Imputation-based meta-analysis of severe malaria

The initial study and data description are published in: Band G et al . (2013). Imputation-based meta-analysis of severe malaria in three African populations . PLoS Genet. 9:e1003509. This data release contains three separate data packages of SNP genotype data for cases and controls from three populations: Gambia, Kenya and Malawi. This data has been deposited in the European Genotyping Archive under EGA Study Code EGAS00001000807. All cases have been diagnosed with malaria in a hospital. Controls were samples from within the general population and from new births. All samples are unrelated (but see Readme files for further details). The information provided here is common to each of the three country datasets and where differences exist these are noted. Data set structure Each data package contains: Samples Genotypes Other Files Files are all in the 'oxford' format suitable for use with SNPTEST v2: http://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html For a more detailed description of the file formats used in SNPTEST, see http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html Samples Gambia_650Y_HM3_information.sample Kenya_HM3_information.sample Malawi_1M_HM3.sample These are space-delimited files. These files contain information on the samples. The table below gives an example of the data: ID_1 ID_2 missing sex ethnicity country control MALARIA rs334 PCA_1 ... PCA_2 0 0 0 D D D B B D C C C WTCCC130585 WTCCC130585 0.076 M MANDINKA GM 0 1 TT 0.0481 ... -0.00276 0 = N/A D = discrete variable C = continuous variable Row 3 onwards are the sample data and they are listed in the same row order as in the other files in this dataset. Please do not change the sample sort order of this file or the other files. Headers: ID_1 and ID_2 describe the sample_ids and are identical Missing: proportion of SNP data missing Sex: M = male, F = female, NA = missing Ethnicity: only ethnic information for the major ethnic groups is provided and all other groups have been pooled together and labelled as "OTHER" Country_code: GM, KE, MW (ISO code for Gambia, Kenya and Malawi respectively) Control: sample collected from the general population (0=NO, 1=YES) Malaria: sample collected from a patient with severe malaria (0=NO, 1=YES) rs334: probable HbS (rs334) genotype for each individual typed using the Sequenom iPLEX platform. For further details on this SNP see:http://www.ensembl.org/Homo_sapiens/Variation/Explore?r=11:5226502-5227502;v=rs334;vdb=variation;vf=328 and http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs334 The genotype data are provided with respect to the plus '+' strand T: Major allele/ancestral allele/reference allele A: Minor allele/alternative allele/non-reference allele The genome position with respect to the GRCh36 is 11:5204808 Where we were unable to determine a genotype the data are represented by NA PCA_x: PCA_1 to PCA_10 are the first 10 principal components used in the above paper to control for population structure in Genome Wide Association Analysis (GWAS). Missing values are set to NA; samples with missing PCs are those that were excluded from GWAS analyses in the the above paper; these samples also appear in the exclusion lists. Excluded samples: Gambia_650Y_HM3_samples.excluded Kenya_HM3_samples.excluded Malawi_1M_HM3_samples.excluded These files contain lists of samples that were excluded from final analysis due to various QC criteria including: pass_rate heterozygosity Note that there are no header line or column data-type rows at the beginning of these files. Genotypes These files contain posterior probabilities of genotyping calls from imputation using IMPUTE2 into the HapMap 3 (release #2) reference panel obtained from the IMPUTE webpage (http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference). Coordinates refer to NCBI build 36. A Directory called 'gen' contains the SNP data by chromosome. Files are provide per chromosome of the name format: Gambia_650Y_HM3_imputed.??.gen.gz Kenya_650Y_HM3_imputed.??.gen.gz Malawi_HM3_imputed.??.gen.gz where ?? represents the chromosome number with zero-padded prefix. Each file contains the posterior probabilities of genotyping calls for HapMap3 SNPs. The file format is as per SNPTEST v2: SNP1 rs1 1000 A C 1 0 0 1 0 0 ... SNP2 rs2 2000 G T 1 0 0 0 1 0 ... SNP3 rs3 3000 C T 1 0 0 0 1 0 ... There are no header rows. Columns correspond to: Column1: SNP name Column2: rs id Column3: chromosomal position Column4 and 5: SNP alleles from Illumina Manifests Column6 ... ColumnN: contain the posterior probabilities of imputation. Each individual is represented by 3 values corresponding to the genotypes AA, AB and BB respectively. Other files A ReadMe file: ReadMe_Gambia_Illumina-Imputation_data_EGAS00001000807.txt ReadMe_Kenya_Illumina-Imputation_data_EGAS00001000807.txt ReadMe_Malawi_Illumina-Imputation_data_EGAS00001000807.txt A directory called 'bgen': Gambia_650Y_HM3_imputed.bgen Kenya_650Y_HM3_imputed.bgen Malawi_HM3_imputed.bgen Genotype probabilities of imputation output in bgen format (http://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html#input_file_formats) A directory called 'info': Gambia_650Y_HM3_imputed.info.gz Kenya_650Y_HM3_imputed.info.gz Malawi_HM3_imputed.info.gz These files provide imputation information. Note: The .bgen file can be converted into other formats using qctool, e.g. bgen to gen formatsee qctool manual for more details (http://www.well.ox.ac.uk/~gav/qctool/#tutorial) example command: ./qctool -g Gambia_650Y_HM3_imputed.bgen -og Gambia_650Y_HM3_imputed.gen Extra information specific to Kenya Kenya_HM3_information.families This is file describes samples in trios or part trios. Example format: family_ID sample_ID father_ID mother_ID family_member Kenya_fam_02 MLCP1_1M1300381 MLCP1_1M1424842 MLCP1_1M1424843 Index Kenya_fam_02 MLCP1_1M1424842 NA NA Father Kenya_fam_02 MLCP1_1M1424843 NA NA Mother family_id: id to group family members sample_id: unique individual_id that maps to the Kenya_HM3_information.samples file father_id: individual_id of the father that maps to the individual_id field mother_id: individual_id of the mother that maps to the individual_id field family_member: relationship of the individual to the family index member