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Hong SC, Muyas F, Cortés-Ciriano I, Hormoz S. scAI-SNP: a method for inferring ancestry from single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594208. [PMID: 38798590 PMCID: PMC11118306 DOI: 10.1101/2024.05.14.594208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Collaborative efforts, such as the Human Cell Atlas, are rapidly accumulating large amounts of single-cell data. To ensure that single-cell atlases are representative of human genetic diversity, we need to determine the ancestry of the donors from whom single-cell data are generated. Self-reporting of race and ethnicity, although important, can be biased and is not always available for the datasets already collected. Here, we introduce scAI-SNP, a tool to infer ancestry directly from single-cell genomics data. To train scAI-SNP, we identified 4.5 million ancestry-informative single-nucleotide polymorphisms (SNPs) in the 1000 Genomes Project dataset across 3201 individuals from 26 population groups. For a query single-cell data set, scAI-SNP uses these ancestry-informative SNPs to compute the contribution of each of the 26 population groups to the ancestry of the donor from whom the cells were obtained. Using diverse single-cell data sets with matched whole-genome sequencing data, we show that scAI-SNP is robust to the sparsity of single-cell data, can accurately and consistently infer ancestry from samples derived from diverse types of tissues and cancer cells, and can be applied to different modalities of single-cell profiling assays, such as single-cell RNA-seq and single-cell ATAC-seq. Finally, we argue that ensuring that single-cell atlases represent diverse ancestry, ideally alongside race and ethnicity, is ultimately important for improved and equitable health outcomes by accounting for human diversity.
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Affiliation(s)
- Sung Chul Hong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Sahand Hormoz
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Gartner V, Redelings BD, Gaither C, Parr JB, Kalonji A, Phanzu F, Brazeau NF, Juliano JJ, Wray GA. Genomic insights into Plasmodium vivax population structure and diversity in central Africa. Malar J 2024; 23:27. [PMID: 38238806 PMCID: PMC10797969 DOI: 10.1186/s12936-024-04852-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Though Plasmodium vivax is the second most common malaria species to infect humans, it has not traditionally been considered a major human health concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility that P. vivax is evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. METHODS Whole genome sequencing of one new P. vivax isolate from the Democratic Republic of the Congo (DRC) was performed and used in population genomics analyses to assess how this central African isolate fits into the global context of this species. RESULTS Plasmodium vivax from DRC is similar to other African populations and is not closely related to the non-human primate parasite P. vivax-like. Evidence is found for a duplication of the gene PvDBP and a single copy of PvDBP2. CONCLUSION These results suggest an endemic P. vivax population is present in central Africa. Intentional sampling of P. vivax across Africa would further contextualize this sample within African P. vivax diversity and shed light on the mechanisms of infection in Duffy negative individuals. These results are limited by the uncertainty of how representative this single sample is of the larger population of P. vivax in central Africa.
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Affiliation(s)
- Valerie Gartner
- Biology Department, Duke University, Durham, NC, 27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, 27708, USA
| | - Benjamin D Redelings
- Biology Department, Duke University, Durham, NC, 27708, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Ronin Institute, Durham, NC, 27705, USA
| | | | | | - Albert Kalonji
- SANRU Asbl, 149 A/B, Boulevard du 30 Juin, Kinshasa, Gombe, Democratic Republic of Congo
| | - Fernandine Phanzu
- SANRU Asbl, 149 A/B, Boulevard du 30 Juin, Kinshasa, Gombe, Democratic Republic of Congo
| | | | | | - Gregory A Wray
- Biology Department, Duke University, Durham, NC, 27708, USA.
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Panigrahi M, Rajawat D, Nayak SS, Ghildiyal K, Sharma A, Jain K, Lei C, Bhushan B, Mishra BP, Dutt T. Landmarks in the history of selective sweeps. Anim Genet 2023; 54:667-688. [PMID: 37710403 DOI: 10.1111/age.13355] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
Half a century ago, a seminal article on the hitchhiking effect by Smith and Haigh inaugurated the concept of the selection signature. Selective sweeps are characterised by the rapid spread of an advantageous genetic variant through a population and hence play an important role in shaping evolution and research on genetic diversity. The process by which a beneficial allele arises and becomes fixed in a population, leading to a increase in the frequency of other linked alleles, is known as genetic hitchhiking or genetic draft. Kimura's neutral theory and hitchhiking theory are complementary, with Kimura's neutral evolution as the 'null model' and positive selection as the 'signal'. Both are widely accepted in evolution, especially with genomics enabling precise measurements. Significant advances in genomic technologies, such as next-generation sequencing, high-density SNP arrays and powerful bioinformatics tools, have made it possible to systematically investigate selection signatures in a variety of species. Although the history of selection signatures is relatively recent, progress has been made in the last two decades, owing to the increasing availability of large-scale genomic data and the development of computational methods. In this review, we embark on a journey through the history of research on selective sweeps, ranging from early theoretical work to recent empirical studies that utilise genomic data.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | | | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu Prasad Mishra
- Division of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Bareilly, India
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Osborne A, Phelan JE, Vanheer LN, Manjurano A, Gitaka J, Drakeley CJ, Kaneko A, Kita K, Campino S, Clark TG. High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing. Sci Rep 2023; 13:12062. [PMID: 37495620 PMCID: PMC10371994 DOI: 10.1038/s41598-023-39233-z] [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: 01/04/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Malaria has exhibited the strongest known selective pressure on the human genome in recent history and is the evolutionary driving force behind genetic conditions, such as sickle-cell disease, glucose-6-phosphatase deficiency, and some other erythrocyte defects. Genomic studies (e.g., The 1000 Genomes project) have provided an invaluable baseline for human genetics, but with an estimated two thousand ethno-linguistic groups thought to exist across the African continent, our understanding of the genetic differences between indigenous populations and their implications on disease is still limited. Low-cost sequencing-based approaches make it possible to target specific molecular markers and genes of interest, leading to potential insights into genetic diversity. Here we demonstrate the versatility of custom dual-indexing technology and Illumina next generation sequencing to generate a genetic profile of human polymorphisms associated with malaria pathology. For 100 individuals diagnosed with severe malaria in Northeast Tanzania, variants were successfully characterised on the haemoglobin subunit beta (HBB), glucose-6-phosphate dehydrogenase (G6PD), atypical chemokine receptor 1 (ACKR1) genes, and the intergenic Dantu genetic blood variant, then validated using pre-existing genotyping data. High sequencing coverage was observed across all amplicon targets in HBB, G6PD, ACKR1, and the Dantu blood group, with variants identified at frequencies previously observed within this region of Tanzania. Sequencing data exhibited high concordance rates to pre-existing genotyping data (> 99.5%). Our work demonstrates the potential utility of amplicon sequencing for applications in human genetics, including to personalise medicine and understand the genetic diversity of loci linked to important host phenotypes, such as malaria susceptibility.
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Affiliation(s)
- Ashley Osborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Alphaxard Manjurano
- Mwanza Medical Research Centre, National Institute for Medical Research, Mwanza, Tanzania
- Joint Malaria Program, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Christopher J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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Tobler R, Souilmi Y, Huber CD, Bean N, Turney CSM, Grey ST, Cooper A. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proc Natl Acad Sci U S A 2023; 120:e2213061120. [PMID: 37220274 PMCID: PMC10235988 DOI: 10.1073/pnas.2213061120] [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: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 05/25/2023] Open
Abstract
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
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Affiliation(s)
- Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Environment Institute, The University of Adelaide, Adelaide, SA5005, Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Nigel Bean
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA5005, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Chris S. M. Turney
- Division of Research, University of Technology Sydney, Ultimo, NSW2007, Australia
| | - Shane T. Grey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW2052, Australia
- Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW2010, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Blue Sky Genetics, Ashton, SA5137, Australia
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6
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Sezgin E, Kaplan E. Diverse selection pressures shaping the genetic architecture of behçet disease susceptibility. Front Genet 2022; 13:983646. [PMID: 36246630 PMCID: PMC9561091 DOI: 10.3389/fgene.2022.983646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Behçet disease (BD) is a polygenic, multifactorial, multisystem inflammatory condition with unknown etiology. Global distribution of BD is geographically structured, highest prevalence observed among East Asian, Middle Eastern, and Mediterranean populations. Although adaptive selection on a few BD susceptibility loci is speculated, a thorough evolutionary analysis on the genetic architecture of BD is lacking. We aimed to understand whether increased BD risk in the human populations with high prevalence is due to past selection on BD associated genes. We performed population genetics analyses with East Asian (high BD prevalence), European (low/very low BD prevalence), and African (very low/no BD prevalence) populations. Comparison of ancestral and derived alleles’ frequencies versus their reported susceptible or protective effect on BD showed both derived and ancestral alleles are associated with increased BD risk. Variants showing higher risk to and more significant association with BD had smaller allele frequency differences, and showed less population differentiation compared to variants that showed smaller risk and less significant association with BD. Results suggest BD alleles are not unique to East Asians but are also found in other world populations at appreciable frequencies, and argue against selection favoring these variants only in populations with high BD prevalence. BD associated gene analyses showed similar evolutionary histories driven by neutral processes for many genes or balancing selection for HLA (Human Leukocyte Antigen) genes in all three populations studied. However, nucleotide diversity in several HLA region genes was much higher in East Asians suggesting selection for high nucleotide and haplotype diversity in East Asians. Recent selective sweep for genes involved in antigen recognition, peptide processing, immune and cellular differentiation regulation was observed only in East Asians. We conclude that the evolutionary processes shaping the genetic diversity in BD risk genes are diverse, and elucidating the underlying specific selection mechanisms is complex. Several of the genes examined in this study are risk factors (such as ERAP1, IL23R, HLA-G) for other inflammatory diseases. Thus, our conclusions are not only limited to BD but may have broader implications for other inflammatory diseases.
