24-SNP barcode data from two trials in Zambia (Daniels et al., 2020)

Source: R/data.R

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

Rapid diagnostic test-positive samples were obtained from household-level data collection during two community-randomized trials conducted in the same geographical region of Southern Province of Zambia between 2012 and 2016. the first sample set (n = 836 children younger than 6 years) was collected during the peak malaria transmission season (April–May) in both 2012 and 2013 (baseline) as part of a community-randomized controlled trial designed to assess the impact of three rounds of an MTAT intervention that used RDTs for testing and artemether–lumefantrine for treatment. The second sample set (n = 784 individuals 3 months or older) was obtained from an 18-month longitudinal cohort study, with monthly follow-up visits, conducted from December 2014 to May 2016 (cohort). The cohort was designed to evaluate a cluster randomized controlled trial for assessing the impact of four rounds of community-wide MDA and household-level (focal) MDA (fMDA) with DHAp compared with that of no mass treatment (control).
Samples were genotyped 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_2020B)

Format

A dataframe with 34 columns, giving the sample ID, collection date, study type, (TODO), study batch and arm (columns 1:6), the genomic data over all 24 SNPs (columns 7:30), and details of missingness and designated mono/polyclonality (columns 31:34). Heterozygous genotyping calls are identified by "N", and missing alleles are identified by "X". Note, the original downloaded data contained 18 samples with missing genotypic data, which have been removed to leave the 1620 samples referred to in the main paper.

References

Daniels RF, Schaffner SF, Bennett A, Porter TR, Yukich JO, Mulube C, Mambwe B, Mwenda MC, Chishimba S, Bridges DJ, Moonga H, Hamainza B, Chizema Kawesha E, Miller JM, Steketee RW, Wirth DF, Eisele TP, Hartl DL, Volkman SK (2020). “Evidence for Reduced Malaria Parasite Population after Application of Population-Level Antimalarial Drug Strategies in Southern Province, Zambia.” The American Journal of Tropical Medicine and Hygiene, 103(2 Suppl), 66--73. ISSN 0002-9637, doi: 10.4269/ajtmh.19-0666 , https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7416975/.