific variant exerts substantial risk on Parkinson's disease as compared with common variation identified through GWAS and it was found to be present in 39% of the cases assessed in this study. This finding highlights the importance of understanding ancestry-specific genetic risk in complex diseases, a particularly crucial point as the Parkinson's disease field moves towards targeted treatments in clinical trials. The distinctive genetics of African populations highlights the need for equitable inclusion of ancestrally diverse groups in future trials, which will be a valuable step towards gaining insights into novel genetic determinants underlying the causes of Parkinson's disease. This finding opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk of Parkinson's disease. The Global Parkinson's Genetics Program, which is funded by the Aligning Science Across Parkinson's initiative, and The Michael J Fox Foundation for Parkinson's Research.

The moderator effect of socioeconomic status on the relationship between parental financial teaching and financial literacy

The primary aim of this research was to investigate the potential moderating effect of parental Socioeconomic status (SES) on the association between parental financial education and the financial literacy of young black African individuals. Financial literacy was measured through financial knowledge, financial behaviour, financial attitudes, and financial decision-making. Parental SES was measured by parental income. A quantitative approach was adopted for this study. A self-administered questionnaire was used to collect data from young adults in South Africa. Moderated regression analysis was used to analyse data. The results showed that parental income did not moderate the relationship between parental financial teaching and financial decision-making. Furthermore, the results indicated that parental income moderated the relationship between parental financial teaching and financial knowledge, financial behaviour, and financial attitude. Therefore, the overall results indicated that the relationship between parental financial teaching and financial literacy is moderated by parental SES. This study represents one of the initial attempts to examine the moderated association between parental financial instruction, financial literacy, and parental socioeconomic status (SES). Government must improve parental SES as it influences parental financial teaching and financial literacy. This study concluded that parental SES is important as it moderates the relationship between parental financial teaching and financial literacy.

Life years lost associated with mental illness: A cohort study of beneficiaries of a South African medical insurance scheme

BackgroundPeople with mental illness have a reduced life expectancy, but the extent of the mortality gap and the contribution of natural and unnatural causes to excess mortality among people with mental illness in South Africa are unknown. MethodsWe analysed reimbursement claims from South African medical insurance scheme beneficiaries aged 15–85 years. We estimated excess life years lost (LYL) associated with organic, substance use, psychotic, mood, anxiety, eating, personality, developmental or any mental disorders. ResultsWe followed 1,070,183 beneficiaries for a median of three years, of whom 282,926 (26.4 %) received mental health diagnoses. Men with a mental health diagnosis lost 3.83 life years (95 % CI 3.58–4.10) compared to men without. Women with a mental health diagnosis lost 2.19 life years (1.97–2.41) compared to women without. Excess mortality varied by sex and diagnosis, from 11.50 LYL (95 % CI 9.79–13.07) among men with alcohol use disorder to 0.87 LYL (0.40–1.43) among women with generalised anxiety disorder. Most LYL were attributable to natural causes (men: 3.42, women: 1.94). A considerable number of LYL were attributable to unnatural causes among men with bipolar (1.52) or substance use (2.45) disorder. LimitationsMental diagnoses are based on reimbursement claims. ConclusionsPremature mortality among South African individuals with mental disorders is high. Our findings support interventions for the prevention, early detection, and treatment of physical comorbidities in this population. Targeted programs for suicide prevention and substance use treatment, particularly among men, can help reduce excess mortality from unnatural causes.

ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden

BackgroundCurated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines.MethodsUsing archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6 years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD.ResultsWhile the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar’s lower false-positive rate.ConclusionsConsidering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.

Evaluation of Blood Pressure in African and Caucasian Race Individuals

Evaluation of Blood Pressure in African and Caucasian Race Individuals

Diversity and disparity in the treatment and care of sarcoidosis.