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Affiliation(s)
- Efe Sezgin
- Department of Food Engineering, Izmir Institute of Technology, Izmir, Turkey
- Biotechnology Interdisciplinary Program, Izmir Institute of Technology, Izmir, Turkey
- *Correspondence: Efe Sezgin,
| | - Elif Kaplan
- Biotechnology Interdisciplinary Program, Izmir Institute of Technology, Izmir, Turkey
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7
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Cuadros-Espinoza S, Laval G, Quintana-Murci L, Patin E. The genomic signatures of natural selection in admixed human populations. Am J Hum Genet 2022; 109:710-726. [PMID: 35259336 DOI: 10.1016/j.ajhg.2022.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
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Katar Y, Usman E, Aliska G. Genetic Variation of the CYP2C9 Genetic of Minangkabau as a Predictor of Side Effect Providing Indications of Non-steroidal Anti-inflammatory Drugs. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.8853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND: Non-steroidal Anti-inflammatory Drugs (NSAID) activity showed a varied response based on the genetic polymorphism of the CYP29C enzyme. Metabolism of some NSAIDs such as celecoxib, diclofenac, and ibuprofen is highly dependent on CYP2C9. This enzyme has several variants of the heterozygous and homozygous genotypes such as CYP2C9 *2/2 and CYP2C9 *1/*3 which differ for each population. Genetic testing for specific variations of this allele will help determine whether the drug is a valid pharmacotherapeutic option for the patient or not.
AIM: This study aims to analyze the genetic variation of the CYP2C9 gene from the Minangkabau ethnic, West Sumatra, Indonesia, which can later be used as a determinant of selecting the right NSAID with optimal effectiveness and to minimalize side effects.
MATERIAL AND METHODS: Respondents of this study were users of NSAID drugs obtained from several hospitals in Padang City and were of Minang ethnicity. Blood samples taken from patients were stored in EDTA tubes and DNA was isolated using a genomic DNA isolation kit, DNAzol® Genomic DNA Kits (Thermofischer Scientific). PCR primer and sequencing were designed using Primer Blast (NCBI) software. The synthesized primer was purified by HPLC. DNA fragment application was carried out using the PCR method. The amplicon DNA was purified and prepared as much as 500 ng for sequencing using Illumina’s Next Generation Sequencing method. This analysis was performed with the help of SPSS software.
RESULTS: When analyzing the CYP2C9 gene on Primer F23, 44 people were found to be homozygous for the normal allele (AA genotype), and 11 people were heterozygous (GT genotype), 45 people were normal allele (TT genotype), five people were heterozygous (CG genotype), 49 people were normal allele (AA genotype), and five people were heterozygous (GA genotype).
CONCLUSION: This study concluded that relationship between CYP29C genetic variation and NSAID drug metabolism is found at the genotypic frequency rs229837 and rs1934969.
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Ahmed S, Khan H, Khan A, Bangash MH, Hussain A, Qayum M, Hamdard MH. Inter-ethnic genetic variations and novel variant identification in the partial sequences of CYP2B6 gene in Pakistani population. PeerJ 2021; 9:e11149. [PMID: 34386299 PMCID: PMC8312491 DOI: 10.7717/peerj.11149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background Some single nucleotide polymorphisms (SNPs) in the cytochrome P450 (CYP)2B6 gene lead to decreased enzyme activity and have an impact on drug metabolism. The present study was designed to investigate the patterns of genetic distinction across a hypervariable region of the CYP2B6 gene, known to contain important SNPs, i.e. rs4803419 and rs3745274, among five major ethnic groups of the Pakistani population. Methods Arlequin v3.5.DnaSPv6.12. and network 5 resources were used to analyze population genetic variance in the partial CYP2B6 gene sequences obtained from 104 human samples belonging to Punjabi, Pathan, Sindhi, Seraiki and Baloch ethnicities of Pakistan. The partial CYP2B6 gene region analyzed in the current study is previously known to possess important SNPs. Results The data analyses revealed that genetic variance among samples mainly came from differentiation within the ethnic groups. However, significant genetic variation was also found among the various ethnic groups. The high pairwise Fst genetic distinction was observed between Seraiki and Sindhi ethnic groups (Fst = 0.13392, P-value = 0.026) as well as between Seraiki and Balochi groups (Fst = 0.04303, P-value = −0.0030). However, the degree of genetic distinction was low between Pathan and Punjabi ethnic groups. Some SNPs, including rs3745274 and rs4803419, which are previously shown in strong association with increased plasma Efavirenz level, were found in high frequency. Besides, a novel SNP, which was not found in dbSNP and Ensemble databases, was identified in the Balochi ethnicity. This novel SNP is predicted to affect the CYP2B6 splicing pattern. Conclusion These results may have significant implications in Pakistani ethnicities in the context of drugs metabolized by CYP2B6, especially in Seraiki and Balochi ethnicity. The novel heterogeneous SNP, found in the present study, might lead to altered drug-metabolizing potential of CYP2B6 and, therefore, may be implicated in non-responder phenomenon.
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Affiliation(s)
- Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Hizbullah Khan
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | | | - Abrar Hussain
- Baluchistan University of Information Technology and Management Sciences, Quetta, Pakistan
| | - Mughal Qayum
- Department of Pharmacy, Kohat University of Science & Technology, Kohat, Pakistan
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Lo E, Russo G, Pestana K, Kepple D, Abagero BR, Dongho GBD, Gunalan K, Miller LH, Hamid MMA, Yewhalaw D, Paganotti GM. Contrasting epidemiology and genetic variation of Plasmodium vivax infecting Duffy-negative individuals across Africa. Int J Infect Dis 2021; 108:63-71. [PMID: 33991680 DOI: 10.1016/j.ijid.2021.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Plasmodium vivax malaria was thought to be rare in Africans who lack the Duffy blood group antigen expression. However, recent studies indicate that P. vivax can infect Duffy-negative individuals and has spread into areas of high Duffy negativity across Africa. Our study compared epidemiological and genetic features of P. vivax between African regions. METHODS A standardized approach was used to identify and quantify P. vivax from Botswana, Ethiopia, and Sudan, where Duffy-positive and Duffy-negative individuals coexist. The study involved sequencing the Duffy binding protein (DBP) gene and inferring genetic relationships among P. vivax populations across Africa. RESULTS Among 1215 febrile patients, the proportions of Duffy negativity ranged from 20-36% in East Africa to 84% in southern Africa. Average P. vivax prevalence among Duffy-negative populations ranged from 9.2% in Sudan to 86% in Botswana. Parasite density in Duffy-negative infections was significantly lower than in Duffy-positive infections. P. vivax in Duffy-negative populations were not monophyletic, with P. vivax in Duffy-negative and Duffy-positive populations sharing similar DBP haplotypes and occurring in multiple, well-supported clades. CONCLUSIONS Duffy-negative Africans are not resistant to P. vivax, and the public health significance of this should not be neglected. Our study highlights the need for a standardized approach and more resources/training directed towards the diagnosis of vivax malaria in Africa.
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Affiliation(s)
- Eugenia Lo
- Biological Sciences, University of North Carolina at Charlotte, USA.
| | - Gianluca Russo
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy.
| | - Kareen Pestana
- Biological Sciences, University of North Carolina at Charlotte, USA
| | - Daniel Kepple
- Biological Sciences, University of North Carolina at Charlotte, USA
| | - Beka Raya Abagero
- Tropical Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | - Ghyslaine Bruna Djeunang Dongho
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy; Evangelical University of Cameroon, Bandjoun, Cameroon
| | | | - Louis H Miller
- Laboratory of Malaria and Vector Research, NIAID/NIH, Bethesda, USA
| | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Delenasaw Yewhalaw
- Tropical Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana; Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
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11
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African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet 2021; 22:284-306. [PMID: 33432191 DOI: 10.1038/s41576-020-00306-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/29/2023]
Abstract
The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.
