Research Topics
Genomes and Genes | Dominic P KwiatkowskiSummaryAffiliation: University of Oxford Country: UK Publications
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Publications
Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samplesMeera Venkatesan
Howard Hughes Medical Institute, University of Maryland School of Medicine, Baltimore, MD, USA
Malar J 11:41. 2012..This study was undertaken to determine whether CF11 columns could be adapted to isolate Plasmodium falciparum DNA from parasitized whole blood and achieve current quantity and purity requirements for Illumina sequencing...- Host candidate gene polymorphisms and clearance of drug-resistant Plasmodium falciparum parasitesMahamadou Diakite
Malaria Research and Training Centre, Faculty of Medicine, Pharmacy and Odontostomatology, University of Bamako, Mali
Malar J 10:250. 2011..This study aimed to identify molecular markers in the human genome that correlate with the clearance of malaria parasites after drug treatment, despite the drug resistance profile of the protozoan as predicted by molecular approaches... - Innate immunity in ocular Chlamydia trachomatis infection: contribution of IL8 and CSF2 gene variants to risk of trachomatous scarring in GambiansAngels Natividad
London School of Hygiene and Tropical Medicine, London University, London, UK
BMC Med Genet 10:138. 2009.... - Large-scale association analysis of TNF/LTA gene region polymorphisms in type 2 diabetesVesna Boraska
Department of Medical Biology, University of Split School of Medicine, Split, Croatia
BMC Med Genet 11:69. 2010..The purpose of this study is to examine T2D association of tag SNPs in the TNF/LTA region capturing the majority of common variation in a large-scale sample set of UK/Irish origin... 
Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populationsNeil Hanchard
Tropical Metabolism Research Unit, Tropical Medicine Research Institute, University of the West Indies, Kingston, Jamaica
BMC Genet 8:52. 2007..Here we evaluate the haplotype similarity of classical betas haplotypes over 400 kb in population samples from Jamaica, The Gambia, and among the Yoruba of Nigeria (Hapmap YRI)...- How malaria has affected the human genome and what human genetics can teach us about malariaDominic P Kwiatkowski
Wellcome Trust Centre for Human Genetics and University Department of Paediatrics, Oxford, United Kingdom
Am J Hum Genet 77:171-92. 2005.... 
The complexity of genetic variation in a simple immune systemDominic P Kwiatkowski
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK OX3 7BN
Trends Genet 21:197-9. 2005..However, the effects of individual polymorphisms on the resistance phenotype were modest, and epistatic interactions appeared to be common. What might these findings tell us about genetic resistance to infection in humans?..- TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expressionSusana Campino
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Malar J 8:44. 2009..Although TLR9 activation by malaria parasites is well reported, the implication to the susceptibility to severe malaria is not clear. The aim of this study was to assess the contribution of genetic variation at TLR9 to severe malaria... - Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populationsTaane G Clark
Wellcome Trust Centre for Human Genetics, University of Oxford, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
J Infect Dis 199:569-75. 2009..Therefore, more-detailed mapping of variants across TNF/LTA genes and their flanking regions in the Gambian and allied populations may need to be undertaken to find any causal polymorphisms... - Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populationsValentina D Mangano
Childhood Infection Group, The Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
PLoS ONE 4:e4206. 2009..Our results offer no evidence that the molecular pathways regulated by the transcription factor IRF-1 are involved in the immune-based pathogenesis of severe malaria... - Association of the GNAS locus with severe malariaSarah Auburn
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
Hum Genet 124:499-506. 2008..88 (0.81-0.96), P = 0.005 and OR = 1.12 (1.03-1.20), P = 0.005]. The evidence presented here indicates that the influence of G-alpha-s on erythrocyte invasion efficacy may, indeed, alter individual susceptibility to disease... - Assessing genuine parents-offspring trios for genetic association studiesYik Y Teo
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Hum Hered 67:26-37. 2009..Here, we introduce a method for evaluating the authenticity of nuclear family trios... - Further evidence supporting a role for gs signal transduction in severe malaria pathogenesisSarah Auburn
Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
PLoS ONE 5:e10017. 2010..Our results provide further evidence supporting a role of the Gs signal transduction pathway in the regulation of severe malaria, and request further exploration of this pathway in future studies... - Genome-wide comparisons of variation in linkage disequilibriumYik Y Teo
Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
Genome Res 19:1849-60. 2009.... - Positive selection of a CD36 nonsense variant in sub-Saharan Africa, but no association with severe malaria phenotypesAndrew E Fry
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
Hum Mol Genet 18:2683-92. 2009..98). These results suggest a range of possible explanations including the existence of alternative selection pressures on CD36, co-evolution between host and parasite or confounding caused by allelic heterogeneity of CD36 deficiency... - Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populationsSusana Campino
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
PLoS ONE 3:e4105. 2008..A complementary approach is to use an Allele-Specific Expression (ASE) assay, which is more robust to the effects of environmental variation and trans-acting genetic factors... 