Clinical presentation and outcomes in patients with sarcoidosis vary by race, gender, ethnicity, and geolocation. African Americans and female individuals have the highest incidence of disease. They are also more likely to present with advanced and more severe forms of disease, and to die from sarcoidosis. African American female individuals have the highest disease-associated mortality, yet this varies by geolocation. The diverse presentation and outcomes in sarcoidosis have often been attributed to genetics and biology, yet this may not be entirely so. Several studies have shown that African Americans and female individuals are more likely to earn less and be more socioeconomically disadvantaged in society. Patients with sarcoidosis earning in the lowest income strata presented with the most severe disease and reported more barriers to care. It is plausible that the racial, gender, and geospatial differences in sarcoidosis are more reflective of healthcare disparities than genetics or biology alone. Preventable differences in the burden of disease and in the opportunities to achieve optimal health outcomes that are differentially experienced by groups of people disadvantaged by race, gender, ethnicity, or socioeconomic background should be identified and addressed.

Ethnic Minority Microparticles have Distinct Pro-Thrombotic and Pro-Oxidative Phenotypes and Interact Differentially with Endothelial Cells in vitro: Implications for Risk to Cardiovascular Disease

Ethnic minority individuals are disproportionately susceptible to endothelial dysfunction and cardiovascular disease (CVD). Microparticles (MP) are biologically active membrane-bound nanovesicles released from cells that act as biomolecular shuttles. Plasma MP was isolated from healthy White, Black African, and South Asian individuals and analysed using flow cytometry. Their effects and interactions were assessed using fluorescence, confocal, and scanning electron microscopy. Total MP and a sub-population of smaller MP associated with dysfunction and disease progression were significantly increased in Black African individuals. Pro-thrombotic and pro-oxidant MP were substantially more numerous in Black African individuals. The tissue factor activity of ethnic minority MP was significantly greater than White MP. Ethnic minority MP induced significantly greater functional changes and morphology to an endothelial cell line in vitro and integrated into endothelial cells noticeably more than White MP. These data imply distinct differences in ethnic minority MP, suggesting a role in CVD susceptibility.

Prevalence and functional profile of SARS-CoV-2 T cells in asymptomatic Kenyan adults.

SARS-CoV-2 infection in Africa has been characterized by less severe disease than elsewhere but the profile of SARS-CoV-2 specific adaptive immunity in this largely asymptomatic spread has not been studied. We collected blood and nasopharyngeal samples from rural Kenyans (n=80) without respiratory symptoms since 2019, had no contact with COVID-19 cases or received COVID-19 vaccines and were negative for current SARS-CoV-2 infection. We analyzed spike-specific antibodies and T cells specific for SARS-CoV-2 structural (membrane, nucleocapsid and spike) and accessory (ORF3a, ORF7, ORF8) proteins. Pre-pandemic samples collected in urban Nairobi, Kenya (n=13) between 2015-2016 and samples of mild-moderately symptomatic COVID-19 convalescents (n=36) living in the urban environment of Singapore were also studied. Among asymptomatic Kenyans, we detected anti-spike antibodies in 41.0% and T cell responses against ≥2 SARS-CoV-2 proteins in 82.5%. The pre-pandemic samples from Nairobi had low-level, monospecific responses. Furthermore, distinct from cellular immunity in European and Asian COVID-19 convalescents, strong T cell immunogenicity was observed against viral accessory proteins (ORF3a, ORF8) and not structural proteins, as well as a higher IL-10/IFN-γ ratio cytokine profile. The high incidence of T cell responses against different SARS-CoV-2 proteins in largely seronegative participants suggests that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. Similar observations have been made with other coronavirus infections such as MERS and SARS-CoV-1. The functional and antigen-specific profile of SARS-CoV-2 specific T cells in these African individuals suggests that genetic or environmental factors play a role in the development of protective antiviral immunity. U.S. Centers for Disease Control and Prevention, Division of Global Health Protection; the Singapore Ministry of Health's National Medical Research Council.