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Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
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13
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Hamid I, Korunes KL, Beleza S, Goldberg A. Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde. eLife 2021; 10:e63177. [PMID: 33393457 PMCID: PMC7815310 DOI: 10.7554/elife.63177] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Humans have undergone large migrations over the past hundreds to thousands of years, exposing ourselves to new environments and selective pressures. Yet, evidence of ongoing or recent selection in humans is difficult to detect. Many of these migrations also resulted in gene flow between previously separated populations. These recently admixed populations provide unique opportunities to study rapid evolution in humans. Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ~20 generations. We estimate that the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference. Our study provides evidence of adaptation in a human population on historical timescales.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | | | - Sandra Beleza
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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14
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Oboh MA, Oyebola KM, Idowu ET, Badiane AS, Otubanjo OA, Ndiaye D. Rising report of Plasmodium vivax in sub-Saharan Africa: Implications for malaria elimination agenda. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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15
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Buczek K, Deryło K, Kutyła M, Rybicka-Jasińska K, Gryko D, Borsuk G, Rodzik B, Trytek M. Impact of Protoporphyrin Lysine Derivatives on the Ability of Nosema ceranae Spores to Infect Honeybees. INSECTS 2020; 11:insects11080504. [PMID: 32764215 PMCID: PMC7469180 DOI: 10.3390/insects11080504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Honeybees, which are important for the development and maintenance of natural ecosystems, are infected by microsporidia, Nosema apis and N. ceranae. These parasites induce a disease named nosemosis contributing to the impairment of digestion and nutrient absorption, ultimately leading to total colony collapse. The need for research into the control of N. ceranae has become increasingly important. Promising compounds for the treatment of nosemosis are porphyrins. In the present study, we examined the effects of three different porphyrins on the infectivity of N. ceranae microsporidia. A significantly lower level of infection was observed in the bees infected with the porphyrin-treated spores than in the control bees (infected with untreated spores). We showed that protoporphyrin lysine derivatives in particular prevented the development of Nosema spores and simultaneously extended bee life spans (up to 50%). The results also indicate that these porphyrins may contribute to the reduction in digestive nutrient absorption disorders in bees. The present findings can be used to develop a new class of drugs for combating nosemosis. These compounds may serve as preventive or disinfection agents through direct inactivation of Nosema both in the midgut and outside the host body, i.e., in the hive. Abstract The effect of two protoporphyrin IX derivatives conjugated with single (PP[Lys(TFA)-OH)]2) or double (PP[Lys(TFA)-Lys(TFA)-OH]2) lysine moieties on the infectious capacity of Nosema ceranae spores was examined, and their efficacies were compared with those of a cationic porphyrin (H2TTMePP). Honeybees were inoculated with spores preincubated with porphyrins or with untreated spores (control). A significantly lower level of infection was observed in the bees infected with the porphyrin-treated spores than in the infected control. Porphyrins 1 and 2 reduced the infectious capability of microsporidia more efficiently than porphyrin 3, with bee mortality declining to almost 50%. Confocal analysis of the midguts of infected bees revealed distinct differences in the number of spores between the control group and the group infected with PP[Lys(TFA)-Lys(TFA)-OH]2-treated spores. Notably, bees with a reduced level of infection consumed less sucrose syrup than the control bees, indicating a reduction in digestive disorders and an improvement in food absorption.
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Affiliation(s)
- Katarzyna Buczek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (K.B.); (M.K.)
| | - Kamil Deryło
- Department of Molecular Biology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Mateusz Kutyła
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (K.B.); (M.K.)
| | - Katarzyna Rybicka-Jasińska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; (K.R.-J.); (D.G.)
| | - Dorota Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; (K.R.-J.); (D.G.)
| | - Grzegorz Borsuk
- Institute of Biological Basis of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland;
| | - Beata Rodzik
- Department of Applied Mathematics, Faculty of Mathematics, Maria Curie-Skłodowska University, Plac Marii Curie-Skłodowskiej 1, 20-031 Lublin, Poland;
| | - Mariusz Trytek
- Department of Industrial and Environmental Microbiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; (K.B.); (M.K.)
- Correspondence: ; Tel.: +48-81-537-5933
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16
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Werren EA, Garcia O, Bigham AW. Identifying adaptive alleles in the human genome: from selection mapping to functional validation. Hum Genet 2020; 140:241-276. [PMID: 32728809 DOI: 10.1007/s00439-020-02206-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022]
Abstract
The suite of phenotypic diversity across geographically distributed human populations is the outcome of genetic drift, gene flow, and natural selection throughout human evolution. Human genetic variation underlying local biological adaptations to selective pressures is incompletely characterized. With the emergence of population genetics modeling of large-scale genomic data derived from diverse populations, scientists are able to map signatures of natural selection in the genome in a process known as selection mapping. Inferred selection signals further can be used to identify candidate functional alleles that underlie putative adaptive phenotypes. Phenotypic association, fine mapping, and functional experiments facilitate the identification of candidate adaptive alleles. Functional investigation of candidate adaptive variation using novel techniques in molecular biology is slowly beginning to unravel how selection signals translate to changes in biology that underlie the phenotypic spectrum of our species. In addition to informing evolutionary hypotheses of adaptation, the discovery and functional annotation of adaptive alleles also may be of clinical significance. While selection mapping efforts in non-European populations are growing, there remains a stark under-representation of diverse human populations in current public genomic databases, of both clinical and non-clinical cohorts. This lack of inclusion limits the study of human biological variation. Identifying and functionally validating candidate adaptive alleles in more global populations is necessary for understanding basic human biology and human disease.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI, USA
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed Garcia
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California Los Angeles, 341 Haines Hall, Los Angeles, CA, 90095, USA.
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17
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Waskow G, Rodrigues MMDO, Höher G, Onsten T, Lindenau JDR, Fiegenbaum M, Almeida S. Genetic variability of blood groups in southern Brazil. Genet Mol Biol 2020; 43:e20180327. [PMID: 32478792 PMCID: PMC7263432 DOI: 10.1590/1678-4685-gmb-2018-0327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/08/2019] [Indexed: 12/03/2022] Open
Abstract
We evaluated genetic variability among the blood groups Kell
(c.578C > T and
c.1790T > C), Kidd
(c.838A > G), Duffy
(c.125A > G, c.265C >
T and c.1-67T > C),
Diego (c.2561C > T), MNS
(c.143T > C) and Rh
(c.676G > C) in Rio Grande do Sul in
southern Brazil. Genetic profiling from 382 volunteer blood donors was performed
through allelic discrimination assays using a hydrolysis probe (TaqMan®) with a
real-time PCR system. The sample was divided into two groups: Euro-Brazilian and
Afro-Brazilian. A comparison with studies from other regions of Brazil and the
1000 Genomes Database showed significant differences for almost all
polymorphisms evaluated in our population. Population differentiation between
the Euro- and Afro-Brazilian groups was low (FST value 0.055). However, when each locus was evaluated individually,
KEL*06 and FY*02N.01 allele frequencies
were significantly higher in the Afro-Brazilian group than in the Euro-Brazilian
group. Ethnic classification that uses phenotypic criteria to find blood units
with rare antigens may be important when there is a need to detect blood units
with an absence of Duffy antigens. There is also a greater probability of
finding donors in the Afro-Brazilian group. Taken together, the data indicate
strong European and African contributions to the gene pool, with intense
admixture.
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Affiliation(s)
- Gabriela Waskow
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Programa de Pós-Graduação em Biociências, Porto Alegre, RS, Brazil
| | | | - Gabriela Höher
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Programa de Pós-Graduação em Biociências, Porto Alegre, RS, Brazil
| | - Tor Onsten
- Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, RS, Brazil
| | - Juliana Dal-Ri Lindenau
- Universidade Federal de Santa Catarina (UFSC), Departamento de Biologia Celular, Embriologia e Genética, Florianópolis, SC, Brazil
| | - Marilu Fiegenbaum
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Programa de Pós-Graduação em Biociências, Porto Alegre, RS, Brazil.,Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Departamento de Ciências Básicas da Saúde, Porto Alegre, RS, Brazil
| | - Silvana Almeida
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Programa de Pós-Graduação em Biociências, Porto Alegre, RS, Brazil.,Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Departamento de Ciências Básicas da Saúde, Porto Alegre, RS, Brazil
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18
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Gurdasani D, Carstensen T, Fatumo S, Chen G, Franklin CS, Prado-Martinez J, Bouman H, Abascal F, Haber M, Tachmazidou I, Mathieson I, Ekoru K, DeGorter MK, Nsubuga RN, Finan C, Wheeler E, Chen L, Cooper DN, Schiffels S, Chen Y, Ritchie GRS, Pollard MO, Fortune MD, Mentzer AJ, Garrison E, Bergström A, Hatzikotoulas K, Adeyemo A, Doumatey A, Elding H, Wain LV, Ehret G, Auer PL, Kooperberg CL, Reiner AP, Franceschini N, Maher D, Montgomery SB, Kadie C, Widmer C, Xue Y, Seeley J, Asiki G, Kamali A, Young EH, Pomilla C, Soranzo N, Zeggini E, Pirie F, Morris AP, Heckerman D, Tyler-Smith C, Motala AA, Rotimi C, Kaleebu P, Barroso I, Sandhu MS. Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa. Cell 2020; 179:984-1002.e36. [PMID: 31675503 DOI: 10.1016/j.cell.2019.10.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/03/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
Genomic studies in African populations provide unique opportunities to understand disease etiology, human diversity, and population history. In the largest study of its kind, comprising genome-wide data from 6,400 individuals and whole-genome sequences from 1,978 individuals from rural Uganda, we find evidence of geographically correlated fine-scale population substructure. Historically, the ancestry of modern Ugandans was best represented by a mixture of ancient East African pastoralists. We demonstrate the value of the largest sequence panel from Africa to date as an imputation resource. Examining 34 cardiometabolic traits, we show systematic differences in trait heritability between European and African populations, probably reflecting the differential impact of genes and environment. In a multi-trait pan-African GWAS of up to 14,126 individuals, we identify novel loci associated with anthropometric, hematological, lipid, and glycemic traits. We find that several functionally important signals are driven by Africa-specific variants, highlighting the value of studying diverse populations across the region.
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Affiliation(s)
- Deepti Gurdasani
- William Harvey Research Institute, Queen Mary's University of London, London, UK
| | | | - Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Center for Genomics Research and Innovation (CGRI)/National Biotechnology Development Agency CGRI/NABDA, Abuja, Nigeria
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | | | | | | | - Marc Haber
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ioanna Tachmazidou
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage Hertfordshire SG1 2NY, UK
| | - Iain Mathieson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth Ekoru
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rebecca N Nsubuga
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Chris Finan
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Eleanor Wheeler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Li Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Yuan Chen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Alex J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Konstantinos Hatzikotoulas
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA
| | | | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Georg Ehret
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14, Switzerland
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Charles L Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Dermot Maher
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Stephen B Montgomery
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Yali Xue
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet Seeley
- London School of Hygiene and Tropical Medicine, London, UK; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Elizabeth H Young
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew P Morris
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK; Department of Biostatistics, University of Liverpool, Liverpool, UK
| | | | | | - Ayesha A Motala
- Department of Diabetes and Endocrinology, University of KwaZulu-Natal, Durban, South Africa.
