24-SNP barcode data from Richard Toll, Senegal (Daniels et al., 2020)

Data from Daniels et al. (2020). Here we give a brief summary of the data - see the original paper for full details.

Samples were obtained from routine case investigation carried out in Richard Toll, Senegal between September 2012 and December 2015. Rapid diagnostic tests (RDTs) were used to diagnose malaria cases either through facility-based passive case detection (PCD) or through reactive case detection (RACD). A standardized questionnaire was also filled out for all participants to collect information on basic demographic information including travel history. RDTs were used to genotype malaria infections using a 24-SNP barcode. Samples were designated polygenomic if multiple alleles were observed at two or more positions, otherwise they were designated monogenomic. Samples with missing data at 5 or more loci were deemed to have "failed" for the purposes of subsequent analyses, but are included in the data anyway.

data(Daniels_2020C)

Format

A dataframe with 30 columns, giving sample ID and year (columns 1:2), genomic data at 24 SNPs (columns 3:26), and details of missingness and designated mono/polyclonality (columns 27:30). Heterozygous genotyping calls are identified by "N", and missing alleles are identified by "X".

Source

Supplementary materials

References

Daniels RF, Schaffner SF, Dieye Y, Dieng G, Hainsworth M, Fall FB, Diouf CN, Ndiop M, Cisse M, Gueye AB, Sarr O, Guinot P, Deme AB, Bei AK, Sy M, Thwing J, MacInnis B, Earle D, Guinovart C, Sene D, Hartl DL, Ndiaye D, Steketee RW, Wirth DF, Volkman SK (2020). “Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal.” Malaria Journal, 19(1), 276. ISSN 1475-2875, doi: 10.1186/s12936-020-03346-x , https://malariajournal.biomedcentral.com/articles/10.1186/s12936-020-03346-x.