African Groups Research Articles

Completing the web: identifying sampling bias and knowledge gaps within South African spider surveys (Arachnida, Araneae)

Species distribution datasets are fundamental for macroecological studies, although there is an overarching need to ensure that these datasets are representative of the entire community. Shortfalls, or knowledge gaps, within biodiversity datasets originate for a range of reasons, and can lead to incorrect conclusions or recommendations being drawn. Spatial scale influences the interpretations of diversity patterns and thus is an important aspect to consider. South Africa has a rich history of spider sampling and as such, it is possible to investigate the influence that scale, both spatial and taxonomic, has on the overall interpretations of how complete the spider knowledge base is in the country. To do this, we draw on curated natural history spider collections and determine how complete the spider assemblages are across twelve unique combinations of taxonomic and spatial scales. Overall, we received 121 605 usable records from seven collections, with spider records and diversity, being concentrated along the eastern and coastal regions of South Africa. We show that assemblage completeness increases with both increasing taxonomic and spatial scales, and as such, knowledge of the distribution of spider families at the biome level is largely complete. Moreover, we show that our fine-scale knowledge of spider assemblages in South Africa is relatively poor, yet we do identify, even at fine scales, assemblages in South Africa that can be considered complete. We identify under-sampled regions of the country, which in turn are congruent with the distribution of under-sampled regions found in other South African invertebrate groups. We show that the scaling of completeness can only be interpreted in one direction: as scale increases so does completeness. These findings will have important implications for spider research and conservation in South Africa, given that regions where completeness is highest correspond strongly to areas in South Africa with the highest threats to biodiversity.

Insects in the far West: Burial practices on El Hierro Island (Canary Islands, Spain; ca. 6th-11th centuries) reconstructed via funerary archaeoentomology

The Canary Islands were first settled by North African groups in the first millennium CE and, after a few centuries of interconnections with the mainland and between islands, remained isolated until the late medieval European expansion into the Atlantic. El Hierro is a small island located in the westernmost part of the archipelago that was inhabited by the bimbapes from the 2nd century CE until the 15th century European conquest. The archaeological records, including marine food processing sites and cave burials, illustrate their adaptation to the environment: the dependence on marine resources for its economy owing the island's isolation and the scarcity of arable land and the use of the natural landscape to dispose of deads. La Lajura Cave, a collective burial site used from the 6th to 11th centuries CE, revealed significant anthropological and entomological findings. The archaeoentomological analysis of the sediment samples revealed 5816 insect remains, primarily Diptera and Coleoptera, with relatively small numbers of Hymenoptera, Heteroptera, Lepidoptera, and Arachnida. These findings shed light on decomposition processes and funerary practices as well as the distribution of the cadaveric entomofauna present in the western limit of the Palearctic region before the modern era. This study highlights the role of insects in cadaveric decomposition and their ecological behaviors, offering valuable insights into the funerary practices of Bimbape society in a unique ecological context.

Epidemiologic study on prostate cancer in Sudanese men across African ethnic groups

This study sought to investigate the demographic and clinical characteristics of Sudanese men diagnosed with prostate cancer (PCa) to highlight differences in diagnosis among the three major ethnolinguistic groups. A total of 532 patients with confirmed PCa diagnosis through biopsy were enrolled from six medical centers in Sudan. The majority of patients, comprising 84.2% (448/532), were diagnosed with advanced-stage disease, with a Grade group above 3. There were no discernible differences in PCa aggressiveness among the ethnolinguistic groups. However, higher levels of prostate-specific antigen (PSA) were observed in the Niger-Congo group, where 55.2% had PSA values exceeding 50 ng/ml. Patients from this group were also diagnosed at a younger age. In contrast, 90.5% of Afro-Asiatic patients are over 60 years old. Further analysis conducted within an age-matched subgroup of patients (n = 273) revealed a higher incidence of perineural invasion in the Afro-Asiatic group. This research represents the first investigation of PCa across different African ethnic groups and associates a higher incidence of perineural invasion with a specific ethnic group. While recent efforts have been made to establish African-relevant risk models to mitigate PCa health disparities, there remains a need for further investigation into genetically distinct populations within the African continent.