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Institute of Health, Bethesda, MD, USA.
| | - Pontiano Kaleebu
- London School of Hygiene and Tropical Medicine, London, UK; Uganda Medical Informatics Centre (UMIC), MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Hygiene & Tropical Medicine Uganda Research Unit on AIDS, Entebbe, Uganda.
| | - Inês Barroso
- Wellcome Sanger Institute, Hinxton, Cambridge, UK; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Manj S Sandhu
- Department of Medicine, University of Cambridge, Cambridge, UK.
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19
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Genetic variations in drug-metabolizing enzyme CYP2C9 among major ethnic groups of Pakistani population. Gene 2020; 746:144659. [PMID: 32276000 DOI: 10.1016/j.gene.2020.144659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 01/31/2023]
Abstract
The genetic polymorphism of cytochrome P450 (CYPs)drug-metabolizing enzymes are well studied in human populations for drug safety and efficacy. CYP2C9 is a highly polymorphic CYP enzyme that oxidizing the indigenous compounds and xenobiotics. The present study was pursued to evaluate the genetic variation across the CYP2C9 gene among major groups of the Pakistani population. The CYP2C9 genomic region holding important warfarin drug-metabolizing SNPs was sequenced from 159 individuals belong from five major ethnic groups of Pakistani population. The population genetic analyses of the high-quality sequences data was performed using Arlequin v3.5, DnaSP v6.12 and Network 5 resources. The data analyses unveiled that genetic variance among samples mainly arose from population-scale differentiation among these ethnic groups with global Fst of 0.78, P-value < 0.0001. The highest pairwise population genetic variation observed between Saraiki and Baloch groups based on different statistical tests. Whereas, uniform genetic composition across CYP2C9 loci was inferred among Punjabi, Pathan and Sindhi groups with minimal genetic differentiation. Several SNPs, including the previously reported warfarin associated variants, i.e. rs2860905, rs1799853 (CYP2C9*2) and rs72558189 (CYP2C9*14) were detected in these population groups with diverse allelic frequencies. Besides, a novel intronic SNP, i.e. not available in dbSNP and Ensemble databases, was identified for a Sindhi individual sample. This novel SNP predicted to influence the CYP2C9 alternative transcript splicing. The pharmacogeneticsassessment of the CYP2C9 genetic variations identified in current study may important to test against the warfarin efficacy for different ethnicity of Pakistani population.
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20
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de Silva JR, Amir A, Lau YL, Ooi CH, Fong MY. Distribution of the Duffy genotypes in Malaysian Borneo and its relation to Plasmodium knowlesi malaria susceptibility. PLoS One 2019; 14:e0222681. [PMID: 31536563 PMCID: PMC6752761 DOI: 10.1371/journal.pone.0222681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/03/2019] [Indexed: 12/01/2022] Open
Abstract
The Duffy blood group plays a key role in Plasmodium knowlesi and Plasmodium vivax invasion into human erythrocytes. The geographical distribution of the Duffy alleles differs between regions with the FY*A allele having high frequencies in many Asian populations, the FY*B allele is found predominately in European populations and the FY*Bes allele found predominantly in African regions. A previous study in Peninsular Malaysia indicated high homogeneity of the dominant FY*A/FY*A genotype. However, the distribution of the Duffy genotypes in Malaysian Borneo is currently unknown. In the present study, the distribution of Duffy blood group genotypes and allelic frequencies among P. knowlesi infected patients as well as healthy individuals in Malaysian Borneo were determined. A total of 79 P. knowlesi patient blood samples and 76 healthy donor samples were genotyped using allele specific polymerase chain reaction (ASP-PCR). Subsequently a P. knowlesi invasion assay was carried out on FY*AB/ FY*A and FY*A/ FY*A Duffy genotype blood to investigate if either genotype conferred increased susceptibility to P. knowlesi invasion. Our results show almost equal distribution between the homozygous FY*A/FY*A and heterozygous FY*A/FY*B genotypes. This is in stark contrast to the Duffy distribution in Peninsular Malaysia and the surrounding Southeast Asian region which is dominantly FY*A/FY*A. The mean percent invasion of FY*A/FY*A and FY*A/FY*B blood was not significantly different indicating that neither blood group confers increased susceptibility to P. knowlesi invasion.
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Affiliation(s)
- Jeremy Ryan de Silva
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Amirah Amir
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choo-Huck Ooi
- Sarawak State Health Department, Jalan Diplomatik, Off Jalan Bako, Kuching, Sarawak, Malaysia
| | - Mun Yik Fong
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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21
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Ely ZA, Moon JM, Sliwoski GR, Sangha AK, Shen XX, Labella AL, Meiler J, Capra JA, Rokas A. The Impact of Natural Selection on the Evolution and Function of Placentally Expressed Galectins. Genome Biol Evol 2019; 11:2574-2592. [PMID: 31504490 PMCID: PMC6751361 DOI: 10.1093/gbe/evz183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 01/03/2023] Open
Abstract
Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to primates, are involved in placental development. To comprehensively study the molecular evolution of these galectins, both across mammals and within humans, we conducted a series of between- and within-species evolutionary analyses. By examining patterns of sequence evolution between species, we found that primate-specific galectins showed uniformly high substitution rates, whereas two of the four other galectins experienced accelerated evolution in primates. By examining human population genomic variation, we found that galectin genes and variants, including variants previously linked to immune diseases, showed signatures of recent positive selection in specific human populations. By examining one nonsynonymous variant in Galectin-8 previously associated with autoimmune diseases, we further discovered that it is tightly linked to three other nonsynonymous variants; surprisingly, the global frequency of this four-variant haplotype is ∼50%. To begin understanding the impact of this major haplotype on Galectin-8 protein structure, we modeled its 3D protein structure and found that it differed substantially from the reference protein structure. These results suggest that placentally expressed galectins experienced both ancient and more recent selection in a lineage- and population-specific manner. Furthermore, our discovery that the major Galectin-8 haplotype is structurally distinct from and more commonly found than the reference haplotype illustrates the significance of understanding the evolutionary processes that sculpted variants associated with human genetic disease.
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Affiliation(s)
- Zackery A Ely
- Department of Biological Sciences, Vanderbilt University
| | - Jiyun M Moon
- Department of Biological Sciences, Vanderbilt University
| | | | - Amandeep K Sangha
- Department of Chemistry, Vanderbilt University
- Center for Structural Biology, Vanderbilt University
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University
- Center for Structural Biology, Vanderbilt University
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University
- Department of Biomedical Informatics, Vanderbilt University School of Medicine
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
- Department of Biomedical Informatics, Vanderbilt University School of Medicine
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22
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Casillas S, Mulet R, Villegas-Mirón P, Hervas S, Sanz E, Velasco D, Bertranpetit J, Laayouni H, Barbadilla A. PopHuman: the human population genomics browser. Nucleic Acids Res 2019; 46:D1003-D1010. [PMID: 29059408 PMCID: PMC5753332 DOI: 10.1093/nar/gkx943] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/04/2017] [Indexed: 12/17/2022] Open
Abstract
The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.
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Affiliation(s)
- Sònia Casillas
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- To whom correspondence should be addressed. Sònia Casillas. Tel: +34 93 5868958; Fax: +34 93 5812011; . Correspondence may also be addressed to Antonio Barbadilla.
| | - Roger Mulet
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pablo Villegas-Mirón
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Sergi Hervas
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Esteve Sanz
- Servei de Genòmica i Bioinformàtica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Daniel Velasco
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003 Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003 Barcelona, Spain
| | - Antonio Barbadilla
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Servei de Genòmica i Bioinformàtica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- To whom correspondence should be addressed. Sònia Casillas. Tel: +34 93 5868958; Fax: +34 93 5812011; . Correspondence may also be addressed to Antonio Barbadilla.
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Szpak M, Xue Y, Ayub Q, Tyler‐Smith C. How well do we understand the basis of classic selective sweeps in humans? FEBS Lett 2019; 593:1431-1448. [DOI: 10.1002/1873-3468.13447] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/29/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
| | - Yali Xue
- The Wellcome Sanger Institute Hinxton UK
| | - Qasim Ayub
- School of Science Monash University Malaysia Bandar Sunway Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform Monash University Malaysia Genomics Facility Bandar Sunway Malaysia
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24
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Han C, Li Q, Liu J, Hao Z, Huang J, Zhang Y. Characterization, evolution, and expression analysis of TLR7 gene subfamily members in Mastacembelus armatus (Synbranchiformes: Mastacembelidae). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 95:77-88. [PMID: 30742850 DOI: 10.1016/j.dci.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/03/2019] [Accepted: 02/03/2019] [Indexed: 06/09/2023]
Abstract
TLR7 subfamily members are important pattern recognition receptors participating in the recognition of pathogen-associated molecular patterns. In this study, we successfully identified 3 members of TLR7 subfamily from the spiny eel Mastacembelus armatus (MaTLR7, MaTLR8 and MaTLR9). The amino acid sequence identities of MaTLR7 and MaTLR8 with Monopterus albus TLR7 were 87.2% and 76.5%, respectively and the identity of MaTLR9 with Seriola lalandi TLR9 was 74.7%. The phylogenetic analysis revealed MaTLRs showed close relationship to other species in Synbranchiformes or Perciformes. Quantitative real-time PCR analysis revealed that they were expressed in all tested tissues and higher expression was found in spleen or gill. After infection with Aeromonas veronii, expression of MaTLR7, MaTLR8 and MaTLR9 were all significantly downregulated in spleen and kidney. Evolutionary analysis suggested that the ancestral lineages of teleost TLR8 and TLR9 had been subject to positive selection pressures and multiple Maximum likelihood methods recovered 3 positively selected sites in teleost TLR7, 4 in TLR8 and 8 in TLR9. Domain distribution revealed most positively selected sites were located in leucine-rich repeat domain. Our results will contribute to better understanding the antibacterial mechanism of TLRs and their co-evolution with pathogens.
