Wellcome Open Research

Version 2 of data for "Geographic-genetic analysis of Plasmodium falciparum parasite populations from surveys of primary school children in Western Kenya"

Posted on 2017-08-31 - 11:06
Dataset 1: Genotyping results for 111 single nucleotide polymorphisms (SNPs) typed in 2486 Plasmodium falciparum samples collected from primary school children during a parasitological survey in western Kenya in 2009 and 2010.
The columns contain the following information: sample_id, unique sample identifier; admin1, provincial location of school; district_name, district location of school; date_visit, date of sample collection; assay_code, name of assay; allele1 and allele2, alternative alleles at a specific SNP position; result, genotype call after processing; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass=1) or lack of a valid genotype (fail=0). Geospatial data for individual school locations is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee at dgc@kemri-wellcome.org. The criteria for such access is specified in detail in the data sharing guidelines under which the DGC operates, and relates to a) addressing health research, b)operating within the bounds of informed consent, c)complying with confidentiality procedures, d) mitigating potential harm to participants in research.

Dataset 2: Single nucleotide polymorphisms (SNPs) and distance differences between Plasmodium falciparum parasite pairs sampled during a parasitological survey of primary school children in western Kenya.
Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of SNP differences between parasite pairs; distance represents geographical distance, in kilometres, between parasite pairs.


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