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Manske M Miotto O Campino S Auburn S Almagro-Garcia J Maslen G O'Brien J Djimde A Doumbo O Zongo I Ouedraogo JB Michon P Mueller I Siba P Nzila A Borrmann S Kiara SM Marsh K Jiang H Su XZ Amaratunga C Fairhurst R Socheat D Nosten F Imwong M White NJ Sanders M Anastasi E Alcock D Drury E Oyola S Quail MA Turner DJ Ruano-Rubio V Jyothi D Amenga-Etego L Hubbart C Jeffreys A Rowlands K Sutherland C Roper C Mangano V Modiano D Tan JC Ferdig MT Amambua-Ngwa A Conway DJ Takala-Harrison S Plowe CV 《Nature》2012,487(7407):375-379
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. 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. 相似文献
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