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Thami PK, Choga WT, Dandara C, O’Brien SJ, Essex M, Gaseitsiwe S, Chimusa ER. Whole genome sequencing reveals population diversity and variation in HIV-1 specific host genes. Front Genet 2023; 14:1290624. [PMID: 38179408 PMCID: PMC10765519 DOI: 10.3389/fgene.2023.1290624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/20/2023] [Indexed: 01/06/2024] Open
Abstract
HIV infection continues to be a major global public health issue. The population heterogeneity in susceptibility or resistance to HIV-1 and progression upon infection is attributable to, among other factors, host genetic variation. Therefore, identifying population-specific variation and genetic modifiers of HIV infectivity can catapult the invention of effective strategies against HIV-1 in African populations. Here, we investigated whole genome sequences of 390 unrelated HIV-positive and -negative individuals from Botswana. We report 27.7 million single nucleotide variations (SNVs) in the complete genomes of Botswana nationals, of which 2.8 million were missing in public databases. Our population structure analysis revealed a largely homogenous structure in the Botswana population. Admixture analysis showed elevated components shared between the Botswana population and the Niger-Congo (65.9%), Khoe-San (32.9%), and Europeans (1.1%) ancestries in the population of Botswana. Statistical significance of the mutational burden of deleterious and loss-of-function variants per gene against a null model was estimated. The most deleterious variants were enriched in five genes: ACTRT2 (the Actin Related Protein T2), HOXD12 (homeobox D12), ABCB5 (ATP binding cassette subfamily B member 5), ATP8B4 (ATPase phospholipid transporting 8B4) and ABCC12 (ATP Binding Cassette Subfamily C Member 12). These genes are enriched in the glycolysis and gluconeogenesis (p < 2.84e-6) pathways and therefore, may contribute to the emerging field of immunometabolism in which therapy against HIV-1 infection is being evaluated. Published transcriptomic evidence supports the role of the glycolysis/gluconeogenesis pathways in the regulation of susceptibility to HIV, and that cumulative effects of genetic modifiers in glycolysis/gluconeogenesis pathways may potentially have effects on the expression and clinical variability of HIV-1. Identified genes and pathways provide novel avenues for other interventions, with the potential for informing the design of new therapeutics.
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Affiliation(s)
- Prisca K. Thami
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wonderful T. Choga
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- UCT/SAMRC Platform for Pharmacogenomics Research and Translation (PREMED) Unit, South African Medical Research Council, Cape Town, South Africa
| | - Stephen J. O’Brien
- Laboratory of Genomics Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
- Guy Harvey Oceanographic Center Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Myron Essex
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health AIDS Initiative, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health AIDS Initiative, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Emile R. Chimusa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
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2
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Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
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Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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3
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Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A, Baker S, Pollard AJ, Khor CC, Dolecek C, Basnyat B, Dunstan SJ, Holt KE, Inouye M. Direct inference and control of genetic population structure from RNA sequencing data. Commun Biol 2023; 6:804. [PMID: 37532769 PMCID: PMC10397182 DOI: 10.1038/s42003-023-05171-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/24/2023] [Indexed: 08/04/2023] Open
Abstract
RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data.
