Kwiatkowski Group

Selected publications

Miotto O, Almagro-Garcia J, Manske M, Macinnis B, Campino S, Rockett KA, Amaratunga C, Lim P, Suon S, Sreng S, Anderson JM, Duong S, Nguon C, Chuor CM, Saunders D, Se Y, Lon C, Fukuda MM, Amenga-Etego L, Hodgson AV, Asoala V, Imwong M, Takala-Harrison S, Nosten F, Su XZ, Ringwald P, Ariey F, Dolecek C, Hien TT, Boni MF, Thai CQ, Amambua-Ngwa A, Conway DJ, Djimdé AA, Doumbo OK, Zongo I, Ouedraogo JB, Alcock D, Drury E, Auburn S, Koch O, Sanders M, Hubbart C, Maslen G, Ruano-Rubio V, Jyothi D, Miles A, O'Brien J, Gamble C, Oyola SO, Rayner JC, Newbold CI, Berriman M, Spencer CC, McVean G, Day NP, White NJ, Bethell D, Dondorp AM, Plowe CV, Fairhurst RM, Kwiatkowski DP Nature Genetics (2013). Multiple populations of artemisinin-resistant Plasmodium falciparumin Cambodia. Nature Genetics (2013). PMID: 23624527 Further information

Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O'Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo JB, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara SM, Marsh K, Jiang H, Su XZ, Amaratunga C, Fairhurst R, Socheat D, Nosten F, Imwong M, White NJ, Sanders M, Anastasi E, Alcock D, Drury E, Oyola S, Quail MA, Turner DJ, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan JC, Ferdig MT, Amambua-Ngwa A, Conway DJ, Takala-Harrison S, Plowe CV, Rayner JC, Rockett KA, Clark TG, Newbold CI, Berriman M, MacInnis B, Kwiatkowski DP. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature (2012). PMID: 22722859 Further information

de Vries J, Bull SJ, Doumbo O, Ibrahim M, Mercereau-Puijalon O, Kwiatkowski D, Parker M. Ethical issues in human genomics research in developing countries. BMC Medical Ethics (2011) 12:5. PMID21418562

Teo YY, Small KS, Kwiatkowski DP. Methodological challenges of genome-wide association analysis in Africa. Nature Reviews Genetics (2010) 11, 149-60
PMID 20084087

Teo YY, Fry AE, Bhattacharya K, Small KS, Kwiatkowski DP, Clark TG. Genome-wide comparisons of variation in linkage disequilibrium.  Genome Research, Nature Genetics (2009) 41, 657-65
PMID19465909

Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M, Sirugo G, Sisay-Joof F, Usen S, Auburn S, Bumpstead SJ, Campino S, Coffey A, Dunham A, Fry AE, Green A, Gwilliam R, Hunt SE, Inouye M, Jeffreys AE, Mendy A, Palotie A, Potter S, Ragoussis J, Rogers J, Rowlands K, Somaskantharajah E, Whittaker P, Widden C, Donnelly P, Howie B, Marchini J, Morris A, Sanjoaquin M, Achidi EA, Agbenyega T, Allen A, Amodu O, Corran P, Djimde A, Dolo A, Doumbo OK, Drakeley C, Dunstan S, Evans J, Farrar J, Fernando D, Hien TT, Horstmann RD, Ibrahim M, Karunaweera N, Kokwaro G, Koram KA, Lemnge M, Makani J, Marsh K, Michon P, Modiano D, Molyneux ME, Mueller I, Parker M, Peshu N, Plowe CV, Puijalon O, Reeder J, Reyburn H, Riley EM, Sakuntabhai A, Singhasivanon P, Sirima S, Tall A, Taylor TE, Thera M, Troye-Blomberg M, Williams TN, Wilson M, Kwiatkowski DP; Wellcome Trust Case Control Consortium; Malaria Genomic Epidemiology Network. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet. 2009 May 24. PMID: 19465909

Campino S, Forton J, Auburn S, Fry A, Diakite M, Richardson A, Hull J, Jallow M, Sisay-Joof F, Pinder M, Molyneux ME, Taylor TE, Rockett K, Clark TG, Kwiatkowski DP. TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression.  Malar J. 2009 Mar 13;8(1):44. PMID: 19284650