Health, Disability, and Economic Inactivity Following a Diagnosis of a Severe Mental Illness: Cohort Study of Electronic Health Records Linked at the Individual-Level, to Census from England.

The association of social and clinical indicators with employment, disability, and health outcomes among individuals with severe mental illnesses (SMI) remains unclear. Existing evidence primarily comes from smaller cohort studies limited by shorter follow-up and high attrition, or registry-based research, which lacks information on important social determinants. We utilized a novel data linkage consisting of clinical records of individuals diagnosed with schizophrenia-spectrum or bipolar disorders from the South London and Maudsley Mental Health Trust, linked at the individual-level to the 2011 UK Census, a rich source for sociodemographic information. Using logistic regression, we estimated adjusted odds ratios (aORs) and 95% confidence intervals to determine associations between socioeconomic and clinical indicators and economic inactivity, self-rated health, and disability outcomes. The sample comprised 8249 people with SMI diagnoses. Economic inactivity (77.3%), disability (68.3%) and poor health (61.1%) were highly prevalent. Longer duration of illness and comorbid substance misuse were associated with economic inactivity, poorer self-rated health, and disability, with associations noted between living alone and all outcomes (aORs and 95% CI: Economic inactivity: 1.72, 1.45-2.03; disability: 1.48, 1.31-1.68; poor health: 1.32, 1.18-1.49). Relative to the White British group, Black African, South Asian, and Other Black groups were more likely to be economically inactive. Black Caribbean and other groups were less likely to report poorer self-rated health or disability. Our findings highlight considerable disability, poorer health, and economic inactivity experienced by people with SMI. Addressing comorbid substance misuse and social isolation could play a role in improving outcomes.

Dissecting the genetic admixture and forensic signatures of ethnolinguistically diverse Chinese populations via a 114-plex NGS InDel panel

Comprehensive characterizations of genetic diversity and demographic models of ethnolinguistically diverse Chinese populations are essential for elucidating their forensic characteristics and evolutionary past. We developed a 114-plex NGS InDel panel to genotype 114 genome-wide markers and investigated the genetic structures of Zhuang, Hui, Miao, Li, Tibetan, Yi, and Mongolian populations, encompassing five language families. This panel demonstrated robust performance, with exceptional potential for forensic individual identification and paternity testing, evidenced by the combined power of discrimination for 77 autosomal InDels (ranged from 1-3.6400 × 10–30 to 1-3.5713 × 10–32) and the combined power of exclusion (ranged from 1-2.1863 × 10–6 to 1-2.1261 × 10–7). The cumulative mean exclusion chance for 32 X-chromosomal InDels varied between 0.99996 and 0.99999 for trios and 0.99760 to 0.99898 for duos. We also analyzed genetic similarities and differences between these populations and 27 global populations, revealing distinct clusters among African, South Asian, East Asian, and European groups, with a close genetic affinity to East Asians. Notably, we identified geography-related genetic substructures: Inner Mongolia Mongolians and Gansu Huis formed a northern branch, Tibetans and Yis from Sichuan constituted a highland branch, and Guangxi Zhuangs exhibited close ties with Hainan Lis and Guangxi Miaos in the southern branch. Additionally, many InDels proved to be ancestry-informative markers for biogeographic ancestry inference. Collectively, these findings underscore the utility of the 114-plex NGS InDel panel as a complementary tool for forensic investigations and as a source of insights into the genetic architecture of ethnolinguistically distinct Chinese populations.

Range contraction and expansion of the African buffalo under climate change scenarios

ABSTRACT Climate change is one of the leading causes of global biodiversity declines and extinctions. Yet knowledge of its impact on African buffalo distribution on the continent is lacking. In this study, we apply ensemble species distribution modelling to predict the distribution of two coarsely defined African buffalo functional groups under current and future climate scenarios (Shared Socioeconmic Pathway, SSP245 and SSP585 in 2100) and estimate habitat representation within protected areas. Model predictions indicate significant range contraction and expansion in the savanna and the forest buffalo functional groups, respectively. Also, the proportion of suitable habitats for both functional groups is represented poorly within protected areas, with the current coverage expected to decline further. Our findings reveal plausible implications of climate change on African buffalo conservation and zoonotic diseases. Overall, this climate-based approach could be applied to model the distribution of African buffalo subspecies at local geographical scales in countries with adequately sampled occurrence data to support conservation decision-making.