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Affiliation(s)
- Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Mila Shakya
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Kar Seng Sim
- Genome Institute of Singapore, Singapore, Singapore
| | - Susan Tonks
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Patan Academy of Health Sciences, Patan Hospital, Lalitpur, Nepal
| | | | - Agus Salim
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, Australia
- Department of Population Health, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | | | - Christiane Dolecek
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
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4
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Maseng MJ, Tawe L, Thami PK, Moyo S, Kasvosve I, Novitsky V, Essex M, Russo G, Gaseitsiwe S, Paganotti GM. The role of CYP2B6 516G>T polymorphism on efavirenz/nevirapine toxicity. Implications on treatment outcomes: Lessons from Botswana. Medicine (Baltimore) 2022; 101:e29066. [PMID: 35512066 PMCID: PMC9276322 DOI: 10.1097/md.0000000000029066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/25/2022] [Indexed: 01/04/2023] Open
Abstract
The two non-nucleoside reverse transcriptase inhibitors (NNRTIs), efavirenz (EFV) and nevirapine (NVP), are currently the core antiretroviral drugs for treatment of HIV in sub-Saharan Africa including Botswana. The drugs are metabolized by Cytochrome P450 2B6 (CYP2B6) liver enzyme. The CYP2B6 gene that encodes for metabolism of these drugs is known to be highly polymorphic. One of the polymorphism in the CYP2B6 gene, 516G>T, particularly the 516T allele, is known to confer poor metabolism of EFV and NVP. This may lead to high levels of plasma drug concentrations and development of treatment toxicities, like central nervous system toxicities, and cutaneous and hepatic toxicities, for EFV and NVP, respectively. The CYP2B6 516G allele on the other hand is associated with an extensive metabolism of the two NNRTIs drugs. We sought to establish association between possible developments of NNRTIs toxicities with CYP2B6 516G>T variation in Botswana.A total of 316 peripheral blood mononuclear cells samples were used in a retrospective view. All the samples were from participants on EFV/NVP-containing regimen with known toxicity output. TaqMan Real-Time PCR approach was applied for assessing CYP2B6 516 allele variation in cases with treatment toxicity and those without. Analysis was performed by chi-square statistics and logistic regression analysis.The rate of poor metabolizers among participants with toxicity and those without toxicity was 18.4% and 15.1%, respectively. The CYP2B6 516 genotype distribution comparisons between the participants with toxicity and those without were not statistically different (chi-square = .326; P = .568).CYP2B6 516 variation was not associated with NNRTI toxicity. No other factors were associated with toxicity when considering age, baseline body mass index, baseline CD4, baseline HIV viral load and adherence. The results were discussed in the context of all the studies done in Botswana to date.
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Affiliation(s)
- Monkgomotsi J. Maseng
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, UB Campus, Block 246, Gaborone, Botswana
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
| | - Leabaneng Tawe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, UB Campus, Block 246, Gaborone, Botswana
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
- Botswana-University of Pennsylvania Partnership, UB Campus, Block 244G, Gaborone, Botswana
| | - Prisca K. Thami
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road Observatory, Cape Town, South Africa
| | - Sikhulile Moyo
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Hungtinton Avenue, Boston, MA
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, UB Campus, Block 246, Gaborone, Botswana
| | - Vladimir Novitsky
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Hungtinton Avenue, Boston, MA
| | - Max Essex
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Hungtinton Avenue, Boston, MA
| | - Gianluca Russo
- Department of Public Health and Infectious Disease, Faculty of Medicine, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Simani Gaseitsiwe
- Botswana-Harvard AIDS Institute Partnership, Plot 1836 North Ring Road, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Hungtinton Avenue, Boston, MA
| | - Giacomo M. Paganotti
- Botswana-University of Pennsylvania Partnership, UB Campus, Block 244G, Gaborone, Botswana
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, 3120-2740 Hamilton Walk, Philadelphia, PA
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, UB Campus, Block 246, Gaborone, Botswana
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5
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Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. Proc Natl Acad Sci U S A 2021; 118:2107830118. [PMID: 34782459 DOI: 10.1073/pnas.2107830118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 11/18/2022] Open
Abstract
Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.