Methodological challenges of genome-wide association analysis in AfricaYik Ying Teo
Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
Nat Rev Genet 11:149-60. 2010..We review the methodological challenges and consider how GWA studies in Africa will be transformed by new approaches in statistical imputation and large-scale genome sequencing...- Power consequences of linkage disequilibrium variation between populationsYik Y Teo
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Genet Epidemiol 33:128-35. 2009.... - Screening for recently selected alleles by analysis of human haplotype similarityNeil A Hanchard
Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
Am J Hum Genet 78:153-9. 2006..Using this method, we also evaluated >4,000 SNPs on chromosome 20, indicating the applicability of the method to regional data sets... - Association of Fcgamma receptor IIa (CD32) polymorphism with severe malaria in West AfricaGraham S Cooke
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
Am J Trop Med Hyg 69:565-8. 2003..This is the first evidence for an association between CD32 polymorphism and severe malaria and provides an example of balancing selective pressures from different infectious diseases operating at the same genetic locus... - Haplotype homozygosity and derived alleles in the human genomeAndrew E Fry
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
Am J Hum Genet 78:1053-9. 2006..Our results support the use of haplotype-based techniques, such as extended haplotypic homozygosity, to assess the age of alleles... - Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patientsTimothy Robinson
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
PLoS ONE 6:e23204. 2011..falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity... - Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malariaAndrew E Fry
The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
Hum Mol Genet 17:567-76. 2008..5-99.9th centile). This low F(ST) region may be a signal of long-standing balancing selection at the ABO locus, caused by multiple infectious pathogens including P. falciparum... - Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mappingJulian T Forton
Department of Paediatrics, Oxford University, Oxford OX3 7BN, United Kingdom
Genome Res 17:82-7. 2007..As this method is unaffected by other sources of variation, such as environmental and trans-acting genetic factors, it provides a tractable approach for dissecting the complexities of genetic variation in gene regulation... - Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibilityTaane G Clark
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Eur J Hum Genet 17:1080-5. 2009..Our results highlight some of the consequences of allelic heterogeneity, particularly the increased type I error. They also suggest that G6PD-deficient male hemizygotes and female heterozygotes are protected from severe malaria... - Allele-specific repression of lymphotoxin-alpha by activated B cell factor-1Julian C Knight
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
Nat Genet 36:394-9. 2004..These findings provide a molecular model of how LTA expression may be genetically regulated by allele-specific recruitment of the transcriptional repressor ABF-1... - Haplotype mapping of the bronchiolitis susceptibility locus near IL8Jeremy Hull
University Department of Paediatrics, Level 4, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
Hum Genet 114:272-9. 2004..In between these two genes there is only one structural feature of interest, a novel gene RASSF6, which is predicted to encode a Ras effector protein... - In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loadingJulian C Knight
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
Nat Genet 33:469-75. 2003..The haploChIP method may be useful in high-throughput screening for common DNA polymorphisms that affect gene regulation in vivo... - Tumor necrosis factor SNP haplotypes are associated with iron deficiency anemia in West African childrenSarah H Atkinson
Medical Research Council MRC Keneba and MRC Laboratories, Banjul, The Gambia
Blood 112:4276-83. 2008..Thus, TNF appears to be a risk factor for iron deficiency and IDA in children in a malaria-endemic environment and this is likely to be due to a TNF-alpha-induced block in iron absorption... - Valid consent for genomic epidemiology in developing countriesDave A Chokshi
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
PLoS Med 4:e95. 2007 - A genotype calling algorithm for the Illumina BeadArray platformYik Y Teo
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Bioinformatics 23:2741-6. 2007..As the technology moves towards assaying millions of genetic polymorphisms simultaneously, there is a need for an integrated and easy-to-use software for calling genotypes... - Genomewide analysis of the host response to malaria in Kenyan childrenMichael J Griffiths
Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
J Infect Dis 191:1599-611. 2005..The delineation of subjects on the basis of patterns of gene expression provides a molecular perspective of the host response to malaria and further functional insight into the underlying processes of pathogenesis... - Nucleotide and haplotypic diversity of the NOS2A promoter region and its relationship to cerebral malariaDavid Burgner
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX2 7BN, UK
Hum Genet 112:379-86. 2003..Despite high linkage disequilibrium across the region studied, this association would not have been detected without the initial construction of a dense marker set for haplotype tagging... - Data sharing and intellectual property in a genomic epidemiology network: policies for large-scale research collaborationDave A Chokshi
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England
Bull World Health Organ 84:382-7. 2006..We outline some pragmatic solutions founded on the basic principles of promoting innovation and access... - Haptoglobin genotype, anaemia and malaria in Gambian childrenSharon E Cox
MRC International Nutrition Group, London School of Hygiene and Tropical Medicine, UK