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Affiliation(s)
- Chong Han
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Qiang Li
- School of Life Sciences, Guangzhou University, Guangzhou, PR China
| | - Jinmei Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Zhiqiang Hao
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Jianrong Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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25
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Grignard L, Mair C, Curry J, Mahey L, Bastiaens GJH, Tiono AB, Okebe J, Coulibaly SA, Gonçalves BP, Affara M, Ouédraogo A, Bougouma EC, Sanou GS, Nébié I, Lanke KHW, Sirima SB, d'Alessandro U, Clark TG, Campino S, Bousema T, Drakeley C. Bead-based assays to simultaneously detect multiple human inherited blood disorders associated with malaria. Malar J 2019; 18:14. [PMID: 30665411 PMCID: PMC6341711 DOI: 10.1186/s12936-019-2648-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/12/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Glucose-6-phosphate dehydrogenase deficiency (G6PDd), haemoglobin C (HbC) and S (HbS) are inherited blood disorders (IBD) common in populations in malaria endemic areas. All are associated to some degree with protection against clinical malaria whilst additionally G6PDd is associated with haemolysis following treatment with 8-aminoquinolines. Measuring the prevalence of these inherited blood disorders in affected populations can improve understanding of disease epidemiology. Current methodologies in epidemiological studies commonly rely on individual target amplification and visualization; here a method is presented to simultaneously detect the polymorphisms and that can be expanded to include other single nucleotide polymorphisms (SNPs) of interest. METHODS Human DNA from whole blood samples was amplified in a novel, multiplex PCR reaction and extended with SNP-specific probes in an allele specific primer extension (ASPE) to simultaneously detect four epidemiologically important human markers including G6PD SNPs (G202A and A376G) and common haemoglobin mutations (HbS and HbC). The products were hybridized to magnetic beads and the median fluorescence intensity (MFI) was read on MAGPIX® (Luminex corp.). Genotyping data was compared to phenotypical data generated by flow cytometry and to established genotyping methods. RESULTS Seventy-five samples from Burkina Faso (n = 75/78, 96.2%) and 58 samples from The Gambia (n = 58/61, 95.1%) had a G6PD and a HBB genotype successfully assigned by the bead-based assay. Flow cytometry data available for n = 61 samples further supported the concordance between % G6PD normal/deficient cells and genotype. CONCLUSIONS The bead based assay compares well to alternative measures of genotyping and phenotyping for G6PD. The screening is high throughput, adaptable to inclusion of multiple targets of interest and easily standardized.
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Affiliation(s)
- Lynn Grignard
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK.
| | - Catherine Mair
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Guide J H Bastiaens
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Alfred B Tiono
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Joseph Okebe
- Disease Control & Elimination Theme, Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Sam A Coulibaly
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Bronner P Gonçalves
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Muna Affara
- Disease Control & Elimination Theme, Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Alphonse Ouédraogo
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Edith C Bougouma
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Guillaume S Sanou
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Issa Nébié
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kjerstin H W Lanke
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sodiomon B Sirima
- Department of Biomedical Sciences, Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Umberto d'Alessandro
- Disease Control & Elimination Theme, Medical Research Council Unit at London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Teun Bousema
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Chris Drakeley
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
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26
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Oboh MA, Badiane AS, Ntadom G, Ndiaye YD, Diongue K, Diallo MA, Ndiaye D. Molecular identification of Plasmodium species responsible for malaria reveals Plasmodium vivax isolates in Duffy negative individuals from southwestern Nigeria. Malar J 2018; 17:439. [PMID: 30486887 PMCID: PMC6263541 DOI: 10.1186/s12936-018-2588-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/22/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Malaria in Nigeria is principally due to Plasmodium falciparum and, to a lesser extent to Plasmodium malariae and Plasmodium ovale. Plasmodium vivax is thought to be absent in Nigeria in particular and sub-Saharan Africa in general, due to the near fixation of the Duffy negative gene in this population. Nevertheless, there are frequent reports of P. vivax infection in Duffy negative individuals in the sub-region, including reports from two countries sharing border with Nigeria to the west (Republic of Benin) and east (Cameroon). Additionally, there were two cases of microscopic vivax-like malaria from Nigerian indigenous population. Hence molecular surveillance of the circulating Plasmodium species in two states (Lagos and Edo) of southwestern Nigeria was carried out. METHODS A cross-sectional survey between September 2016 and March 2017 was conducted. 436 febrile patients were included for the present work. Venous blood of these patients was subjected to RDT as well as microscopy. Further, parasite DNA was isolated from positive samples and PCR diagnostic was employed followed by direct sequencing of the 18S rRNA of Plasmodium species as well as sequencing of a portion of the promoter region of the Duffy antigen receptor for chemokines. Samples positive for P. vivax were re-amplified several times and finally using the High Fidelity Taq to rule out any bias introduced. RESULTS Of the 256 (58.7%) amplifiable malaria parasite DNA, P. falciparum was, as expected, the major cause of infection, either alone 85.5% (219/256; 97 from Edo and 122 from Lagos), or mixed with P. malariae 6.3% (16/256) or with P. vivax 1.6% (4/256). Only one of the five P. vivax isolates was found to be a single infection. DNA sequencing and subsequent alignment of the 18S rRNA of P. vivax with the reference strains displayed very high similarities (100%). Remarkably, the T-33C was identified in all P. vivax samples, thus confirming that all vivax-infected patients in the current study are Duffy negative. CONCLUSION The present study gave the first molecular evidence of P. vivax in Nigeria in Duffy negative individuals. Though restricted to two states; Edo in South-South and Lagos in South-west Nigeria, the real burden of this species in Nigeria and sub-Saharan Africa might have been underestimated, hence there is need to put in place a country-wide, as well as a sub-Saharan Africa-wide surveillance and appropriate control measures.
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MESH Headings
- Child, Preschool
- Cross-Sectional Studies
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Duffy Blood-Group System/genetics
- Female
- Humans
- Infant
- Infant, Newborn
- Malaria, Vivax/epidemiology
- Malaria, Vivax/parasitology
- Male
- Nigeria/epidemiology
- Plasmodium vivax/classification
- Plasmodium vivax/genetics
- Plasmodium vivax/isolation & purification
- RNA, Ribosomal, 18S/genetics
- Receptors, Cell Surface/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Mary Aigbiremo Oboh
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal.
| | - Aida Sadikh Badiane
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Godwin Ntadom
- National Malaria Elimination Programme/Epidemiology Division, Department of Public Health, Federal Ministry of Health, Abuja, Nigeria
| | - Yaye Die Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Khadim Diongue
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Mamadou Alpha Diallo
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Daouda Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
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27
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Ahmed S, Zhou J, Zhou Z, Chen SQ. Genetic Polymorphisms and In Silico Mutagenesis Analyses of CYP2C9, CYP2D6, and CYPOR Genes in the Pakistani Population. Genes (Basel) 2018; 9:E514. [PMID: 30360443 PMCID: PMC6211126 DOI: 10.3390/genes9100514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/18/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022] Open
Abstract
Diverse distributions of pharmacogenetically relevant variants of highly polymorphic CYP2C9, CYP2D6 and CYPOR genes are responsible for some varied drug responses observed across human populations. There is limited data available regarding the pharmacogenetic polymorphisms and frequency distributions of major allele variants in the Pakistani population. The present in silico mutagenesis study conducted on genotype pharmacogenetic variants and comparative analysis with a global population aims to extend the currently limited pharmacogenetic available evidence for the indigenous Pakistani population. Extracted genomic DNA from 244 healthy individuals' venous blood samples were amplified for distinct variant loci in the CYP2C9, CYP2D6 and CYPOR genes. Two-way sequencing results were compared with standard PubMed data and sequence variant loci confirmed by Chromas. This study revealed significant variations in CYP2C9 (rs1799853, rs1057910 and rs72558189), CYP2D6 (rs16947 and rs1135840), and CYPOR (rs1057868, rs781919285 and rs562750402) variants in intraethnic and interethnic frequency distributions. In silico mutagenesis and three-dimensional protein structural alignment analysis approaches clearly exposed the possible varied impact of rare CYPOR (rs781919285 and rs562750402) single nucleotide polymorphisms (SNPs) and confirmed that the influences of CYP2C9 and CYP2D6 variants are consistent with what was found in earlier studies. This investigation highlighted the need to study pharmacogenetic relevance loci and documentation since evidence could be utilized to elucidate genetic backgrounds of drug metabolism, and provide a basis for future pharmacogenomic studies and adequate dose adjustments in Pakistani and global populations.
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Affiliation(s)
- Shabbir Ahmed
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jie Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Shu-Qing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
- International Center for Precision Medicine, Zhejiang California International NanoSystems Institute (ZCNI), Hangzhou 310058, China.
