Links
- ORCID
- ORCID
- ORCID
- ORCID
- Crossref
- [www.ncbi.nlm.nih.gov] | PDF
- [hdl.handle.net]
- [hdl.handle.net]
- [europepmc.org] | PDF
- [www.researchgate.net] | PDF
- [www.ncbi.nlm.nih.gov] | PDF
- [www.ncbi.nlm.nih.gov] | PDF
- [researchonline.lshtm.ac.uk] | PDF
Tools
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
,
Olivo Miotto ,
Susana Campino,
Sarah Auburn,
Jacob Almagro-Garcia,
Gareth Maslen,
Jack O'Brien,
Jack O’Brien,
Abdoulaye Djimde,
Ogobara Doumbo,
Issaka Zongo,
Jean-Bosco Ouedraogo,
Pascal Michon,
Ivo Mueller,
Peter Siba
and other authors.
Abstract
Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance(1,2). Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.