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Genome-wide study of resistance to severe malaria in eleven populations (version 2)

Released on 15 Aug 2019.

Human

This data release contains SNP genotype data and association test results from our analysis of severe malaria in eleven populations. Data for eleven populations (Gambia, Mali, Burkina Faso, Ghana, Nigeria, Cameroon, Tanzania, Malawi, Kenya, Vietnam and Papua New Guinea) are available.

The datasets available include raw Illumina Omni 2.5M genotype data from each population analysed in the above manuscript. In addition, we provide a set of processed data for a subset of samples that passed our quality control process, including phased and imputed SNP genotypes and a set of association test summary statistics.

A set of genotypes at selected genetic variants generated using the Sequenom MassArray platform on a larger set of individuals is also available.

Data sets

Kenya

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001742 (1,738 controls; 1,944 cases; 180 parents; 3 other)

Method: Illumina Omni 2.5M genotyping

Gambia

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001738 (2,786 controls; 2,807 cases; 1 parents)

Method: Illumina Omni 2.5M genotyping

Malawi

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001741 (1,498 controls; 1,590 cases)

Method: Illumina Omni 2.5M genotyping

Mali

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001737 (394 controls; 475 cases; 31 parents)

Method: Illumina Omni 2.5M genotyping

Burkina Faso

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001739 (639 controls; 807 cases)

Method: Illumina Omni 2.5M genotyping

Ghana

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001734 (342 controls; 422 cases; 18 parents)

Method: Illumina Omni 2.5M genotyping

Nigeria

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001736 (131 controls; 288 cases)

Method: Illumina Omni 2.5M genotyping

Cameroon

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001740 (778 controls; 693 cases)

Method: Illumina Omni 2.5M genotyping

Tanzania

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001743 (494 controls; 485 cases)

Method: Illumina Omni 2.5M genotyping

Vietnam

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001733 (868 controls; 860 cases)

Method: Illumina Omni 2.5M genotyping

Papua New Guinea

EGA Study ID: EGAS00001001311

EGA Data Set ID: EGAD00010001735 (395 controls; 420 cases)

Method: Illumina Omni 2.5M genotyping

Genome-wide phased genotypes for eleven populations

EGA Study ID: EGAS00001001311

8,666 controls; 9,077 cases; 215 parents; 2 other

Method: Illumina Omni 2.5M SNP genotypes phased using SHAPEIT2

Raw genotypes from individual populations are also available as separate datasets (see below).

Sequenom MassArray genotypes

EGA Study ID: EGAD00010001799

19,845 controls; 15,865 cases; 3,341 parents; 773 whole genome sequenced individuals (CP3/GGVP); 196 HapMap; 9 other

Method: Sequenom MassArray (Agena Bioscience)

Gambia HLA typing

EGA Study ID: EGAS00001001311
EGA Dataset ID: EGAD00010001818 (32 family trios)
Method: HLA typing by Sanger sequencing

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Citations

If you use these data, please cite:

Malaria Genomic Epidemiology Network. Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nat Commun 10, 5732 (2019) doi:10.1038/s41467-019-13480-z