Performance of Polygenic Risk Scores for Primary Open-Angle Glaucoma in Populations of African Descent

Primary open-angle glaucoma (POAG) polygenic risk scores (PRSs) continue to be evaluated in primarily European-ancestry populations despite higher prevalence and worse outcomes in African-ancestry populations. To evaluate how established POAG PRSs perform in African-ancestry samples from the Genetics in Glaucoma Patients of African Descent (GIGA), Genetics of Glaucoma in Individuals of African Descent (GGLAD), and Million Veteran Program (MVP) datasets and compare these with European-ancestry samples. This was a multicenter, cross-sectional study of POAG cases and controls from Tanzania, South Africa, Nigeria, Ghana, and the US. Included were individuals of African descent from South Africa and Tanzania from the GIGA dataset; individuals of African descent from Ghana, Nigeria, and the US from the GGLAD dataset; and individuals of African or European descent from the US in the MVP dataset. Data were analyzed from January 2022 to July 2023. Three PRSs derived from large meta-analyses of European and Asian populations, namely Gharahkhani et al (Gharahkhani PRS), Han et al (Han PRS), and Craig et al (Craig PRS). Odds ratios (ORs) for POAG risk stratification comparing the highest and lowest quintiles; area under the receiver operating characteristic curve (AUROC), and liability coefficient of determination (R2) for the addition of PRS to a baseline of age, sex, and first 5 principal components. A total of 11 673 cases and 66 432 controls were included in this study across 7 ancestral groups. Mean (SD) age of the total participants was 76.9 (8.7) years, with 74 304 males (95.1%). The following were included in each dataset: GIGA (663 cases, 476 controls), GGLAD (1471 cases, 1482 controls), and MVP (9559 cases, 64 474 controls). Increases in ORs were found for the highest POAG risk quintile ranging from an OR of 1.68 (95% CI, 1.17-2.43) in Ghanaians to 7.05 (95% CI, 2.73-19.6) in the South African multiple ancestry group (which derives from at least 5 distinct ancestral groups: Khoisan, Bantus, Europeans, Indians, and Southeast Asians) with the Gharahkhani PRS. The Han PRS showed OR increases for the highest POAG risk quintile ranging from 2.27 (95% CI, 1.49-3.47) in African American individuals in the GGLAD dataset to 7.24 (95% CI, 6.47-8.12) in Europeans. The Craig PRS predicted OR increases in the highest quintile for all groups ranging from 1.51 (95% CI, 1.05-2.18) in Ghanaians to 6.31 (95% CI, 5.67-7.04) in Europeans. However, AUROC and R2 increases above baseline were lower for all African-ancestry compared with European-ancestry groups in the 3 tested PRSs. In this cross-sectional study, despite some improvements in OR-based risk stratification using the Gharahkhani PRSs, Han PRSs, and Craig PRSs, consistently lower improvements in AUROC and R2 for African-ancestry compared with European-ancestry groups highlight the need for risk prediction models tailored to diverse populations.

Comparative analysis of White and African American groups reveals unique lipid and inflammatory features of diabetes.