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28
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Yin Q, Srivastava K, Gebremedhin A, Makuria AT, Flegel WA. Long-range haplotype analysis of the malaria parasite receptor gene ACKR1 in an East-African population. Hum Genome Var 2018; 5:26. [PMID: 30245840 PMCID: PMC6138691 DOI: 10.1038/s41439-018-0024-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/13/2018] [Indexed: 12/18/2022] Open
Abstract
The human ACKR1 gene encodes a glycoprotein expressing the Duffy blood group antigens (Fy). The Duffy protein acts as a receptor for distinct pro-inflammatory cytokines and malaria parasites. We determined the haplotypes of the ACKR1 gene in a population inhabiting a malaria-endemic area. We collected blood samples from 60 healthy volunteers in Ethiopia’s southwestern low-altitude tropical region. An assay was devised to amplify the ACKR1 gene as a single amplicon and determine its genomic sequence. All haplotypes were resolved at 5178 nucleotides each, covering the coding sequence (CDS) of the ACKR1 gene and including the 5′- and 3′-untranslated regions (UTR), intron 1, and the 5′- and 3′-flanking regions. When necessary, allele-specific PCR with nucleotide sequencing or length polymorphism analysis was applied. Among the 120 chromosomes analyzed, 18 ACKR1 alleles were confirmed without ambiguity. We found 18 single-nucleotide polymorphisms (SNPs); only one SNP was novel. The non-coding sequences harbored 14 SNPs. No SNP, other than c.-67T>C, indicative of a non-functional allele, was detected. We described haplotypes of the ACKR1 gene in an autochthonous East-African population and found 18 distinct ACKR1 alleles. These long-range alleles are useful as templates to phase and analyze next-generation sequencing data, thus enhancing the reliability of clinical diagnostics. Researchers have surveyed genetic diversity related to malaria resistance in a region of Ethiopia where malaria is endemic. Duffy antigens, a component of blood type, are encoded by the ACKR1 gene, and individuals with the Duffy-negative blood type are resistant to malaria. Although the genes encoding resistant types have been identified, they have not been fully surveyed in malaria-endemic regions, where novel types are most likely to be found. Willy Flegel at the National Institutes of Health, Bethesda, USA, and co-workers sequenced ACKR1 in 60 people from Gambela, Ethiopia, where malaria is endemic. They detected 18 variants, including one never before documented. Almost all (16 of 18) of the variants encoded the Duffy-negative blood type. The authors plan to compare the genetic diversity in this region with a nearby region where malaria is not endemic.
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Affiliation(s)
- Qinan Yin
- 1Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Kshitij Srivastava
- 1Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD USA
| | | | - Addisalem Taye Makuria
- 1Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD USA.,3U.S. Food and Drug Administration, Silver Spring, MD USA
| | - Willy Albert Flegel
- 1Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD USA
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29
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Yao S, Hong CC, Ruiz-Narváez EA, Evans SS, Zhu Q, Schaefer BA, Yan L, Coignet MV, Lunetta KL, Sucheston-Campbell LE, Lee K, Bandera EV, Troester MA, Rosenberg L, Palmer JR, Olshan AF, Ambrosone CB. Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors. PLoS Genet 2018; 14:e1007368. [PMID: 29879116 PMCID: PMC5991662 DOI: 10.1371/journal.pgen.1007368] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/18/2018] [Indexed: 01/09/2023] Open
Abstract
Selection pressure due to exposure to infectious pathogens endemic to Africa may explain distinct genetic variations in immune response genes. However, the impact of those genetic variations on human immunity remains understudied, especially within the context of modern lifestyles and living environments, which are drastically different from early humans in sub Saharan Africa. There are few data on population differences in constitutional immune environment, where genetic ancestry and environment are likely two primary sources of variation. In a study integrating genetic, molecular and epidemiologic data, we examined population differences in plasma levels of 14 cytokines involved in innate and adaptive immunity, including those implicated in chronic inflammation, and possible contributing factors to such differences, in 914 AA and 855 EA women. We observed significant differences in 7 cytokines, including higher plasma levels of CCL2, CCL11, IL4 and IL10 in EAs and higher levels of IL1RA and IFNα2 in AAs. Analyses of a wide range of demographic and lifestyle factors showed significant impact, with age, education level, obesity, smoking, and alcohol intake, accounting for some, but not all, observed population differences for the cytokines examined. Levels of two pro-inflammatory chemokines, CCL2 and CCL11, were strongly associated with percent of African ancestry among AAs. Through admixture mapping, the signal was pinpointed to local ancestry at 1q23, with fine-mapping analysis refined to the Duffy-null allele of rs2814778. In AA women, this variant was a major determinant of systemic levels of CCL2 (p = 1.1e-58) and CCL11 (p = 2.2e-110), accounting for 19% and 40% of the phenotypic variance, respectively. Our data reveal strong ancestral footprints in inflammatory chemokine regulation. The Duffy-null allele may indicate a loss of the buffering function for chemokine levels. The substantial immune differences by ancestry may have broad implications to health disparities between AA and EA populations.
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Affiliation(s)
- Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Edward A. Ruiz-Narváez
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States of America
| | - Sharon S. Evans
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Beverly A. Schaefer
- Department of Pediatric Hematology & Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
- Department of Pediatric Hematology & Oncology, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, United States of America
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Marie V. Coignet
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | | | - Kelvin Lee
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
| | - Elisa V. Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, The State University of New Jersey, New Brunswick, NJ, United States of America
| | - Melissa A. Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Lynn Rosenberg
- Slone Epidemiology Center at Boston University, Boston, MA, United States of America
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, United States of America
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States of America
- * E-mail:
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30
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Cazzola M, Calzetta L, Matera MG, Hanania NA, Rogliani P. How does race/ethnicity influence pharmacological response to asthma therapies? Expert Opin Drug Metab Toxicol 2018. [DOI: 10.1080/17425255.2018.1449833] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mario Cazzola
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Luigino Calzetta
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Maria Gabriella Matera
- Department of Experimental Medicine, Unit of Pharmacology, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Nicola A Hanania
- Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paola Rogliani
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
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Pierron D, Heiske M, Razafindrazaka H, Pereda-Loth V, Sanchez J, Alva O, Arachiche A, Boland A, Olaso R, Deleuze JF, Ricaut FX, Rakotoarisoa JA, Radimilahy C, Stoneking M, Letellier T. Strong selection during the last millennium for African ancestry in the admixed population of Madagascar. Nat Commun 2018; 9:932. [PMID: 29500350 PMCID: PMC5834599 DOI: 10.1038/s41467-018-03342-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/06/2018] [Indexed: 01/24/2023] Open
Abstract
While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.
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Affiliation(s)
- Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France.
| | - Margit Heiske
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
- Aix Marseille Univ., CNRS, EFS, ADES, Marseille, France
| | - Veronica Pereda-Loth
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Jazmin Sanchez
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Omar Alva
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Amal Arachiche
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000, Evry, France
| | - Robert Olaso
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000, Evry, France
| | - Jean-Francois Deleuze
- Commissariat à l'Energie Atomique, Institut Génomique, Centre National de Génotypage, 91000, Evry, France
| | - Francois-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
| | - Jean-Aimé Rakotoarisoa
- Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, 101, Antananarivo, Madagascar
| | - Chantal Radimilahy
- Institut de Civilisations/Musée d'Art et d'Archéologie, Université d'Antananarivo, 101, Antananarivo, Madagascar
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288 CNRS, Université de Toulouse, 31073, Toulouse, France
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Laso-Jadart R, Harmant C, Quach H, Zidane N, Tyler-Smith C, Mehdi Q, Ayub Q, Quintana-Murci L, Patin E. The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan. Am J Hum Genet 2017; 101:977-984. [PMID: 29129317 DOI: 10.1016/j.ajhg.2017.09.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022] Open
Abstract
From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their history of admixture and natural selection remains largely undefined. Here, we studied the genome-wide diversity of the African-descent Makranis, who reside on the Arabian Sea coast of Pakistan, as well that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics, and tempo of the Indian Ocean slave trade. We show that the Makranis are the result of an admixture event between local Baluch tribes and Bantu-speaking populations from eastern or southeastern Africa; we dated this event to ∼300 years ago during the Omani Empire domination. Levels of parental relatedness, measured through runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at traits evolving under positive selection, including skin color, lactase persistence, and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group-believed to confer resistance against Plasmodium vivax infection-was recently introduced to Pakistan through the slave trade and evolved adaptively in this P. vivax malaria-endemic region. Our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations.
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Han C, Li Q, Zhang Z, Huang J. Characterization, expression, and evolutionary analysis of new TLR3 and TLR5M genes cloned from the spiny eel Mastacembelus armatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:174-187. [PMID: 28821419 DOI: 10.1016/j.dci.2017.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/12/2017] [Accepted: 08/13/2017] [Indexed: 06/07/2023]
Abstract
Toll-like receptors (TLRs) play an important role in innate and adaptive immunity. Here, we identify two new TLRs from the spiny eel Mastacembelus armatus (TLR3 and membrane TLR5M). Both MaTLR3 and MaTLR5M were expressed in all tested tissues; expression was highest in liver and spleen, respectively. After infection with Vibrio parahaemolyticus, expression of both TLRs fluctuated and differed significantly from controls at several time points. The predicted three-dimensional model of the MaTLR3 and MaTLR5M proteins indicates that most sites under positive selection were located in the extracellular domains of TLRs. Evolutionary analysis detected positively selected sites in the ancestral lineages of vertebrates, amphibians and reptiles. Multiple ML methods recovered 10 positively selected sites in teleost TLR3 and 24 in TLR5M, and most sites were located in leucine-rich repeat domain, possibly related to an "arms-race" co-evolution with pathogens.
