Dataset Information

WTCCC2 Visceral Leishmaniasis (VL) samples

ABSTRACT: A WTCCC2 project genome-wide association study for visceral leishmaniasis (VL) in individuals from India, Brazil and Sudan, genotyped on the custom Illumina 670k array. The WTCCC2 analysis of the Brazilian and Indian samples is described in Fakiola et al. [Nat Genet. 2013 Feb;45(2):208-13]. It should be noted that due to expected family structure in the data, normal analyses of these data should include an estimation of the relatedness between the samples. For more details about sample collection for the project please refer to the Methods section of the paper above. The samples from India were all collected from Bihar state in northeastern India. The Brazilian samples were collected from a wide area of northern Brazil, and managed at two laboratories in Natal and Belem. For more details on the geographic distribution of the Brazil samples please see Jamieson et al. [Genes Immun. 2007 Jan;8(1):84-90]. We have not generated qc_passed or info files for the Sudanese data, a preliminary scan of the data indicated that there may be DNA quality issues with these samples.

PROVIDER: EGAS00001000773 | EGA |

REPOSITORIES: EGA

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Publications

Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.

Fakiola Michaela M Strange Amy A Cordell Heather J HJ Miller E Nancy EN Pirinen Matti M Su Zhan Z Mishra Anshuman A Mehrotra Sanjana S Monteiro Gloria R GR Band Gavin G Bellenguez Céline C Dronov Serge S Edkins Sarah S Freeman Colin C Giannoulatou Eleni E Gray Emma E Hunt Sarah E SE Lacerda Henio G HG Langford Cordelia C Pearson Richard R Pontes Núbia N NN Rai Madhukar M Singh Shri P SP Smith Linda L Sousa Olivia O Vukcevic Damjan D Bramon Elvira E Brown Matthew A MA Casas Juan P JP Corvin Aiden A Duncanson Audrey A Jankowski Janusz J Markus Hugh S HS Mathew Christopher G CG Palmer Colin N A CN Plomin Robert R Rautanen Anna A Sawcer Stephen J SJ Trembath Richard C RC Viswanathan Ananth C AC Wood Nicholas W NW Wilson Mary E ME Deloukas Panos P Peltonen Leena L Christiansen Frank F Witt Campbell C Jeronimo Selma M B SM Sundar Shyam S Spencer Chris C A CC Blackwell Jenefer M JM Donnelly Peter P

Nature genetics 20130106 2

To identify susceptibility loci for visceral leishmaniasis, we undertook genome-wide association studies in two populations: 989 cases and 1,089 controls from India and 357 cases in 308 Brazilian families (1,970 individuals). The HLA-DRB1-HLA-DQA1 locus was the only region to show strong evidence of association in both populations. Replication at this region was undertaken in a second Indian population comprising 941 cases and 990 controls, and combined analysis across the three cohorts for rs92 ...[more]

PMID: 23291585

Dataset Information

WTCCC2 Visceral Leishmaniasis (VL) samples

Publications

Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis.

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