24-SNP barcode data from clonal outbreak in Panama (Obaldia et al., 2015)

Data from Obaldia et al. (2015). Here we give a brief summary of the data - see the original paper for full details.

This study focused on 37 P. falciparum isolates collected during 2003–2008 from individuals in malaria-endemic provinces in eastern Panama, along with 20 isolates collected during 2011–2012 from healthcare facilities in 3 malaria endemic sites in Colombia. Samples were sequenced using a 24-SNP barcode. Samples were considered polyclonal if they contained multiple alleles at two or more loci, otherwise they were considered monoclonal. Samples were clustered into major groups using STRUCTURE software.

data(Obaldia_2015)

Format

A dataframe with 30 columns, giving sample characteristics (columns 1:5), genomic data at 24 SNPs (columns 6:29), and major group membership (column 30). Heterozygous genotyping calls are identified by "N", and missing alleles are identified by "NA".

Source

Data extracted manually from paper

References

Obaldia N, Baro NK, Calzada JE, Santamaria AM, Daniels R, Wong W, Chang H, Hamilton EJ, Arevalo-Herrera M, Herrera S, Wirth DF, Hartl DL, Marti M, Volkman SK (2015). “Clonal Outbreak of Plasmodium falciparum Infection in Eastern Panama.” Journal of Infectious Diseases, 211(7), 1087--1096. ISSN 0022-1899, 1537-6613, doi: 10.1093/infdis/jiu575 , https://academic.oup.com/jid/article-lookup/doi/10.1093/infdis/jiu575.