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Tawe L, Grover S, Zetola N, Robertson ES, Gaseitsiwe S, Moyo S, Kasvosve I, Paganotti GM, Narasimhamurthy M. Promoter Hypermethylation Analysis of Host Genes in Cervical Cancer Patients With and Without Human Immunodeficiency Virus in Botswana. Front Oncol 2021; 11:560296. [PMID: 33718129 PMCID: PMC7952881 DOI: 10.3389/fonc.2021.560296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Epidemics of human immunodeficiency virus (HIV) and cervical cancer are interconnected. DNA hypermethylation of host genes' promoter in cervical lesions has also been recognized as a contributor to cervical cancer progression. Methods: For this purpose we analyzed promoter methylation of four tumor suppressor genes (RARB, CADM1, DAPK1 and PAX1) and explored their possible association with cervical cancer in Botswana among women of known HIV status. Overall, 228 cervical specimens (128 cervical cancers and 100 non-cancer subjects) were used. Yates-corrected chi-square test and Fisher's exact test were used to explore the association of promoter methylation for each host gene and cancer status. Subsequently, a logistic regression analysis was performed to find which factors, HIV status, high risk-HPV genotypes, patient's age and promoter methylation, were associated with the following dependent variables: cancer status, cervical cancer stage and promoter methylation rate. Results: In patients with cervical cancer the rate of promoter methylation observed was greater than 64% in all the genes studied. Analysis also showed a higher risk of cervical cancer according to the increased number of methylated promoter genes (OR = 6.20; 95% CI: 3.66–10.51; P < 0.001). RARB methylation showed the strongest association with cervical cancer compared to other genes (OR = 15.25; 95% CI: 6.06–40.0; P < 0.001). Cervical cancer and promoter methylation of RARB and DAPK1 genes were associated with increasing age (OR = 1.12; 95% CI: 1.01-1.26; P = 0.037 and OR = 1.05; 95% CI: 1.00-1.10; P = 0.040). The presence of epigenetic changes at those genes appeared to be independent of HIV status among subjects with cervical cancer. Moreover, we found that cervical cancer stage was influenced by RARB (χ2= 7.32; P = 0.002) and CADM1 (χ2=12.68; P = 0.013) hypermethylation, and HIV status (χ2= 19.93; P = 0.001). Conclusion: This study confirms the association between invasive cervical cancer and promoter gene methylation of tumor suppressing genes at the site of cancer. HIV infection did not show any association to methylation changes in this group of cervical cancer patients from Botswana. Further studies are needed to better understand the role of HIV in methylation of host genes among cancer subjects leading to cervical cancer progression.
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Affiliation(s)
- Leabaneng Tawe
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana.,Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Surbhi Grover
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicola Zetola
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
| | - Erle S Robertson
- Department of Otorhinolaryngology-Head and Neck Surgery, and the Tumor Virology Program, Abramson Comprehensive Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, United States
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Giacomo M Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Mohan Narasimhamurthy
- Department of Pathology, Faculty of Medicine, University of Botswana, Gaborone, Botswana
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7
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Oosthuizen J, Kotze MJ, Van Der Merwe N, Myburgh EJ, Bester P, van der Merwe NC. Globally Rare BRCA2 Variants With Founder Haplotypes in the South African Population: Implications for Point-of-Care Testing Based on a Single-Institution BRCA1/2 Next-Generation Sequencing Study. Front Oncol 2021; 10:619469. [PMID: 33643918 PMCID: PMC7908826 DOI: 10.3389/fonc.2020.619469] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Breast cancer patients historically benefitted from population-based genetic research performed in South Africa, which led to the development of founder-based BRCA1/2 diagnostic tests. With the advent of next-generation sequencing (NGS) technologies, the clinical utility of limited, targeted genetic assays were questioned. The study focused on mining NGS data obtained from an extensive single-institution NGS series (n=763). The aims were to determine (i) the prevalence of the most common recurrent/founder variants in patients referred for NGS directly; and (ii) to explore the data for inferred haplotypes associated with previous and potential new recurrent/founder variants. The identification of additional founder variants was essential for promoting and potentially advancing to rapid founder-based BRCA1/2 point-of-care (POC) technology as a time- and cost-effective alternative. NGS revealed actionable BRCA1/2 variants in 11.1% of patients tested (BRCA1 - 4.7%; BRCA2 - 6.4%), of which 22.4% represented variants currently screened for using first-tier targeted genetic testing. A retrospective investigation into the overall mutation-positive rate for an extended cohort (n=1906), which included first-tier test results, revealed that targeted genetic testing identified 74% of all pathogenic variants. This percentage justified the use of targeted genetic testing as a first-tier assay. Inferred haplotype analysis confirmed the founder status of BRCA2 c.5771_5774del (rs80359535) and c.7934del (rs80359688) and revealed an additional African founder variant (BRCA2 c.582G>A - rs80358810). A risk-benefit analysis using a questionnaire-based survey was performed in parallel to determine genetic professionals' views regarding POC testing. This was done to bridge the clinical implementation gap between haplotype analysis and POC testing as a first-tier screen during risk stratification of breast and ovarian cancer patients. The results reflected high acceptance (94%) of BRCA1/2 POC testing when accompanied by genetic counselling. Establishing the founder status for several recurrent BRCA2 variants across ethnic groups supports unselected use of the BRCA POC assay in all SA breast/ovarian cancer patients by recent local and international public health recommendations. Incorporating POC genotyping into the planned NGS screening algorithm of the Department of Health will ensure optimal use of the country's recourses to adhere to the set standards for optimal care and management for all breast cancer patients.
