Abstract
MotivationThe presence of multiple infecting strains of the malarial parasite Plasmodium falciparum affects key phenotypic traits, including drug resistance and risk of severe disease. Advances in protocols and sequencing technology have made it possible to obtain high-coverage genome-wide sequencing data from blood samples and blood spots taken in the field. However, analyzing and interpreting such data is challenging because of the high rate of multiple infections present.ResultsWe have developed a statistical method and implementation for deconvolving multiple genome sequences present in an individual with mixed infections. The software package DEploid uses haplotype structure within a reference panel of clonal isolates as a prior for haplotypes present in a given sample. It estimates the number of strains, their relative proportions and the haplotypes presented in a sample, allowing researchers to study multiple infection in malaria with an unprecedented level of detail.Availability and implementationThe open source implementation DEploid is freely available at https://github.com/mcveanlab/DEploid under the conditions of the GPLv3 license. An R version is available at https://github.com/mcveanlab/DEploid-r.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
Malaria remains one of the top global health problems
We have developed a statistical method and implementation for deconvolving multiple genome sequences present in an individual with mixed infections
The software package DEploid uses haplotype structure within a reference panel of clonal isolates as a prior for haplotypes present in a given sample. It estimates the number of strains, their relative proportions and the haplotypes presented in a sample, allowing researchers to study multiple infection in malaria with an unprecedented level of detail
Summary
Malaria remains one of the top global health problems. The majority of malaria related deaths are caused by the Plasmodium falciparum parasite (WHO, 2016), transmitted by mosquitoes of the genus Anopheles. The presence of multiple strains of P.falciparum makes fine scale analysis of genetic variation challenging, since genetic differences between strains of this haploid organism will appear as heterozygous loci Such mixed calls confound methods that exploit haplotype data to detect, among other phenomena, the occurrence of natural selection or recent demographic events (Harris and Nielsen, 2013; Lawson et al, 2012; Mathieson and McVean, 2014; Sabeti et al, 2002). In light of these difficulties, researchers usually focus on clonal infections or resort to heuristic methods for resolving heterozygous genotypes.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