African Americans have a higher prevalence of Type 2 Diabetes (T2D) compared to White groups. T2D is a health disparity clinically characterized by dysregulation of lipids and chronic inflammation. However, how the relationships among biological and sociological predictors of T2D drive this disparity remains to be addressed. To determine characteristic plasma lipids and systemic inflammatory biomarkers contributing to diabetes presentation between White and African American groups. We performed a cross-sectional retrospective cohort study using pre-existing demographic and clinical data from two diverse studies: Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) and AllofUs. From HANDLS (N=40), we used information from wave 1 (2004). From AllofUs (N=17,339), we used data from the Registered Tier Dataset v7, available in the AllofUs researcher workbench. HANDLS is a population-based cohort study involving 3720 participants in the Baltimore area supported by the Intramural Research Program of the National Institute on Aging. HANDLS is a longitudinal study designed to understand the sources of persistent health disparities in overall longevity and chronic disease in White and African American individuals. The AllofUs study is an NIH funded multicenter study consisting of patient-level data from 331,382 individuals from 35 hospitals in the United States aimed at sampling one million or more people living in the United States to provide a collection of broadly accessible data. The HANDLS subcohort participants (N=40) were divided into four groups equally distributed by race, sex, and diabetes status. Groups were also matched by age, body mass index, and poverty status. The analysis pipeline consisted of evaluating the significance of the variables race and disease status using the 2-way ANOVA test and post-ANOVA comparisons using Fisher LSD test, reporting unadjusted p-values. Additionally, unsupervised (PCA) and supervised (OPLS-DA) clustering analysis was performed to determine putative biological drivers of variability and main immunological and metabolic features characterizing diabetes in White and African American groups from HANDLS. Major clinical findings were validated in a large cohort of White and African American groups with T2D in the AllofUS research study (N=17,339). AllofUs groups were of similar range in age and BMI as HANDLS. Furthermore, a linear regression model was built adjusting for age and BMI to determine differences in clinical findings between White and African American groups with T2D. Primary outcomes using a HANDLS subcohort (N=40) were clinical parameters related to diabetes, plasma lipids determined by lipidomics and measured by mass spectrometry, and cytokine profiling using a customized panel of 52 cytokines and growth factors measured by Luminex. Outcomes evaluated in the AllofUs study (N=17,339) were clinical: cholesterol to HDL ratio, triglycerides, fasting glucose, insulin, and hemoglobin A1C. In the HANDLS subcohort, White individuals with diabetes had elevated cholesterol to HDL ratio (mean difference -1.869, p =0.0053 ) , high-sensitivity C-reactive protein (mean difference -9.135, p =0.0040), and clusters of systemic triglycerides measured by lipidomics, compared to White individuals without diabetes. These clinical markers of dyslipidemia (cholesterol to HDL ratio and triglycerides) and inflammation (hs-CRP) were not significantly elevated in diabetes in African Americans from the HANDLS subcohort. These results persisted even when controlling for statin use. Diabetes in White individuals in the HANDLS cohort was characterized by a marked elevation in plasma lipids, while an inflammatory status characterized by Th17-cytokines was predominant in the African American group from the HANDLS subcohort. We validated the key findings of elevated triglycerides and cholesterol to HDL ratio in White individuals with T2D in a sample (N=17,339) of the AllofUs study. Our results show that diabetes can manifest with healthy lipid profiles, particularly in these cohorts of African Americans. This study suggests that Th17-inflammation associated with diabetes is characteristic of African Americans, while a more classic inflammation is distinctive of White individuals from HANDLS cohort. Further, clinical markers of dyslipidemia seem to characterize diabetes presentation only in White groups, and not in African Americans.

The Process and Current Situation of Islam Localization in Senegal

Islam originated in the Arabian Peninsula and spread to the Maghreb region inhabited by Berbers in the late 7th century and early 8th century, and then spread further to West Africa south of the Sahara from north to south. Around 850 AD, the first group of black Africans converted to Islam. They belonged to the Dya’ogo dynasty of the Tekur Kingdom, which is located in the Senegal River Valley in present-day Senegal. Currently, Senegal is one of the countries with the highest proportion of Muslim population in West Africa, with 94% of its people believing in Islam. Not only that, Senegal has also developed a unique Islamic system dominated by the Brotherhood. This article attempts to sort out the process of Islam localization in Senegal and explain the impact of the Brotherhood on contemporary Senegalese politics and economy.

Abstract 4120763: Predicting Disease Risk Among Variants in Cardiomyopathy-Associated Genes Across Diverse Genetic Ancestries