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Affiliation(s)
- Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Maritha J Kotze
- Department of Pathology, Division of Chemical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.,Division of Chemical Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Nicole Van Der Merwe
- Department of Pathology, Division of Chemical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - Phillip Bester
- Division of Virology, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Nerina C van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
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8
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Bango ZA, Tawe L, Muthoga CW, Paganotti GM. Past and current biological factors affecting malaria in the low transmission setting of Botswana: A review. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104458. [PMID: 32668367 PMCID: PMC7354381 DOI: 10.1016/j.meegid.2020.104458] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 11/29/2022]
Abstract
Malaria continues to be one of the top infectious agents contributing to morbidity and mortality in sub-Saharan Africa. Annually, Botswana accounts only for a small proportion of cases (<<1%). Despite significantly reduced incidence rate, the country still experiences sporadic outbreaks that hamper the goal of malaria elimination. This review evaluated previous and current biological factors that impact malaria in Botswana, specifically focussing on the vectors, the parasite and the host. This was accomplished via a literature review evaluating these variables in Botswana. Current literature suggests that Anopheles arabiensis is the main malaria vector in the country. Several other potential vectors have been found widely distributed throughout Botswana in high numbers, yet remain largely unstudied with regards to their contribution to the country's malaria burden. We also report the most up to date list of all Anopheles species that have been found in Botswana. Plasmodium falciparum is responsible for the vast majority of symptomatic malaria in the country and some drug resistance markers have been documented for this species. Plasmodium vivax has been reported in asymptomatic subjects, even though a large proportion of the Botswana population appears to be Duffy antigen negative. Very little is known about the true distribution of P. vivax and no point of care testing infrastructure for this species exists in Botswana, making it difficult to tailor treatment to address possible recrudescence or relapse. Due to a genetically diverse population with a substantial Khoisan contribution into the Bantu genetic background, several phenotypes that potentially impact prevalence and severity of malaria exist within the country. These include sickle cell trait, Glucose-6-Phosphate Dehydrogenase deficiency, and Duffy negativity. This review highlights the information that currently exists on malaria in Botswana. It also postulates that a comprehensive understanding of these aforementioned biological factors may help to explain malaria persistence in Botswana.
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Affiliation(s)
| | - Leabaneng Tawe
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana; Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana; Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, PA, USA; Department of Biomedical Sciences, University of Botswana, Gaborone, Botswana.
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9
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Pakendorf B, Stoneking M. The genomic prehistory of peoples speaking Khoisan languages. Hum Mol Genet 2020; 30:R49-R55. [PMID: 33075813 PMCID: PMC8117426 DOI: 10.1093/hmg/ddaa221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 11/14/2022] Open
Abstract
Peoples speaking so-called Khoisan languages-that is, indigenous languages of southern Africa that do not belong to the Bantu family-are culturally and linguistically diverse. They comprise herders, hunter-gatherers as well as groups of mixed modes of subsistence, and their languages are classified into three distinct language families. This cultural and linguistic variation is mirrored by extensive genetic diversity. We here review the recent genomics literature and discuss the genetic evidence for a formerly wider geographic spread of peoples with Khoisan-related ancestry, for the deep divergence among populations speaking Khoisan languages overlaid by more recent gene flow among these groups and for the impact of admixture with immigrant food-producers in their prehistory.
