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Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

SprMorn 添加于 2012/6/18 13:46:11  987次阅读 | 0次推荐 | 0个评论

Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance1, 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.

作 者:Magnus Manske, Olivo Miotto, Susana Campino, Sarah Auburn, Jacob Almagro-Garcia, Gareth Maslen, Jack O’Brien, Abdoulaye Djimde, Ogobara Doumbo, Issaka Zongo, Jean-Bosco Ouedraogo, Pascal Michon, Ivo Mueller, Peter Siba, Alexis Nzila, Steffen Borrmann, Steven M. Kiara, Kevin Marsh, Hongying Jiang, Xin-Zhuan Su, Chanaki Amaratunga, Rick Fairhurst, Duong Socheat, Francois Nosten, Mallika Imwong et al.
期刊名称: nature
期卷页: 第卷 第期 ~页
学科领域:生命科学 » 遗传学与生物信息学 » 基因组学
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原文链接:http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11174.html
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相关报道: http://paper.sciencenet.cn/htmlpaper/20126181348378624916.shtm
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