A Mendelian randomization study of genetic liability to post-traumatic stress disorder and risk of ischemic stroke

Observational studies have shown an association between post-traumatic stress disorder (PTSD) and ischemic stroke (IS) but given the susceptibility to confounding it is unclear if these associations represent causal effects. Mendelian randomization (MR) facilitates causal inference that is robust to the influence of confounding. Using two sample MR, we investigated the causal effect of genetic liability to PTSD on IS risk. Ancestry-specific genetic instruments of PTSD and four quantitative sub-phenotypes of PTSD, including hyperarousal, avoidance, re-experiencing, and total symptom severity score (PCL-Total) were obtained from the Million Veteran Programme (MVP) using a threshold P value (P) of <5 × 10−7, clumping distance of 1000 kilobase (Mb) and r2 < 0.01. Genetic association estimates for IS were obtained from the MEGASTROKE consortium (Ncases = 34,217, Ncontrols = 406,111) for European ancestry individuals and from the Consortium of Minority Population Genome-Wide Association Studies of Stroke (COMPASS) (Ncases = 3734, Ncontrols = 18,317) for African ancestry individuals. We used the inverse-variance weighted (IVW) approach as the main analysis and performed MR-Egger and the weighted median methods as pleiotropy-robust sensitivity analyses. In European ancestry individuals, we found evidence of an association between genetic liability to PTSD avoidance, and PCL-Total and increased IS risk (odds ratio (OR)1.04, 95% Confidence Interval (CI) 1.007–1.077, P = 0.017 for avoidance and (OR 1.02, 95% CI 1.010–1.040, P = 7.6 × 10−4 for PCL total). In African ancestry individuals, we found evidence of an association between genetically liability to PCL-Total and reduced IS risk (OR 0.95 (95% CI 0.923–0.991, P = 0.01) and hyperarousal (OR 0.83 (95% CI 0.691–0.991, P = 0.039) but no association was observed for PTSD case-control, avoidance, or re-experiencing. Similar estimates were obtained with MR sensitivity analyses. Our findings suggest that specific sub-phenotypes of PTSD, such as hyperarousal, avoidance, PCL total, may have a causal effect on people of European and African ancestry’s risk of IS. This shows that the molecular mechanisms behind the relationship between IS and PTSD may be connected to symptoms of hyperarousal and avoidance. To clarify the precise biological mechanisms involved and how they may vary between populations, more research is required.

The genetic and phenotypic correlates of mtDNA copy number in a multi-ancestry cohort.

Mitochondrial DNA copy number (mtCN) is often treated as a proxy for mitochondrial (dys-) function and disease risk. Pathological changes in mtCN are common symptoms of rare mitochondrial disorders, but reported associations between mtCN and common diseases vary across studies. To understand the biology of mtCN, we carried out genome- and phenome-wide association studies of mtCN in 30,666 individuals from the Penn Medicine BioBank (PMBB)-a diverse cohort of largely African and European ancestry. We estimated mtCN in peripheral blood using exome sequence data, taking cell composition into account. We replicated known genetic associations of mtCN in the PMBB and found that their effects are highly correlated between individuals of European and African ancestry. However, the heritability of mtCN was much higher among individuals of largely African ancestry compared with European ancestry individuals. Admixture mapping suggests that there are undiscovered variants underlying mtCN that are differentiated in frequency between individuals with African and European ancestry. We show that mtCN is associated with many health-related phenotypes. We discovered robust associations between mtDNA copy number and diseases of metabolically active tissues, such as cardiovascular disease and liver damage, that were consistent across African and European ancestry individuals. Other associations, such as epilepsy and prostate cancer, were only discovered in either individuals with European or African ancestry but not both. We show that mtCN-phenotype associations can be sensitive to blood cell composition and environmental modifiers, explaining why such associations are inconsistent across studies. Thus, mtCN-phenotype associations must be interpreted with care.

Integrating polygenic risk scores into clinical breast cancer models: Influence on prediction in diverse cohorts.