Background: Many cases of cardiomyopathy (CM) are genetically inherited, and the expansion of broad genomic sequencing has opened the door for predicting those at risk for developing disease. However, genetic tools that help determine variant pathogenicity employ genetic data from predominantly European genetic ancestries. Understanding the full diversity of genetic variants in cardiomyopathy genes is central to identifying which variants will cause disease. Hypothesis: Participants of non-European genetic ancestry will have a higher burden of cardiomyopathy gene variants with "VUS" designation in ClinVar but will have equivalent/less penetrance of clinical cardiomyopathy compared to a European ancestry group. Methods: Participants in the AllofUs database with exome sequencing (ES) were queried and a cohort of 230,013 participants were retained after sample quality control filters. Participant genetic ancestry was based on the designated ancestry group determined via AllofUs as previously described (1). Participants were queried for variants in genes with definitive or moderate evidence of hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and arrhythmogenic cardiomyopathy (ACM) in ClinGen. Variants were filtered by ClinVar status (1* and above P/LP, 1* and above B/LB, and VUS). Participant CM disease status was determined via ICD-9/10 code. Results: For each ancestry group, prevalence of cardiomyopathy ranged from 0.34% in the Latino/admixed American ancestry group to 1.09% in the African group, with an average prevalence of 0.91% across all groups. The European group had a statistically significant lower percentage of ClinVar VUS variants at 26%, while all other non-European ancestry groups had a combined VUS prevalence rate of 35% (****p<0.0001). The penetrance of CM in participants with CM VUS variants was lower in combined non-European ancestry groups (0.84%) than European ancestry (1.02%) (*p=0.0156). Conclusion: Prevalence of ClinVar VUS variants varies across different genetic ancestry groups, with European ancestry having a lower burden of VUS variants compared to non-European groups. However, non-European ancestry groups with increased burden of VUS variants have lower disease penetrance. Citations: (1) The All of Us Research Program Genomics Investigators. Genomic data in the All of Us Research Program. Nature 627 , 340–346 (2024). https://doi.org/10.1038/s41586-023-06957-x

Access to psychological therapies amongst patients with a mental health diagnosis in primary care: a data linkage study.

Significant numbers of people in England have fallen into a gap between primary care psychological therapies and specialist mental health services. We aim to examine pathways to care by looking at demographic variation in detection and referral to primary and secondary psychological services in south London. Longitudinal descriptive study using a record linkage between a primary care database (Lambeth DataNet) and a secondary care mental health database (CRIS). We extracted data on mental health diagnosis, prescriptions and episodes of care in mental health services for all patients of working age registered from 1 January 2008 to 1 March 2018 (pre-covid era). Of those with a mental disorder detected in primary care (n = 110,419; 26.8%); 33.7% (n = 37,253) received no treatment; 21.3% (n = 23,548) exclusively accessed psychological treatment within NHS Talking Therapies and 7.6% accessed secondary care psychological therapies. People from minoritised groups were more likely to be prescribed psychotropic medication as the only treatment offered compared to the White British group. Men, Black African and Asian groups were less likely to access NHS Talking Therapies. People with a personality disorder diagnosis had the highest prevalence and number of NHS Talking Therapies treatment episodes (48.0%, n = 960), a similar percentage (44.1%, n = 881) received secondary care psychology treatment. Our study highlights marked inequalities in access to psychological therapies for men and people from some minoritised ethnic groups across primary and secondary care and how individuals with personality disorders are offered multiple short-term courses in NHS Talking Therapies even where this is not recommended treatment.

Exploring ethnic minority and underserved groups’ experiences of Cardiovascular Disease Annual check uptake in North East England: applying a behavioural insights, qualitative approach

BackgroundCardiovascular disease (CVD) is the leading cause of death worldwide, and prevention is a public health priority. In the UK, adults between 40–74 years should be invited to NHS CVD “health check” every 5 years. However, research has demonstrated variable uptake of CVD health checks, with populations most at risk frequently failing to engage. The North East and North Cumbria (NENC) has the lowest healthy life expectancy in England. With higher levels of inequalities in this region, uptake of CVD health checks for ethnic minorities and underserved groups historically has been poor. The aim of this qualitative study was to gather behavioural insights into the experiences, facilitators and barriers towards engagement with CVD health checks in underserved communities of NENC. MethodsQualitative focus groups (n=7, 45 participants) were conducted to understand experiences, barriers and challenges to uptake of CVD health checks in Middlesbrough, UK. Adults from black African, South Asian, and underserved white indigenous groups were recruited through community leaders. Data were analysed using a Behavioural Insight approach with key themes, barriers and enablers categorised according to the four categories of the EAST framework (Ease, Attractiveness, Social, Timeliness). Ethical approval was obtained from Newcastle University. FindingsWe established that disadvantaged communities in NENC find engaging with CVD health checks challenging because of issues related to access of health services, lack of understanding/knowledge and attitudes. Communities identified that harnessing relationships with community champions would raise awareness and confidence in engaging. Making services accessible, ideally in locations where communities gathered, whilst also increasing understanding and knowledge were also recognised as key to engagement in CVD health checks. InterpretationFindings of this study were relayed to local community leaders and commissioners in a debriefing session, which led to the co-design of innovative interventions (eg, social prescribing, translation services, social marketing campaigns) to improve uptake of CVD health checks. Encouraging engagement with prevention approaches to CVD is vital to address the significant health inequalities seen in underserved communities. Understanding the challenges faced by communities and working with them to facilitate access is critical to reduce CVD and improve healthy life expectancy. FundingFunding for this project was provided by the Innovations for Health Inequalities Programme via the Accelerating Access Collaborative (AAC).