Teo YY, Small KS, Fry AE, Wu Y, Kwiatkowski DP, Clark TG.
Power consequences of linkage disequilibrium variation between populations.  Genet Epidemiol. 2009 Feb;33(2):128-35. PMID: 18814308

Diakite M, Clark TG, Auburn S, Campino S, Fry AE, Green A, Morris AP, Richardson A, Jallow M, Sisay-Joof F, Pinder M, Kwiatkowski DP, Rockett KA. A genetic association study in the Gambia using tagging polymorphisms in the major histocompatibility complex class III region implicates a HLA-B associated transcript 2 polymorphism in severe malaria susceptibility. Hum Genet. 2009 Feb;125(1):105-9. Epub 2008 Nov 28. PMID: 19039607

Clark TG, Diakite M, Auburn S, Campino S, Fry AE, Green A, Richardson A, Small K, Teo YY, Wilson J, Jallow M, Sisay-Joof F, Pinder M, Griffiths MJ, Peshu N, Williams TN, Marsh K, Molyneux ME, Taylor TE, Rockett KA, Kwiatkowski DP. Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations.  J Infect Dis. 2009 Feb 15;199(4):569-75. PMID: 19281305

Mangano VD, Clark TG, Auburn S, Campino S, Diakite M, Fry AE, Green A, Richardson A, Jallow M, Sisay-Joof F, Pinder M, Griffiths MJ, Newton C, Peshu N, Williams TN, Marsh K, Molyneux ME, Taylor TE, Modiano D, Kwiatkowski DP, Rockett KA. Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populations.  PLoS ONE. 2009;4(1):e4206. Epub 2009 Jan 15. PMID: 19145247

Malaria Genomic Epidemiology Network. A global network for investigating the genomic epidemiology of malaria.  Nature. 2008 Dec 11;456(7223):732-7. PMID: 19079050 (DK corresponding author)

Clark TG, Fry AE, Auburn S, Campino S, Diakite M, Green A, Richardson A, Teo YY, Small K, Wilson J, Jallow M, Sisay-Joof F, Pinder M, Sabeti P, Kwiatkowski DP, Rockett KA. Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibility.  Eur J Hum Genet. 2009 Feb 18. PMID: 19223928

Teo YY, Fry AE, Sanjoaquin MA, Pederson B, Small KS, Rockett KA, Kwiatkowski DP, Clark TG. Assessing genuine parents-offspring trios for genetic association studies. Hum Hered. 2009;67(1):26-37. Epub 2008 Oct 17. PMID: 18931507

Auburn S, Diakite M, Fry AE, Ghansah A, Campino S, Richardson A, Jallow M, Sisay-Joof F, Pinder M, Griffiths MJ, Peshu N, Williams TN, Marsh K, Molyneux ME, Taylor TE, Koram KA, Oduro AR, Rogers WO, Rockett KA, Haldar K, Kwiatkowski DP. Association of the GNAS locus with severe malaria. Hum Genet. 2008 Dec;124(5):499-506. Epub 2008 Oct 26. PMID: 18951142

Atkinson SH, Rockett KA, Morgan G, Bejon PA, Sirugo G, O'Connell MA, Hanchard N, Kwiatkowski DP, Prentice AM. Tumor necrosis factor SNP haplotypes are associated with iron deficiency anemia in West African children.  Blood. 2008 Nov 15;112(10):4276-83. Epub 2008 Aug 20. PMID: 18716131

Fry AE, Auburn S, Diakite M, Green A, Richardson A, Wilson J, Jallow M, Sisay-Joof F, Pinder M, Griffiths MJ, Peshu N, Williams TN, Marsh K, Molyneux ME, Taylor TE, Rockett KA, Kwiatkowski DP. Variation in the ICAM1 gene is not associated with severe malaria phenotypes. Genes Immun. 2008 Jul;9(5):462-9. Epub 2008 Jun 5. PMID: 18528404