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Affiliation(s)
- Chong Han
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Qiang Li
- School of Life Sciences, Guangzhou University, Guangzhou, PR China
| | - Zhipeng Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Jianrong Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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34
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Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol 2017; 9:3478-3494. [PMID: 29220486 PMCID: PMC5751042 DOI: 10.1093/gbe/evx259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 12/26/2022] Open
Abstract
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
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35
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Byars SG, Huang QQ, Gray LA, Bakshi A, Ripatti S, Abraham G, Stearns SC, Inouye M. Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. PLoS Genet 2017; 13:e1006328. [PMID: 28640878 PMCID: PMC5480811 DOI: 10.1371/journal.pgen.1006328] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.
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Affiliation(s)
- Sean G. Byars
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Qin Qin Huang
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Lesley-Ann Gray
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Bakshi
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Samuli Ripatti
- Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gad Abraham
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stephen C. Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Michael Inouye
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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36
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Quach H, Quintana-Murci L. Living in an adaptive world: Genomic dissection of the genus Homo and its immune response. J Exp Med 2017; 214:877-894. [PMID: 28351985 PMCID: PMC5379985 DOI: 10.1084/jem.20161942] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/14/2017] [Accepted: 03/06/2017] [Indexed: 12/14/2022] Open
Abstract
More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.
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Affiliation(s)
- Hélène Quach
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France .,Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique, URA3012, 75015 Paris, France
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37
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McManus KF, Taravella AM, Henn BM, Bustamante CD, Sikora M, Cornejo OE. Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans. PLoS Genet 2017; 13:e1006560. [PMID: 28282382 PMCID: PMC5365118 DOI: 10.1371/journal.pgen.1006560] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 03/24/2017] [Accepted: 12/30/2016] [Indexed: 12/22/2022] Open
Abstract
The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans. Despite this, details of the timing and mode of selection at DARC remain poorly understood. Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human genomes, to perform a fine-scale investigation of the evolutionary history of DARC. We estimate the time to most recent common ancestor (TMRCA) of the most common FY*O haplotype to be 42 kya (95% CI: 34-49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011-0.18), which is among the strongest estimated in the human genome. We estimate the TMRCA of the FY*A mutation in non-Africans to be 57 kya (95% CI: 48-65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause.
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Affiliation(s)
- Kimberly F. McManus
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Angela M. Taravella
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Brenna M. Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Carlos D. Bustamante
- Department of Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Martin Sikora
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Centre for Geogenetics, Natural History Museum Denmark, Copenhagen, Denmark
| | - Omar E. Cornejo
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Biological Sciences, Washington State University, Pullman, washington, United States of America
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38
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Molecular basis of the Duffy blood group system. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2017; 16:93-100. [PMID: 28151395 DOI: 10.2450/2017.0119-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 12/21/2016] [Indexed: 11/21/2022]
Abstract
ACKR1, located on chromosome 1q23.2, is the gene that encodes a glycoprotein expressing the Duffy blood group antigens. This gene is transcribed in two mRNA variants yielding two isoforms, encoding proteins with 338 and 336 amino acids. This review provides a general overview of the Duffy blood group to characterise and elucidate the genetic basis of this system. The Fya and Fyb antigens are encoded by co-dominant FY*A (FY*01) and FY*B (FY*02) alleles, which differ by c.125G>A (rs12075), defining the Fy(a+b-), Fy(a-b+) and Fy(a+b+) phenotypes. The Fy(a-b-) phenotype that occurs in Africans provides an explanation for the apparent absence of Plasmodium vivax in this region: this phenotype arises from homozygosity for the FY*B allele carrying a point mutation c.1-67T>C (rs2814778), which prevents Fyb antigen expression only in red blood cells. The same mutation has also been found on the FY*A allele, but it is very rare. The Fy(a-b-) phenotype in Europeans and Asians arises from mutations in the coding region of the FY*A or FY*B allele, preventing Duffy antigen expression on any cell in the body and thus are true Duffy null phenotypes. According to the International Society for Blood Transfusion, ten alleles are associated with the null expression of the Fy antigens. Furthermore, different allelic forms of FY*B modify Fyb antigen expression, which may result in very weak or equivocal serology results. The mostly common found variants, c.265C>T (rs34599082) and c.298G>A (rs13962) -previously defined in combination only with the FY*B allele - have already been observed in the FY*A allele. Thus, six alleles have been recognised and associated with weak expression of the Fy antigens. Considering the importance of the Duffy blood group system in clinical medicine, additional studies via molecular biology approaches must be performed to resolve and clarify the discrepant results that are present in the erythrocyte phenotyping.
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Roche B, Rougeron V, Quintana-Murci L, Renaud F, Abbate JL, Prugnolle F. Might Interspecific Interactions between Pathogens Drive Host Evolution? The Case of Plasmodium Species and Duffy-Negativity in Human Populations. Trends Parasitol 2017; 33:21-29. [DOI: 10.1016/j.pt.2016.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/06/2016] [Accepted: 09/23/2016] [Indexed: 12/27/2022]
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40
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Sulovari A, Chen YH, Hudziak JJ, Li D. Atlas of human diseases influenced by genetic variants with extreme allele frequency differences. Hum Genet 2016; 136:39-54. [PMID: 27699474 DOI: 10.1007/s00439-016-1734-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/27/2016] [Indexed: 12/22/2022]
Abstract
Genetic variants with extreme allele frequency differences (EAFD) may underlie some human health disparities across populations. To identify EAFD loci, we systematically analyzed and characterized 81 million genomic variants from 2504 unrelated individuals of 26 world populations (phase III of the 1000 Genomes Project). Our analyses revealed a total of 434 genes, 15 pathways, and 18 diseases and traits influenced by EAFD variants from five continental populations. They included known EAFD genes, such as LCT (lactose tolerance), SLC24A5 (skin pigmentation), and EDAR (hair morphology). We found many novel EAFD genes, including TBC1D2B (autophagy mediator), TRIM40 (gastrointestinal inflammatory regulator), KRT71, KRT75, KRT83, and KRTAP10-1 (hair and epithelial keratin synthesis), PIK3R3 (insulin receptor interaction), DARS (neurological disorders), and NACA2 (skin inflammatory response). Our results also showed four complex diseases significantly associated with EAFD loci, including asthma (adjusted enrichment P = 4 × 10-8), type I diabetes (P = 6 × 10-9), alcohol consumption (P = 0.0002), and attention deficit/hyperactivity disorder (P = 0.003). This study provides a comprehensive atlas of genes, pathways, and human diseases significantly influenced by EAFD variants.
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Affiliation(s)
- Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA
| | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA
| | - James J Hudziak
- Vermont Center for Children, Youth, and Families, Department of Psychiatry, University of Vermont, Burlington, VT, 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA. .,Department of Computer Science, University of Vermont, Burlington, VT, 05405, USA. .,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, 05405, USA.
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41
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Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC. Admixture into and within sub-Saharan Africa. eLife 2016; 5. [PMID: 27324836 PMCID: PMC4915815 DOI: 10.7554/elife.15266] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI:http://dx.doi.org/10.7554/eLife.15266.002
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Affiliation(s)
- George Bj Busby
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit, Serrekunda, The Gambia.,Royal Victoria Teaching Hospital, Banjul, The Gambia
| | - Edith Bougama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Valentina D Mangano
- Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ogobara Doumba
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Chris Ca Spencer
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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Duforet-Frebourg N, Luu K, Laval G, Bazin E, Blum MGB. Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data. Mol Biol Evol 2016; 33:1082-93. [PMID: 26715629 PMCID: PMC4776707 DOI: 10.1093/molbev/msv334] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis (PCA). We show that the common FST index of genetic differentiation between populations can be viewed as the proportion of variance explained by the principal components. Considering the correlations between genetic variants and each principal component provides a conceptual framework to detect genetic variants involved in local adaptation without any prior definition of populations. To validate the PCA-based approach, we consider the 1000 Genomes data (phase 1) considering 850 individuals coming from Africa, Asia, and Europe. The number of genetic variants is of the order of 36 millions obtained with a low-coverage sequencing depth (3×). The correlations between genetic variation and each principal component provide well-known targets for positive selection (EDAR, SLC24A5, SLC45A2, DARC), and also new candidate genes (APPBPP2, TP1A1, RTTN, KCNMA, MYO5C) and noncoding RNAs. In addition to identifying genes involved in biological adaptation, we identify two biological pathways involved in polygenic adaptation that are related to the innate immune system (beta defensins) and to lipid metabolism (fatty acid omega oxidation). An additional analysis of European data shows that a genome scan based on PCA retrieves classical examples of local adaptation even when there are no well-defined populations. PCA-based statistics, implemented in the PCAdapt R package and the PCAdapt fast open-source software, retrieve well-known signals of human adaptation, which is encouraging for future whole-genome sequencing project, especially when defining populations is difficult.