Delays in Presentation, Diagnosis, and Treatment Among Patients With GI Cancer in Southwest Nigeria.

The incidence of GI cancers is increasing in sub-Saharan African countries. We described the oncological care pathway and assessed presentation, diagnosis, and treatment intervals and delays among patients with GI cancer who presented to the Obafemi Awolowo University Teaching Hospitals Complex in Ile-Ife, Nigeria. We analyzed data from 545 patients with GI cancer in the African Research Group for Oncology (ARGO) database. We defined presentation interval as the interval between symptom onset and presentation to tertiary hospital, diagnostic interval as between presentation and diagnosis, and treatment interval as between diagnosis and initiation of treatment. We considered >3 months, >1 month, and >1 month to be presentation, diagnosis, and treatment delays, respectively. We compared lengths of intervals using Mann-Whitney U tests and logistic regression. The most frequent cancer types were pancreatic (32%) and colorectal (28%). Most patients presented at stages III (38%) and IV (30%). The median presentation interval was 84 days (IQR, 56-191), and 49% presented after 3 months or longer. The median diagnosis and treatment intervals were 0 (IQR, 0-8) and 7 (IQR, 0-23) days, respectively. There was no relationship between age, sex, education, or distance to tertiary hospital and presentation delay, but patients with stage III to IV versus I to II had higher odds of presentation delay (odds ratio [OR], 1.68 [95% CI, 1.13 to 2.50]). Among patients with pancreatic cancer, older patients were less likely to have a diagnosis delay (OR, 0.50 [95% CI, 0.25 to 0.98]). About half of patients with GI cancer in Ile-Ife, Nigeria, did not present to tertiary hospitals until more than 90 days after noticing symptoms. Efforts are warranted to improve public knowledge of GI cancer symptoms and to strengthen health systems for prompt diagnosis and referral to specialty care.

In the Midst of the Collective: The Experience and Influence of African American Peer Groups in Graduate School at Predominantly White Institutions

In the Midst of the Collective: The Experience and Influence of African American Peer Groups in Graduate School at Predominantly White Institutions

Harnessing Hope in Digital Spaces for Health Equity: How Group Comparison Information and Supportive Comments Influence Bone Marrow Donor Intentions for African Americans.

Pursuing health equity necessitates recognizing health disparities that disproportionately impact disadvantaged groups and eliminating their barriers to essential health resources. Interactive digital technologies-specifically, popular social media platforms such as blogs and social networks-can be leveraged to engage underserved minority populations in collective social action aimed at addressing key determinants of health disparities and promoting equitable health outcomes. The present research focuses on the plight of African Americans-a minority group facing significant health disparities. Particularly in the domain of bone marrow donation, African Americans remain the group least likely to find a matching donor. Guided by the social comparison framing literature, we conducted an online experiment to investigate how group comparison information (GCI) emphasizing group-based disparities and supportive user comments on social media platforms influence African Americans' intentions to join a bone marrow registry. In doing so, we considered hope as a mediator and group identification as a moderator. Results based on a conditional process analysis showed that GCI led to greater bone marrow donor intentions in the presence of supportive comments through elicitation of hope, particularly among those low in group identification. The current findings demonstrate that it is important to consider the role of supportive message environments and group identification when addressing health disparities with GCI. Theoretical and practical implications are discussed.

