Publication:
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Issued Date

2012-07-19

Resource Type

Article

ISSN

14764687
00280836

DOI

10.1038/nature11174

Other identifier(s)

2-s2.0-84863982076

Rights

Mahidol University

Rights Holder(s)

SCOPUS

Bibliographic Citation

Nature. Vol.487, No.7407 (2012), 375-379

Suggested Citation

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, Nicholas J. White, Mandy Sanders, Elisa Anastasi, Dan Alcock, Eleanor Drury, Samuel Oyola, Michael A. Quail, Daniel J. Turner, Valentin Ruano-Rubio, Dushyanth Jyothi, Lucas Amenga-Etego, Christina Hubbart, Anna Jeffreys, Kate Rowlands, Colin Sutherland, Cally Roper, Valentina Mangano, David Modiano, John C. Tan, Michael T. Ferdig, Alfred Amambua-Ngwa, David J. Conway, Shannon Takala-Harrison, Christopher V. Plowe, Julian C. Rayner, Kirk A. Rockett, Taane G. Clark, Chris I. Newbold, Matthew Berriman, Bronwyn MacInnis, Dominic P. Kwiatkowski Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. Vol.487, No.7407 (2012), 375-379. doi:10.1038/nature11174 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/15243

Research Projects

Organizational Units

Authors

Journal Issue

Thesis

Title

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Author(s)

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
 Nicholas J. White
 Mandy Sanders
 Elisa Anastasi
 Dan Alcock
 Eleanor Drury
 Samuel Oyola
 Michael A. Quail
 Daniel J. Turner
 Valentin Ruano-Rubio
 Dushyanth Jyothi
 Lucas Amenga-Etego
 Christina Hubbart
 Anna Jeffreys
 Kate Rowlands
 Colin Sutherland
 Cally Roper
 Valentina Mangano
 David Modiano
 John C. Tan
 Michael T. Ferdig
 Alfred Amambua-Ngwa
 David J. Conway
 Shannon Takala-Harrison
 Christopher V. Plowe
 Julian C. Rayner
 Kirk A. Rockett
 Taane G. Clark
 Chris I. Newbold
 Matthew Berriman
 Bronwyn MacInnis
 Dominic P. Kwiatkowski

Other Contributor(s)

Wellcome Trust Sanger Institute
 University of Oxford
 Mahidol University
 Menzies School of Health Research
 Wellcome Trust Centre for Human Genetics
 University of Bamako Faculty of Medicine, Pharmacy and Odonto-Stomatology
 Institut de Recherche en Sciences de la Santé
 Papua New Guinea Institute of Medical Research
 Wellcome Trust Research Laboratories Nairobi
 National Institute of Allergy and Infectious Diseases
 Cambodia National Malaria Centre
 Shoklo Malaria Research Unit
 Navrongo Health Centre
 London School of Hygiene & Tropical Medicine
 Universita degli Studi di Roma La Sapienza
 University of Notre Dame
 Medical Research Council Laboratories Gambia
 University of Maryland, Baltimore
 Weatherall Institute of Molecular Medicine

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 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. © 2012 Macmillan Publishers Limited. All rights reserved.

Keyword(s)

Multidisciplinary

Availability

URI

https://repository.li.mahidol.ac.th/handle/20.500.14594/15243

Collections

Scopus 2011-2015