Publications
The first results from MalariaGEN Consortial Projects have now been published. Below is a selection of recent findings by MalariaGEN investigators and some methodological papers from the MalariaGEN Resource Centre.
Consortial Publications
Ethical data-release in genome-wide association studies in developing countries. Michael Parker, Susan Bull, Jantina de Vries, Tsiri Agbenyega, Ogobara Doumbo and Dominic Kwiatkowski. PLoS Medicine 2009, Nov 24. Read more>>
Genome-wide and fine-resolution association analysis of malaria in West Africa. 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. Nature Genetics 2009 May 24. PMID: 19465909
A global network for investigating the genomic epidemiology of malaria. Malaria Genomic Epidemiology Network. Nature 2008 Dec 11; 456 (7223): 732-7. PMID: 19079050. Read more >>
Selection of recent publications by MalariaGEN investigators
TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression. Campino S, Forton J, Auburn S, Fry A, Diakite M, Richardson A, Hull J, Jallow M, Sisey-Joof F, Pinder M, Molyneux ME, Taylor TE, Rockett K, Clark TG, Kwiatkowski DP. Malaria Journal 2009 Mar 13;8(1):44 PMID: 19284650
Allelic heterogeneity of G6PD deficiency in West Africa and severe malaria susceptibility. 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. Eur J Hum Genet. 2009 Feb 18. PMID: 19223928
Tumor necrosis factor and lymphotoxin-alpha polymorphisms and severe malaria in African populations. 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. J Infect Dis. 2009 Feb 15;199(4):569-75. PMID: 19281305
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. 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. Hum Genet. 2009 Feb;125(1):105-9. Epub 2008 Nov 28. PMID: 19039607
Lack of association of interferon regulatory factor 1 with severe malaria in affected child-parental trio studies across three African populations. 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. PLoS ONE. 2009;4(1):e4206. Epub 2009 Jan 15. PMID: 19145247
Association of the GNAS locus with severe malaria. 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. Hum Genet. 2008 Oct 26. PMID: 18951142
Tumor necrosis factor SNP haplotypes are associated with iron deficiency anemia in West African children. Atkinson SH, Rockett KA, Morgan G, Bejon PA, Sirugo G, O'Connell MA, Hanchard N, Kwiatkowski DP, Prentice AM. Blood. 2008 Nov 15;112(10):4276-83. Epub 2008 Aug 20. PMID: 18716131
Variation in the ICAM1 gene is not associated with severe malaria phenotypes. 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. Genes Immun. 2008 Jul;9(5):462-9. Epub 2008 Jun 5. PMID: 18528404
Interferon regulatory factor-1 polymorphisms are associated with the control of Plasmodium falciparum infection. Mangano VD, Luoni G, Rockett KA, Sirima BS, Konaté A, Forton J, Clark TG, Bancone G, Sadighi Akha E, Kwiatkowski DP, Modiano D. Genes Immun. 2008 Jul;9(5):482. PMID: 18648379
Genetic epidemiology of susceptibility to malaria: not only academic exercises. Verra F, Avellino P, Bancone G, Mangano V, Modiano D. Parassitologia. 2008 Jun;50(1-2):147-50. PMID: 18693583
Haemoglobin S and haemoglobin C: 'quick but costly' versus 'slow but gratis' genetic adaptations to Plasmodium falciparum malaria. Modiano D, Bancone G, Ciminelli BM, Pompei F, Blot I, Simporé J, Modiano G. Hum Mol Genet. 2008 Mar 15;17(6):789-99. Epub 2007 Nov 28. Erratum in: Hum Mol Genet. 2008 Jul 1;17(13):2070. PMID: 18048408
Severe anemia in Malawian children. 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. N Engl J Med. 2008 Feb 28;358(9):888-99. PMID: 18305266
Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malaria. 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. Hum Mol Genet. 2008 Feb 15;17(4):567-76. Epub 2007 Nov 13. PMID: 18003641
Haptoglobin genotype, anaemia and malaria in Gambian children. Cox SE, Doherty CP, Atkinson SH, Nweneka CV, Fulford AJ, Sirugo G, Rockett KA, Kwiatkowski DP, Prentice AM. Trop Med Int Health. 2008 Jan;13(1):76-82. PMID: 18291005
New interventions for malaria: mining the human and parasite genomes. Ntoumi F, Kwiatkowski DP, Diakité M, Mutabingwa TK, Duffy PE. Am J Trop Med Hyg. 2007 Dec;77(6 Suppl):270-5. Review. PMID: 18165502
Haemoglobin C and S in natural selection against Plasmodium falciparum malaria: a plethora or a single shared adaptive mechanism? Verra F, Bancone G, Avellino P, Blot I, Simporé J, Modiano D. Parassitologia. 2007 Dec;49(4):209-13. Review. PMID: 18689228
Positive replication and linkage disequilibrium mapping of the chromosome 21q22.1 malaria susceptibility locus. 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. Genes Immun. 2007 Oct;8(7):570-6. Epub 2007 Aug 16. PMID: 17703179
Co-introgression of Y-chromosome haplogroups and the sickle cell gene across Africa's Sahel. Bereir RE, Hassan HY, Salih NA, Underhill PA, Cavalli-Sforza LL, Hussain AA, Kwiatkowski D, Ibrahim ME. Eur J Hum Genet. 2007 Nov;15(11):1183-5. Epub 2007 Aug 15. PMID: 17700630