Abstract C093: Epigenetic insights and gene expression in African pan genome contig sequences

Abstract An often-overlooked component in our cancer genomics workflows is the reference genome. While most genomics analytical tools and findings are based on reference builds GRCh37 and GRCh38, these references are largely Eurocentric, and their representativeness among diverse populations has not been studied comprehensively. A previously published study conducted deep whole genome sequencing of over 900 individuals of African ancestry, where they revealed ∼296 million unique base pairs, assembled into 125,715 African Pan Genome (APG) contig sequences that are not represented in the reference genome. To further characterize these APG contig sequences, we sought to determine the epigenetic and expression potential of these sequences. We have previously reported preliminary efforts to characterize the unexplored epigenetic potential across the 125,715 APG contig sequences, where we have utilized Emboss CpG plot for CpG island prediction. Across all contig sequences, we identified 8,353 potential CpG islands across 6,352 contig sequences, where contigs had 1 to 9 predicted CpG islands. Taken together ∼5% of all APG contigs contained at least 1 predicted CpG island. To determine the expression potential of these contigs, we mapped RNAseq reads from an African ancestry-enriched triple negative breast cancer cohort to APG contigs that previously failed to map to the reference genome. Approximately 9% of APG contigs had transcriptomic reads mapping, and 1106 APG contigs had both reads mapping and predicted CpG islands. Given our RNAseq mapping from our African ancestry enriched cohort, we have begun to explore differential expression measures among contigs by African ancestry population groups, highlighting the potential for differential regulation at these understudied loci. Since the publication of the APG contig sequences, the recent telomere-to-telomere (T2T) reference has filled the gaps of GRCh37 and GRCh38, however, is even less diverse. With T2T containing novel sequences that were not present at the time the APG contigs were assembled, we performed BLASTn queries of APG contigs to the T2T genome, where preliminary analysis shows ∼17% fail to map to T2T. For those with BLASTn mapping results, we are currently assessing the coverage and identity of the mapping results to evaluate the alignment. In conclusion, these APG contig sequences harbor potential epigenetic regulatory function and expressed sequences not represented in our standard reference genomes. While some APG contig sequences are represented in the newer T2T genome, preliminary investigations show that these APG contig sequences map to the T2T genome in regions novel from GRCh37 and GRCh38. As we continue to explore these APG contig sequences, we may find ancestry-specific regulatory mechanisms not yet described. Citation Format: Rachel Martini, Kyriaki Founta, Sebastian Maurice, Jason White, Lisa Newman, Onyinye Balogun, Nyasha Chambwe, Melissa Davis. Epigenetic insights and gene expression in African pan genome contig sequences [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C093.

Gene discovery and biological insights into anxiety disorders from a large-scale multi-ancestry genome-wide association study.

We leveraged information from more than 1.2 million participants, including 97,383 cases, to investigate the genetics of anxiety disorders across five continental groups. Through ancestry-specific and cross-ancestry genome-wide association studies, we identified 51 anxiety-associated loci, 39 of which were novel. In addition, polygenic risk scores derived from individuals of European descent were associated with anxiety in African, admixed American and East Asian groups. The heritability of anxiety was enriched for genes expressed in the limbic system, cerebral cortex, cerebellum, metencephalon, entorhinal cortex and brain stem. Transcriptome-wide and proteome-wide analyses highlighted 115 genes associated with anxiety through brain-specific and cross-tissue regulation. Anxiety also showed global and local genetic correlations with depression, schizophrenia and bipolar disorder and widespread pleiotropy with several physical health domains. Overall, this study expands our knowledge regarding the genetic risk and pathogenesis of anxiety disorders, highlighting the importance of investigating diverse populations and integrating multi-omics information.