Trop Med Int Health 13:76-82. 2008..To retest our previous finding that the haptoglobin (Hp) 22 genotype is associated with seasonal anaemia, and to investigate the role of malaria in this effect... - Searching for the regulators of human gene expressionJulian T Forton
Department of Paediatrics, University of Oxford, UK
Bioessays 28:968-72. 2006..This work gives new insights into the complexities of gene regulation and the plausibility of genome-wide study design... - A coding polymorphism in matrix metalloproteinase 9 reduces risk of scarring sequelae of ocular Chlamydia trachomatis infectionAngels Natividad
London School of Hygiene and Tropical Medicine, London University, London, UK
BMC Med Genet 7:40. 2006..Genetic variation within the MMP9 gene affects in vitro MMP9 expression levels, enzymatic activity and susceptibility to various inflammatory and fibrotic conditions... - Seasonal childhood anaemia in West Africa is associated with the haptoglobin 2-2 genotypeSarah H Atkinson
Medical Research Council Laboratories, Banjul, The Gambia
PLoS Med 3:e172. 2006..Previous studies examined the importance of haptoglobin polymorphism in malaria and iron homeostasis, but it is unknown whether haptoglobin genotype might be a risk factor for anaemia in children in a malaria-endemic area... - Whole genome-amplified DNA: insights and imputationYik Y Teo
Nat Methods 5:279-80. 2008 - Quantitative high-throughput analysis of transcription factor binding specificitiesJane Linnell
Wellcome Trust Centre for Human Genetics, University of Oxford, 7 Roosevelt Drive, Oxford OX3 7BN, UK
Nucleic Acids Res 32:e44. 2004..This approach offers the potential for high-throughput determination of TF binding profiles and predicting the effects of single nucleotide polymorphisms on TF binding affinity. New DNA binding data for OCT-1 are presented... - A Mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosisChiea C Khor
The Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Nat Genet 39:523-8. 2007..6 x 10(-8)). We found that the Mal S180L variant attenuated TLR2 signal transduction... - Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetesEleftheria Zeggini
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
Science 316:1336-41. 2007..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes... - Severe anemia in Malawian childrenJob C J Calis
Malawi Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
N Engl J Med 358:888-99. 2008..Severe anemia is a major cause of sickness and death in African children, yet the causes of anemia in this population have been inadequately studied... - Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's diseaseSheila A Fisher
Department of Medical and Molecular Genetics, King s College London School of Medicine, 8th Floor Guy s Tower, Guy s Hospital, London SE1 9RT, UK
Nat Genet 40:710-2. 2008..These data provide the first detailed illustration of the genetic relationship between these common inflammatory bowel diseases... - Common variants near MC4R are associated with fat mass, weight and risk of obesityRuth J F Loos
MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
Nat Genet 40:768-75. 2008.... - Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variantsPaul R Burton
Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
Nat Genet 39:1329-37. 2007.... - Host genetic factors in resistance and susceptibility to malariaDominic P Kwiatkowski
Parassitologia 48:450-67. 2006 - Haplotypic analysis of the TNF locus by association efficiency and entropyHans Ackerman
Wellcome Trust for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
Genome Biol 4:R24. 2003..3 kilobases in 296 healthy, unrelated Gambian and Malawian adults. We generated 592 high-quality haplotypes by integrating family- and population-based reconstruction methods... - New interventions for malaria: mining the human and parasite genomesFrancine Ntoumi
Research Unit, Hopital Albert Schweitzer, Lambarene, Gabon
Am J Trop Med Hyg 77:270-5. 2007..However, genomics studies of human populations raise important ethical issues, such as the disposition of data related to disease susceptibility or paternity, and the ability of communities to understand the nature of the research... - Context-specific functional effects of IFNGR1 promoter polymorphismOliver Koch
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
Hum Mol Genet 15:1475-81. 2006..These findings suggest a mechanism by which a single genetic variant may cause a broad range of phenotypic consequences... - Investigation of familial segregation of hyperreactive malarial splenomegaly in Kumasi, GhanaRuby Martin-Peprah
Department of Medicine, Komfo Anokye Teaching Hospital, P O Box 1934, Kumasi, Ghana
Trans R Soc Trop Med Hyg 100:68-73. 2006..HMS aetiology in Ghana is likely to be complex, involving multiple genetic and environmental factors... - Susceptibility to sequelae of human ocular chlamydial infection associated with allelic variation in IL10 cis-regulationAngels Natividad
Infectious and Tropical Diseases Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
Hum Mol Genet 17:323-9. 2008..0001). These findings provide a plausible functional explanation for the observed genetic association, and support the hypothesis that an excessive IL10 response to C. trachomatis infection is a risk factor for scarring and blindness... - Improved allelic differentiation using sequence-specific oligonucleotide hybridization incorporating an additional base-analogue mismatchDavid Burgner
Department of Paediatrics, University of Oxford, Oxford, UK
Nucleosides Nucleotides Nucleic Acids 23:755-65. 2004..This improved method increases the usefulness of hybridisation-based methods of rapid genotyping of SNPs and may have implications for array methodologies... - Response of the splenic dendritic cell population to malaria infectionAndrew L Leisewitz
Weatherall Institute of of Molecular Medicine, and University Department of Paediatrics, John Radcliffe Hospital, University of Oxford, Oxford, UK
Infect Immun 72:4233-9. 2004..These findings show that splenic dendritic cells are actively engaged in the earliest phase of malarial infection in vivo and are likely to be critical in shaping the subsequent immune response...