10506 Background: Breast cancer (BC) is the second leading cause of cancer death in women worldwide. Periodic mammography screening has been shown to reduce breast cancer mortality by around 20% in average-risk women and several BC risk models are currently used to identify women at higher risk who can be targeted with increased or earlier screening. However, despite their broad use, these models display only moderate discrimination performance (AUC ranging between 0.51 to 0.68). Here we explore the potential of integrating PRS into a BC risk model using a testing dataset comprising over 175,000 women of diverse ancestry in the UK Biobank and Women Health’s Initiative Cohorts. Methods: We built and validated novel ancestry-specific BC PRSs utilizing novel methodology that leverage multiple Genome Wide Association Studies (GWASs) and linkage disequilibrium maps. We assessed genetic ancestry from 5 continental level ancestry groups across all individuals and applied the PRSs to our testing dataset to assess the clinical implications of integrating genetic information to the Tyrer-Cuzick (TC) breast cancer clinical risk model. Results: The PRSs were well calibrated and displayed high risk stratification (Odds Ratios per Standard Deviation: 1.41 (1.28-1.62) to 1.76 (1.40-2.20; Table) which were comparable or better than benchmarking comparisons with previously published PRS panels. Across genetic ancestries, integrating PRS led to a relative increase of women identified at high lifetime BC risk (20% or higher) from between 1.7 fold (East-Asian ancestry) to around 3 fold (European ancestry). The Net Reclassification Improvement compared to the TC-only model was around 12% for East-Asian (0.001-0.254), European (0.111-0.133), and Admixed American ancestries (0.002-0.228), 17% (0.079-0.266) for South-Asians, and 5% (0.008-0.094) for African ancestry individuals (Table). Conclusions: Our results demonstrate that optimizing PRSs for genetic ancestries and integrating them into BC risk models can lead to a significant improvement in risk stratification. This can enable more targeted use of enhanced screening and prevention strategies improving their cost/benefit ratio.[Table: see text]

SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022.

Intra-host diversity studies are used to characterise the mutational heterogeneity of SARS-CoV-2 infections in order to understand the impact of virus-host adaptations. This study investigated the frequency and diversity of the spike (S) protein mutations within SARS-CoV-2 infected South African individuals. The study included SARS-CoV-2 respiratory samples, from individuals of all ages, received at the National Health Laboratory Service at Charlotte Maxeke Johannesburg Academic hospital, Gauteng, South Africa, from June 2020 to May 2022. Single nucleotide polymorphism (SNP) assays and whole genome sequencing were performed on a random selection of SARS-CoV-2 positive samples. The allele frequency (AF) was determined using TaqMan Genotyper software for SNP PCR analysis and galaxy.eu for analysis of FASTQ reads from sequencing. The SNP assays identified 5.3% (50/948) of Delta cases with heterogeneity at delY144 (4%; 2/50), E484Q (6%; 3/50), N501Y (2%; 1/50) and P681H (88%; 44/50), however only heterogeneity for E484Q and delY144 were confirmed by sequencing. From sequencing we identified 9% (210/2381) of cases with Beta, Delta, Omicron BA.1, BA.2.15, and BA.4 lineages that had heterogeneity in the S protein. Heterogeneity was primarily identified at positions 19 (1.4%) with T19IR (AF 0.2-0.7), 371 (92.3%) with S371FP (AF 0.1-1.0), and 484 (1.9%) with E484AK (0.2-0.7), E484AQ (AF 0.4-0.5) and E484KQ (AF 0.1-0.4). Mutations at heterozygous amino acid positions 19, 371 and 484 are known antibody escape mutations, however the impact of the combination of multiple substitutions identified at the same position is unknown. Therefore, we hypothesise that intra-host SARS-CoV-2 quasispecies with heterogeneity in the S protein facilitate competitive advantage of variants that can completely/partially evade host's natural and vaccine-induced immune responses.