Validation of the parents’ version of the KINDLR and Kiddy Parents questionnaire in a South African context

BackgroundThis study aimed to assess the usefulness of the parent version of the KINDLR and the additional items of the Kiddy Parents questionnaire in the South-African context and to validate it as an appropriate tool for measuring health-related quality of life (HRQoL).MethodThe ExAMIN Youth SA study was designed to investigate lifestyle behaviours, including psychosocial factors that may adversely impact on cardiovascular health of children. Construct validity was examined by using exploratory and confirmatory factor analysis, while internal consistency was tested by Cronbach’s alpha. The final factor structure was confirmed by model fit indices.ResultsThe study included children (n = 1088) aged between 5 and 10 years in North-West, South Africa. The reliability coefficients of the original factors could not be reproduced in this data set, with the Cronbach’s alphas ranging between 0.46 and 0.78. With exploratory factor analysis, including the additional items, our data supported a 7-factor structure with acceptable internal consistency (Cronbach’s alpha: 0.68–0.79; Omega: 0.75–0.85) and acceptable model fit indices (CFI: 0.91; TLI: 0.90; RMSEA: 0.05; SRMR: 0.07). Two factors (emotional wellbeing and everyday functioning) further split into separate factors for positive and negative experiences related to each of these dimensions.ConclusionWe confirmed a new factor structure of the parent version of the KINDLR and the additional items of the Kiddy Parents questionnaire, which can be used in the African context. Although the new factor structure has great overlap with the original structure, some items did not contribute to the factors as expected. Language and cultural differences between the original German group and the current South African study group resulted in a different factor structure.

Prevalence of occipitalisation in a South African Black population: An original study of 1119 skulls with a review of the literature

BackgroundOccipitalisation is the most prevalent congenital abnormality at the craniovertebral junction; however, it is rare in the general population. There is a paucity of literature on osteological prevalence studies within the South African Black and broader African populations. This study aimed to establish baseline data for the prevalence of occipitalisation in the South African Black population group. MethodsOne thousand two hundred thirteen skulls from a South African Black population were initially sampled, and after exclusion criteria were applied, the sample was reduced to 1119 skulls (male 766; female 353). A morphological description of the skulls that exhibited occipitalisation was included in this study. ResultsOccipitalisation was observed in three skulls (3/1119; 0.27 %); two of the skulls were female (2/353; 0.57 %), and one was male (1/766; 0.13 %). The three occipitalised skulls exhibited fusion in three areas of the atlas: the anterior arch, lateral masses, and transverse processes. No skulls exhibited posterior arch fusion of the atlas. ConclusionThis study established a baseline prevalence of occipitalisation in the South African Black population at 0.27 % and found no significant association between sex and occipitalisation (p = 0.236). This study highlights the need for further studies in the other African population affinity groups.

Morphology and morphometry of the patella in a select Black South African sample

BackgroundFor many years, sex determination has been achieved through analysis of skeletal remains in forensic medicine. The patella can be utilized for sex determination in the absence (or damage) of the cranium, upper and lower limbs, and pelvic bones. Additionally, understanding the patella's morphology and morphometry is essential for diagnosing and treating injuries and disorders of the knee joint, as well as knee arthroplasty and patella ligament grafting (Medeiros et al., 2001). This study reviewed the morphology and morphometry of the patella in a Black African population of KwaZulu-Natal and determined if a correlation between the parameters of the patellae and sex exists. Materials and methods154 dry patellae belonging to a South African black population group were utilized to review their morphology and morphometry. The classifications of Wiberg (1941) and Borges et al. (2016) were adapted for the morphology. The seven morphometric measurements were adapted from Dayal and Bidmos (2005) and Borges et al. (2016). A p-value less than 0.05 was considered statistically significant. ResultsAccording to the Wiberg classification: Type 1 patellae were least prevalent (1.9 %), while Type 2 were most common with an incidence of 59.7 %. No statistical difference was recorded with sex (p-value = 0.517). According to Borges et al. (2016) classification: Type 1 (triangular-shaped) patellae were most prevalent in males and females (72.7 %) and Type 3 (irregular shape) patellae were least common in this study. A statistically significant difference between Borges et al. (2016) classification scheme (shape of the patella) and sexes was recorded (p-value = 0.003). A statistically significant relationship between morphometric parameters of the patella and sex was also recorded (p-value <0.001). Patella measurements were greater in males than in females. ConclusionIn this study, the patella displayed sexually dimorphic morphological and morphometric characteristics, which indicated that the patella may be used for sex determination in forensic cases with the KwaZulu-Natal population of South Africa, in addition to clinical applications such as knee arthroplasty, patellar ligament grafting, prosthesis synthesis, and patellar implants.