Teo YY, Small KS, Clark TG, Kwiatkowski DP. Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies.  Ann Hum Genet. 2008 May;72(Pt 3):368-74. Epub 2008 Feb 6. PMID: 18261185

Teo YY, Inouye M, Small KS, Fry AE, Potter SC, Dunstan SJ, Seielstad M, Barroso I, Wareham NJ, Rockett KA, Kwiatkowski DP, Deloukas P. Whole genome-amplified DNA: insights and imputation.  Nat Methods. 2008 Apr;5(4):279-80. PMID: 18376389

Mangano VD, Luoni G, Rockett KA, Sirima BS, Konaté A, Forton J, Clark TG, Bancone G, Sadighi Akha E, Kwiatkowski DP, Modiano D. Interferon regulatory factor-1 polymorphisms are associated with the control of Plasmodium falciparum infection. Genes Immun. 2008 Mar;9(2):122-9. Epub 2008 Jan 17. Erratum in: Genes Immun. 2008 Jul;9(5):482. Akha, E S [corrected to Sadighi Akha, E]. PMID: 18200030

Calis JC, Phiri KS, Faragher EB, Brabin BJ, Bates I, Cuevas LE, de Haan RJ, Phiri AI, Malange P, Khoka M, Hulshof PJ, van Lieshout L, Beld MG, Teo YY, Rockett KA, Richardson A, Kwiatkowski DP, Molyneux ME, van Hensbroek MB. Severe anemia in Malawian children. N Engl J Med. 2008 Feb 28;358(9):888-99. PMID: 18305266

Callaghan MJ, Rockett K, Banner C, Haralambous E, Betts H, Faust S, Maiden MC, Kroll JS, Levin M, Kwiatkowski DP, Pollard AJ. Haplotypic diversity in human CEACAM genes: effects on susceptibility to meningococcal disease. Genes Immun. 2008 Jan;9(1):30-7. Epub 2007 Oct 25. PMID: 17960155

Fry AE, Griffiths MJ, Auburn S, Diakite M, Forton JT, Green A, Richardson A, Wilson J, Jallow M, Sisay-Joof F, Pinder M, Peshu N, Williams TN, Marsh K, Molyneux ME, Taylor TE, Rockett KA, Kwiatkowski DP. Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malaria. Hum Mol Genet. 2008 Feb 15;17(4):567-76. Epub 2007 Nov 13. PMID: 18003641

Natividad A, Holland MJ, Rockett KA, Forton J, Faal N, Joof HM, Mabey DC, Bailey RL, Kwiatkowski DP. Susceptibility to sequelae of human ocular chlamydial infection associated with allelic variation in IL10 cis-regulation. Hum Mol Genet. 2008 Jan 15;17(2):323-9. Epub 2007 Oct 18. PMID: 17947295

Campino S, Forton J, Raj S, Mohr B, Auburn S, Fry A, Mangano VD, Vandiedonck C, Richardson A, Rockett K, Clark TG, Kwiatkowski DP. Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations. PLoS ONE. 2008;3(12):e4105. Epub 2008 Dec 31. PMID: 19116668

Cox SE, Doherty CP, Atkinson SH, Nweneka CV, Fulford AJ, Sirugo G, Rockett KA, Kwiatkowski DP, Prentice AM. Haptoglobin genotype, anaemia and malaria in Gambian children. Trop Med Int Health. 2008 Jan;13(1):76-82. PMID: 18291005

Fry AE, Griffiths MJ, Auburn S, Diakite M, Forton JT, Green A, Richardson A, Wilson J, Jallow M, Sisay-Joof, Pinder M, Peshu N, Williams TN, Marsh K, Molyneux ME, Taylor TE, Rockett K, Kwiatkowski DP. Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium Falciparum malaria. Hum Mol Genet

Wellcome Trust Case Control Consortium. Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet 2007 Nov;39(11):1329-37. Epub 2007 Oct 21 PMID: 17952073

