GenRe-Mekong v1.0

This record contains information about the first GenRe-Mekong project data release (v1.0), comprising Genetic Report Cards data from 9,623 Plasmodium falciparum samples. The v1.0 data release contains details on contributing partner studies, sample metadata and key sample attributes inferred from genomic data. The release is accompanied by a publication, detailing the project and highlighting a number of key analyses and results. This record contains files providing supplementary information, including all methods and protocols used, details of reagents, information about the participating studies, as well as sample information, accession numbers, genotype calls and phenotype predictions. GenRe-Mekong data were produced using the SPOTmalaria genetic surveillance framework. SPOTmalaria implements standardized methodologies and processing pipelines for extracting and nalysed genetic data from small blood samples collected from malaria-infected patients. The methodology defines procedures for every step of the process: ethics submissions, dried blood spots sample collection, sample extraction, quality assurance, and genotyping. SPOTmalaria also provides informatics support for sample management, data processing, storage and delivery. These data are available open access. Publications using these data should acknowledge and cite the source of the data using the following form:‘This publication uses data from the GenRe-Mekong Project, as described in: Jacob CG et al.; Genetic surveillance in the Greater Mekong Subregion and South Asia to support malaria control and elimination. eLife 2021;10:e62997 DOI: 10.7554/eLife.62997’ Data files: Study information: Details of the 12 partner studies contributing to GenRe-Mekong, including study description, contact information and key people. Available as .docx and .pdf. Genotypes, Phenotype predictions and Sample provenance: Sample information including provenance, genotype and phenotype information: for the 9,623 samples analysed. Phenotype rules: details of the heuristics utilized to map genetic markers to drug resistance phenotype predictions. Available as .docx and .pdf. Imputation rules: details of the heuristics utilized fill in missing genotypes in drug resistance-related genes based on genotypes at linked loci. v0.39 and v0.40 are available, with v.040 being the latest. SPOTmalaria Technical Notes and Methods: contains technical details and procedures covering both SPOTmalaria V1 and SPOTmalaria V2 platforms. Available as .docx and .pdf. It references the following supplementary files: Supplementary File 1: Spreadsheet detailing genotyped loci and primer sequences Supplementary File 2: Map of mitochondrial loci used for species detection Supplementary File 3: FASTA file containing the kelch13 nucleotide sequence used