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Affiliation(s)
- Nicolas Duforet-Frebourg
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France Department of Integrative Biology, University of California, Berkeley
| | - Keurcien Luu
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France
| | - Guillaume Laval
- Department of Genomes and Genetics, Institut Pasteur, Human Evolutionary Genetics, Paris, France Centre National De La Recherche Scientifique, URA3012, Paris, France
| | - Eric Bazin
- CNRS, Laboratoire D'ecologie Alpine UMR 5553, Univ. Grenoble Alpes, Grenoble, France
| | - Michael G B Blum
- TIMC-IMAG UMR 5525, Univ. Grenoble Alpes, Grenoble, France CNRS, TIMC-IMAG, Grenoble, France
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43
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Fujikura K. Premature termination codons in modern human genomes. Sci Rep 2016; 6:22468. [PMID: 26932450 PMCID: PMC4773809 DOI: 10.1038/srep22468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 01/14/2016] [Indexed: 12/16/2022] Open
Abstract
The considerable range of genetic variation in human populations may partly reflect distinctive processes of adaptation to variable environmental conditions. However, the adaptive genomic signatures remain to be completely elucidated. This research explores candidate loci under selection at the population level by characterizing recently arisen premature termination codons (PTCs), some of which indicate a human knockout. From a total of 7595 participants from two population exome projects, 246 PTCs were found where natural selection has resulted in new alleles with a high frequency (from 1% to 96%) of derived alleles and various levels of population differentiation (FST = 0.00139–0.626). The PTC genes formed protein and regulatory networks limited to 15 biological processes or gene families, of which seven categories were previously unreported. PTC mutations have a strong tendency to be introduced into members of the same gene family, even during modern human evolution, although the exact nature of the selection is not fully known. The findings here suggest the ongoing evolutionary plasticity of modern humans at the genetic level and also partly provide insights into common human knockouts.
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Affiliation(s)
- Kohei Fujikura
- Kobe University School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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44
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Hodgson JA, Pickrell JK, Pearson LN, Quillen EE, Prista A, Rocha J, Soodyall H, Shriver MD, Perry GH. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar. Proc Biol Sci 2015; 281:20140930. [PMID: 24990677 DOI: 10.1098/rspb.2014.0930] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.
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Affiliation(s)
- Jason A Hodgson
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Joseph K Pickrell
- New York Genome Center, New York, NY 10013, USA Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Laurel N Pearson
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ellen E Quillen
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78245, USA
| | - António Prista
- Faculdade de Educação Física e Desporto, Universidade Pedagógica, Maputo, Moçambique
| | - Jorge Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO), Vairão, Portugal Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Himla Soodyall
- Human Genomic Diversity and Disease Research Unit, Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - George H Perry
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Jha P, Lu D, Yuan Y, Xu S. Signature of positive selection of PTK6 gene in East Asian populations: a cross talk for Helicobacter pylori invasion and gastric cancer endemicity. Mol Genet Genomics 2015; 290:1741-52. [PMID: 25838168 DOI: 10.1007/s00438-015-1032-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 03/20/2015] [Indexed: 01/22/2023]
Abstract
Analysis of natural selection events is an attractive strategy for identification of functional variants shaped by gene-environmental interactions and human adaptation. Here, we identified PTK6, a Src-related tyrosine kinase gene, underlying positive selection in East Asian populations. Interestingly, PTK6 variant showed significant correlation with gastric cancer incidences which was the highest in East Asian populations. The high prevalence of gastric cancer in East Asians was also believed to be strongly affected by Helicobacter pylori infection and dietary habit. Therefore, we speculated a competitive interaction of cancer-associated molecules for activation/reduction, where PTK6 likely plays a role through CagA-driven signaling pathway after H. pylori infection. This hypothesis was also supported by our gene expression analysis and the dating of the selective event which was estimated to be ~16,500 years ago, much later than H. pylori invasion in human 50,000 years ago. Establishment of cross talk between PTK6 and CagA by functional studies may further elucidate the underlying biology of H. pylori-mediated gastric cancer.
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Affiliation(s)
- Pankaj Jha
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dongsheng Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuan Yuan
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTec University, Shanghai, 200031, China.
- Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China.
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Beltrán NAR, Meira CT, de Oliveira HN, Pereira GL, Silva JAIIV, da Mota MDS, Curi RA. Prospection of genomic regions divergently selected in cutting line of Quarter Horses in relation to racing line. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps. Genetics 2015; 200:267-84. [PMID: 25716978 DOI: 10.1534/genetics.115.174912] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
Characterizing the nature of the adaptive process at the genetic level is a central goal for population genetics. In particular, we know little about the sources of adaptive substitution or about the number of adaptive variants currently segregating in nature. Historically, population geneticists have focused attention on the hard-sweep model of adaptation in which a de novo beneficial mutation arises and rapidly fixes in a population. Recently more attention has been given to soft-sweep models, in which alleles that were previously neutral, or nearly so, drift until such a time as the environment shifts and their selection coefficient changes to become beneficial. It remains an active and difficult problem, however, to tease apart the telltale signatures of hard vs. soft sweeps in genomic polymorphism data. Through extensive simulations of hard- and soft-sweep models, here we show that indeed the two might not be separable through the use of simple summary statistics. In particular, it seems that recombination in regions linked to, but distant from, sites of hard sweeps can create patterns of polymorphism that closely mirror what is expected to be found near soft sweeps. We find that a very similar situation arises when using haplotype-based statistics that are aimed at detecting partial or ongoing selective sweeps, such that it is difficult to distinguish the shoulder of a hard sweep from the center of a partial sweep. While knowing the location of the selected site mitigates this problem slightly, we show that stochasticity in signatures of natural selection will frequently cause the signal to reach its zenith far from this site and that this effect is more severe for soft sweeps; thus inferences of the target as well as the mode of positive selection may be inaccurate. In addition, both the time since a sweep ends and biologically realistic levels of allelic gene conversion lead to errors in the classification and identification of selective sweeps. This general problem of "soft shoulders" underscores the difficulty in differentiating soft and partial sweeps from hard-sweep scenarios in molecular population genomics data. The soft-shoulder effect also implies that the more common hard sweeps have been in recent evolutionary history, the more prevalent spurious signatures of soft or partial sweeps may appear in some genome-wide scans.
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Lo E, Yewhalaw D, Zhong D, Zemene E, Degefa T, Tushune K, Ha M, Lee MC, James AA, Yan G. Molecular epidemiology of Plasmodium vivax and Plasmodium falciparum malaria among Duffy-positive and Duffy-negative populations in Ethiopia. Malar J 2015; 14:84. [PMID: 25884875 PMCID: PMC4340780 DOI: 10.1186/s12936-015-0596-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/30/2015] [Indexed: 11/28/2022] Open
Abstract
Background Malaria is the most prevalent communicable disease in Ethiopia, with 75% of the country’s landmass classified as endemic for malaria. Accurate information on the distribution and clinical prevalence of Plasmodium vivax and Plasmodium falciparum malaria in endemic areas, as well as in Duffy-negative populations, is essential to develop integrated control strategies. Methods A total of 390 and 416 community and clinical samples, respectively, representing different localities and age groups across Ethiopia were examined. Malaria prevalence was estimated using nested PCR of the 18S rRNA region. Parasite gene copy number was measured by quantitative real-time PCR and compared between symptomatic and asymptomatic samples, as well as between children/adolescents and adults from the local community. An approximately 500-bp segment of the human DARC gene was amplified and sequenced to identify Duffy genotype at the -33rd nucleotide position for all the clinical and community samples. Results Plasmodium vivax prevalence was higher in the south while P. falciparum was higher in the north. The prevalence of P. vivax and P. falciparum malaria is the highest in children compared to adolescents and adults. Four P. vivax infections were detected among the Duffy-negative samples. Samples from asymptomatic individuals show a significantly lower parasite gene copy number than those from symptomatic infections for P. vivax and P. falciparum. Conclusions Geographical and age differences influence the distribution of P. vivax and P. falciparum malaria in Ethiopia. These findings offer evidence-based guidelines in targeting malaria control efforts in the country. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0596-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugenia Lo
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Endalew Zemene
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Teshome Degefa
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Kora Tushune
- Department of Health Services Management, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Margaret Ha
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Anthony A James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
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Chen H, Hey J, Slatkin M. A hidden Markov model for investigating recent positive selection through haplotype structure. Theor Popul Biol 2015; 99:18-30. [PMID: 25446961 PMCID: PMC4277924 DOI: 10.1016/j.tpb.2014.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 10/24/2014] [Accepted: 11/04/2014] [Indexed: 12/17/2022]
Abstract
Recent positive selection can increase the frequency of an advantageous mutant rapidly enough that a relatively long ancestral haplotype will be remained intact around it. We present a hidden Markov model (HMM) to identify such haplotype structures. With HMM identified haplotype structures, a population genetic model for the extent of ancestral haplotypes is then adopted for parameter inference of the selection intensity and the allele age. Simulations show that this method can detect selection under a wide range of conditions and has higher power than the existing frequency spectrum-based method. In addition, it provides good estimate of the selection coefficients and allele ages for strong selection. The method analyzes large data sets in a reasonable amount of running time. This method is applied to HapMap III data for a genome scan, and identifies a list of candidate regions putatively under recent positive selection. It is also applied to several genes known to be under recent positive selection, including the LCT, KITLG and TYRP1 genes in Northern Europeans, and OCA2 in East Asians, to estimate their allele ages and selection coefficients.
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Affiliation(s)
- Hua Chen
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Center for Computational Genetics and Genomics, Temple University, Philadelphia PA 19122, United States.
| | - Jody Hey
- Center for Computational Genetics and Genomics, Temple University, Philadelphia PA 19122, United States.
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720, United States.
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50
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Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Hum Genet 2015; 134:375-92. [PMID: 25634076 DOI: 10.1007/s00439-014-1525-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 12/25/2014] [Indexed: 10/24/2022]
Abstract
The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
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