Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

M Manske; O Miotto; S Campino; S Auburn; J Almagro-Garcia; G Maslen; J O'Brien; A Djimde; O Doumbo; I Zongo; JB Ouedraogo; P Michon; I Mueller; P Siba; A Nzila; S Borrmann; SM Kiara; K Marsh; H Jiang; XZ Su; C Amaratunga; R Fairhurst; D Socheat; F Nosten; M Imwong; NJ White; M Sanders; E Anastasi; D Alcock; E Drury; S Oyola; MA Quail; DJ Turner; V Ruano-Rubio; D Jyothi; L Amenga-Etego; C Hubbart; A Jeffreys; K Rowlands; C Sutherland; C Roper; V Mangano; D Modiano; JC Tan; MT Ferdig; A Amambua-Ngwa; DJ Conway; S Takala-Harrison; CV Plowe; JC Rayner; KA Rockett; TG Clark; CI Newbold; M Berriman; B MacInnis; DP Kwiatkowski

Journal article

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

M Manske, O Miotto, S Campino, S Auburn, J Almagro-Garcia, G Maslen, J O'Brien, A Djimde, O Doumbo, I Zongo, JB Ouedraogo, P Michon, I Mueller, P Siba, A Nzila, S Borrmann, SM Kiara, K Marsh, H Jiang, XZ Su Show all

Nature | NATURE PUBLISHING GROUP | Published : 2012

DOI: 10.1038/nature11174

Open access

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. 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 i..

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University of Melbourne Researchers

Ivo Mueller Author

Grants

Awarded by Division of Intramural Research, National Institute of Allergy and Infectious Diseases

Funding Acknowledgements

We thank G. Dougan and N. Day for support, and T. Anderson and M. Mackinnon for comments. The sequencing and analysis components of this study were supported by the Wellcome Trust through Sanger Institute core funding (077012/Z/05/Z; 098051) and a Strategic Award (090770/Z/09/Z); the Medical Research Council (MRC) through the MRC Centre for Genomics and Global Health (G0600718) and an MRC Professorship to D.P.K. (G19/9). Other parts of this study were partly supported by the Wellcome Trust including core support to the Wellcome Trust Centre for Human Genetics (075491/Z/04; 090532/Z/09/Z); the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; and a Howard Hughes Medical Institute International Scholarship (55005502) to A.D.