Berier RE, Hassan HY, Salih NA, Underhill PA, Cavalli-Sforza LL, Hussain AA, Kwiatkowski D, Ibrahim ME. Co-introgression of Y-chromosome haplogroups and the sickle cell gene across Africa's Sahel. Eur J Hum Genet. 2007 Nov;15(11):1183-5. Epub 2007 Aug 15. PMID: 17700630

Khor CC, Vannberg FO, Chapman SJ, Walley A, Aucan C, Loke H, White NJ, Peto T, Khor LK, Kwiatkowski D, Day N, Scott A, Berkley JA, Marsh K, Peshu N, Maitland K, Williams TN, Hill AV. Positive replication and linkage disequilibrium mapping of the chromosome 21q22.1 malaria susceptibility locus. Genes Immun. 2007 Oct;8(7):570-6. Epub 2007 Aug 16 PMID: 17703179

Callaghan MJ, Rockett K, Banner C, Haralambous E, Bettes H, Faust S, Maiden MC, Kroll JS, Levin M, Kwiatkowski DP, Pollard AJ. Haplotypic diversity in human CEACAM genes: effects on susceptibility to meningococcal disease. Genes Immun. 25 Oct 2007

Natividad A, Holland MJ, Rockett KA, Forton J, Faal N, Joof HM, Mabey DC, Bailey RL, Kwiatkowski DP. Susceptibility to Sequelae of human ocular chlamydial infection associated with allelic variation in IL-10 cis-regulation. Hum Mol Genet. 18 Oct 2007

Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP, Clark TG. A genotype calling algorithm for the Illumina BeadArray platform. Bioinformatics. 2007 Oct 15;23(20):2741-6. Epub 2007 Sep 10. PMID: 17846035

Dunstan SJ, Hue NT, Rockett K, Forton J, Morris AP, Diakite M, Lanh MN, Phuong LT, House D, Parry CM, Vinh H, Hieu NT, Dougan G, Hein TT, Kwiatkowski D, Farrar JJ. A TNF region haplotype offers protection from typhoid fever in Vietnamese patients. Hum Genet 2007 Aug;122(1):51-61. Epub 2007 May 15 PMID: 17503085

Hanchard N, Elzein A, Trafford C, Rockett K, Pinder M, Jallow M, Harding R, Kwiatkowski D, McKenzie C. Classical beta-globin sickle haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations. BMC Genet 2007 Aug 10;8:52 PMID: 17688704

Hull J, Campino S, Rowlands K, Chan MS, Copley RR, Taylor MS, Rockett K, Elvidge G, Keating B, Knight J, Kwiatkowski D.   Identification of common genetic variation that modulates alternative splicing.  PLoS Genet. 2007 Jun;3(6):e99.

Wellcome Trust Case Control Consortium.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.  Nature 447, 661-678.

Forton JT, Udalova IA, Campino S, Rockett KA, Hull J, Kwiatkowski DP (2007). Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping. Genome Res 17 : 1 : 82-7

Chokshi DA, Thera MA, Parker M, Diakite M, Makani J, Kwiatkowski DP, Doumbo OK. Valid consent for genomic epidemiology in developing countries.  PLoS Med. 2007 Apr;4(4):e95.

Forton JT, Kwiatkowski DP (2006) Searching for the regulators of human gene expression. Bioessays 28 : 10 : 968-72

Taylor T, Olola C, Valim C, Agbenyega T, Kremsner P, Krishna S, Kwiatkowski D, Newton C, Missinou M, Pinder M, Wypij D (2006) Standardized data collection for multi-center clinical studies of severe malaria in African children: establishing the SMAC network. Trans R Soc Trop Med Hyg 100 : 7 : 615-22

Fry AE, Trafford CJ, Kimber MA, Chan MS, Rockett KA, Kwiatkowski DP (2006) Haplotype homozygosity and derived alleles in the human genome.  Am J Hum Genet 78 : 6 : 1053-9

Atkinson SH, Rockett K, Sirugo G, Bejon PA, Fulford A, O'connell MA, Bailey R, Kwiatkowski DP, Prentice AM (2006) Seasonal Childhood Anaemia in West Africa Is Associated with the Haptoglobin 2-2 Genotype. PLoS Med 3 : 5 : e172