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Affiliation(s)
- Brigitte Pakendorf
- Dynamique du Langage, UMR5596, CNRS & Université de Lyon, 14 avenue Berthelot, 69007 Lyon, France
| | - Mark Stoneking
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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10
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Bility MT, Agarwal Y, Ho S, Castronova I, Beatty C, Biradar S, Narala V, Periyapatna N, Chen Y, Nachega J. WITHDRAWN: Can Traditional Chinese Medicine provide insights into controlling the COVID-19 pandemic: Serpentinization-induced lithospheric long-wavelength magnetic anomalies in Proterozoic bedrocks in a weakened geomagnetic field mediate the aberrant transformation of biogenic molecules in COVID-19 via magnetic catalysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020:142830. [PMID: 33071142 PMCID: PMC7543923 DOI: 10.1016/j.scitotenv.2020.142830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
This article has been withdrawn at the request of the authors and the editors. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Moses Turkle Bility
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America.
| | - Yash Agarwal
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Sara Ho
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Isabella Castronova
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Cole Beatty
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Shivkumar Biradar
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Vanshika Narala
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Nivitha Periyapatna
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Yue Chen
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
| | - Jean Nachega
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America; Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Public Health, 130 DeSoto Street, Pittsburgh, PA 15261, United States of America
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11
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Kader F, Ghai M, Zhou M. Ethnicity, age and disease-associated variation in body fluid-specific CpG sites in a diverse South African cohort. Forensic Sci Int 2020; 314:110372. [PMID: 32623090 DOI: 10.1016/j.forsciint.2020.110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/11/2022]
Abstract
Tissue-specific differential DNA methylation has been an attractive target for the development of markers for discrimination of body fluids found at crime scenes. Though mostly stable, DNA methylation patterns have been shown to vary between different ethnic groups, in different age groups as well as between healthy and diseased individuals. To the best of our knowledge, none of the markers for body fluid identification have been applied to different ethnic groups to ascertain if variability exists. In the present study, saliva and blood were collected to determine the effects of ethnicity (Blacks, Whites, Coloureds and Indians), age (20-30 years, 40-50years and above 60 years) and diabetes on methylation profiles of potential saliva- and blood-specific DMSs. Both DMSs were previously shown to exhibit hypermethylation in their target body fluids at single CpG sites, however in the present study, additional CpG sites flanking the reported sites were also screened. Bisulfite sequencing revealed that Coloureds showed highest methylation levels for both body fluids, and blacks displayed significant differences between other ethnic groups in the blood-specific CpG sites. A decline in methylation for both potential DMRs was observed with increasing age. Heavily methylated CpG sites in different ethnic groups and previously reported DMSs displayed hypomethylation with increasing age and disease status. Diabetic status did not show any significant difference in methylation when compared to healthy counterparts. Thus, the use of methylation markers for forensics needs thorough investigation of influence of external factors and ideally, several CpG sites should be co-analysed instead of a single DMS.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
| | - Marvellous Zhou
- South African Sugarcane Research Institute, Mount Edgecombe, Durban, South Africa; University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa.
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12
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Human leukocyte antigen class I (A, B, C) and class II (DPB1, DQB1, DRB1) allele and haplotype variation in Black South African individuals. Hum Immunol 2019; 81:6-7. [PMID: 31843212 DOI: 10.1016/j.humimm.2019.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
South Africa has a population of 58.78 million, of which 80.7% are Black African individuals, representing 9 predominant ethnic/linguistic groups (Zulu, Xhosa, Pedi, Tswana, South Sotho, Tsonga, Swati, Venda and Ndebele). HIV-1 and Mycobacterium tuberculosis infection are the leading causes of death (7.8% and 5.9%, respectively) in this population group. To provide reference HLA allele and haplotype data for studies of gene-associations with infectious/non-infectious diseases or vaccine development, we have updated previously published HLA class I (A, B, C) and class II DRB1 genotypes and determined high-resolution class II (DPB1, DQB1) genotypes for n = 142 healthy, unrelated Black South African individuals.
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