Haemoglobin C and S role in acquired immunity against Plasmodium falciparum malaria. Verra F, Simpore J, Warimwe GM, Tetteh KK, Howard T, Osier FH, Bancone G, Avellino P, Blot I, Fegan G, Bull PC, Williams TN, Conway DJ, Marsh K, Modiano D. PLoS ONE. 2007 Oct 3;2(10):e978. PMID: 17912355
Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations. Hanchard N, Elzein A, Trafford C, Rockett K, Pinder M, Jallow M, Harding R, Kwiatkowski D, McKenzie C. BMC Genet. 2007 Aug 10;8:52. PMID: 17688704
Associations between alpha+-thalassemia and Plasmodium falciparum malarial infection in northeastern Tanzania. Enevold A, Alifrangis M, Sanchez JJ, Carneiro I, Roper C, Børsting C, Lusingu J, Vestergaard LS, Lemnge MM, Morling N, Riley E, Drakeley CJ. J Infect Dis. 2007 Aug 1;196(3):451-9. Epub 2007 Jun 20. PMID: 17597460
Haplotype association between haptoglobin (Hp2) and Hp promoter SNP (A-61C) may explain previous controversy of haptoglobin and malaria protection. Cox SE, Doherty C, Atkinson SH, Nweneka CV, Fulford AJ, Ghattas H, Rockett KA, Kwiatkowski DP, Prentice AM. PLoS ONE. 2007 Apr 11;2(4):e362. PMID: 17426810
Valid consent for genomic epidemiology in developing countries. Chokshi DA, Thera MA, Parker M, Diakite M, Makani J, Kwiatkowski DP, Doumbo OK. PLoS Med. 2007 Apr;4(4):e95. Review. PMID: 17455985
The haptoglobin 2-2 genotype is associated with a reduced incidence of Plasmodium falciparum malaria in children on the coast of Kenya. Atkinson SH, Mwangi TW, Uyoga SM, Ogada E, Macharia AW, Marsh K, Prentice AM, Williams TN. Clin Infect Dis. 2007 Mar 15;44(6):802-9. Epub 2007 Feb 7. PMID: 17304451
Host genetic factors in resistance and susceptibility to malaria. Kwiatkowski DP, Luoni G. Parassitologia. 2006 Dec;48(4):450-67. Review. PMID: 17688174
Standardized data collection for multi-center clinical studies of severe malaria in African children: establishing the SMAC network. Taylor T, Olola C, Valim C, Agbenyega T, Kremsner P, Krishna S, Kwiatkowski D, Newton C, Missinou M, Pinder M, Wypij D. Trans R Soc Trop Med Hyg. 2006 Jul;100(7):615-22. Epub 2006 Mar 23. PMID: 16551469
Frequencies of peripheral blood myeloid cells in healthy Kenyan children with alpha+ thalassemia and the sickle cell trait. Urban BC, Shafi MJ, Cordery DV, Macharia A, Lowe B, Marsh K, Williams TN. Am J Trop Med Hyg. 2006 Apr;74(4):578-84. PMID: 16606987
The effect of alpha+-thalassaemia on the incidence of malaria and other diseases in children living on the coast of Kenya. Wambua S, Mwangi TW, Kortok M, Uyoga SM, Macharia AW, Mwacharo JK, Weatherall DJ, Snow RW, Marsh K, Williams TN. PLoS Med. 2006 May;3(5):e158. Epub 2006 Apr 18.
A polymorphism of intercellular adhesion molecule-1 is associated with a reduced incidence of nonmalarial febrile illness in Kenyan children. Jenkins NE, Mwangi TW, Kortok M, Marsh K, Craig AG, Williams TN. Clin Infect Dis. 2005 Dec 15;41(12):1817-9. Epub 2005 Nov 8. PMID: 16288410
Negative epistasis between the malaria-protective effects of alpha+-thalassemia and the sickle cell trait. Williams TN, Mwangi TW, Wambua S, Peto TE, Weatherall DJ, Gupta S, Recker M, Penman BS, Uyoga S, Macharia A, Mwacharo JK, Snow RW, Marsh K. Nat Genet. 2005 Nov;37(11):1253-7. Epub 2005 Oct 16. PMID: 16227994
Methodological publications from the MalariaGEN Resource Centre
LookSeq: a browser-based viewer for deep sequencing data. Manske HM, Kwiatkowski DP. Genome Research, Epub ahead of print. PMID: 19679872
SNP-o-matic. Manske HM, Kwiatkowski DP. Bioinformatics. PMID: 19574284
Genome-wide comparisons of variation in linkage disequilibrium. Teo YY, Fry AE, Bhattacharya K, Small KS, Kwiatkowski DP, Clark TG. Genome Research. PMID: 19541915
Assessing genuine parents-offspring trios for genetic association studies. Teo YY, Fry AE, Sanjoaquin MA, Pederson B, Small KS, Rockett KA, Kwiatkowski DP, Clark TG. Human Heredity 2009;67(1):26-37. Epub 2008 Oct 17. PMID: 18931507
Power consequences of linkage disequilibrium variation between populations. Teo YY, Small KS, Fry AE, Wu Y, Kwiatkowski DP, Clark TG. Genet Epidemiol. 2008 Sep 22. PMID: 18814308
A genotype calling algorithm for the Illumina BeadArray platform. Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP, Clark TG. Bioinformatics. 2007 Oct 15;23(20):2741-6. Epub 2007 Sep 10. PMID: 17846035
Whole genome-amplified DNA: insights and imputation. Teo YY, Inouye M, Small KS, Fry AE, Potter SC, Dunstan SJ, Seielstad M, Barroso I, Wareham NJ, Rockett KA, Kwiatkowski DP, Deloukas P. Nat Methods. 2008 Apr;5(4):279-80. PMID: 18376389
Perturbation analysis: a simple method for filtering SNPs with erroneous genotyping in genome-wide association studies. Teo YY, Small KS, Clark TG, Kwiatkowski DP. Ann Hum Genet. 2008 May;72(Pt 3):368-74. Epub 2008 Feb 6. PMID: 18261185