Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
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 par...
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th-mahidol.152432018-06-11T12:27:39Z Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing 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 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 Multidisciplinary 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. 2018-06-11T05:27:39Z 2018-06-11T05:27:39Z 2012-07-19 Article Nature. Vol.487, No.7407 (2012), 375-379 10.1038/nature11174 14764687 00280836 2-s2.0-84863982076 https://repository.li.mahidol.ac.th/handle/123456789/15243 Mahidol University SCOPUS https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=84863982076&origin=inward |
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Multidisciplinary 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 |
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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. |
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Wellcome Trust Sanger Institute |
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Wellcome Trust Sanger Institute 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 |
format |
Article |
author |
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 |
author_sort |
Magnus Manske |
title |
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing |
title_short |
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing |
title_full |
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing |
title_fullStr |
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing |
title_full_unstemmed |
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing |
title_sort |
analysis of plasmodium falciparum diversity in natural infections by deep sequencing |
publishDate |
2018 |
url |
https://repository.li.mahidol.ac.th/handle/123456789/15243 |
_version_ |
1763497357367836672 |