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. 1,2 Here we describe methods for large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of par...

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Main Authors:	Manske, Magnus, Miotto, Olivo, Campino, Susana, Auburn, Sarah, Almagro-Garcia, Jacob, Maslen, Gareth, O’Brien, Jack, Djimde, Abdoulaye, Doumbo, Ogobara, Zongo, Issaka, Ouedraogo, Jean-Bosco, Michon, Pascal, Mueller, Ivo, Siba, Peter, Nzila, Alexis, Borrmann, Steffen, Kiara, Steven M., Marsh, Kevin, Jiang, Hongying, Su, Xin-Zhuan, Amaratunga, Chanaki, Fairhurst, Rick, Socheat, Duong, Nosten, Francois, Imwong, Mallika, White, Nicholas J., Sanders, Mandy, Anastasi, Elisa, Alcock, Dan, Drury, Eleanor, Oyola, Samuel, Quail, Michael A., Turner, Daniel J., Rubio, Valentin Ruano, Jyothi, Dushyanth, Amenga-Etego, Lucas, Hubbart, Christina, Jeffreys, Anna, Rowlands, Kate, Sutherland, Colin, Roper, Cally, Mangano, Valentina, Modiano, David, Tan, John C., Ferdig, Michael T., Amambua-Ngwa, Alfred, Conway, David J., Takala-Harrison, Shannon, Plowe, Christopher V., Rayner, Julian C., Rockett, Kirk A., Clark, Taane G., Newbold, Chris I., Berriman, Matthew, MacInnis, Bronwyn, Kwiatkowski, Dominic P.
Format:	Online
Language:	English
Published:	2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738909/

id	pubmed-3738909
recordtype	oai_dc
spelling	pubmed-37389092013-08-09 Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing Manske, Magnus Miotto, Olivo Campino, Susana Auburn, Sarah Almagro-Garcia, Jacob Maslen, Gareth O’Brien, Jack Djimde, Abdoulaye Doumbo, Ogobara Zongo, Issaka Ouedraogo, Jean-Bosco Michon, Pascal Mueller, Ivo Siba, Peter Nzila, Alexis Borrmann, Steffen Kiara, Steven M. Marsh, Kevin Jiang, Hongying Su, Xin-Zhuan Amaratunga, Chanaki Fairhurst, Rick Socheat, Duong Nosten, Francois Imwong, Mallika White, Nicholas J. Sanders, Mandy Anastasi, Elisa Alcock, Dan Drury, Eleanor Oyola, Samuel Quail, Michael A. Turner, Daniel J. Rubio, Valentin Ruano Jyothi, Dushyanth Amenga-Etego, Lucas Hubbart, Christina Jeffreys, Anna Rowlands, Kate Sutherland, Colin Roper, Cally Mangano, Valentina Modiano, David Tan, John C. Ferdig, Michael T. Amambua-Ngwa, Alfred Conway, David J. Takala-Harrison, Shannon Plowe, Christopher V. Rayner, Julian C. Rockett, Kirk A. Clark, Taane G. Newbold, Chris I. Berriman, Matthew MacInnis, Bronwyn Kwiatkowski, Dominic P. Article 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. 1,2 Here we describe methods for 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 SNPs 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 exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome. 2012-07-19 /pmc/articles/PMC3738909/ /pubmed/22722859 http://dx.doi.org/10.1038/nature11174 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Manske, Magnus Miotto, Olivo Campino, Susana Auburn, Sarah Almagro-Garcia, Jacob Maslen, Gareth O’Brien, Jack Djimde, Abdoulaye Doumbo, Ogobara Zongo, Issaka Ouedraogo, Jean-Bosco Michon, Pascal Mueller, Ivo Siba, Peter Nzila, Alexis Borrmann, Steffen Kiara, Steven M. Marsh, Kevin Jiang, Hongying Su, Xin-Zhuan Amaratunga, Chanaki Fairhurst, Rick Socheat, Duong Nosten, Francois Imwong, Mallika White, Nicholas J. Sanders, Mandy Anastasi, Elisa Alcock, Dan Drury, Eleanor Oyola, Samuel Quail, Michael A. Turner, Daniel J. Rubio, Valentin Ruano Jyothi, Dushyanth Amenga-Etego, Lucas Hubbart, Christina Jeffreys, Anna Rowlands, Kate Sutherland, Colin Roper, Cally Mangano, Valentina Modiano, David Tan, John C. Ferdig, Michael T. Amambua-Ngwa, Alfred Conway, David J. Takala-Harrison, Shannon Plowe, Christopher V. Rayner, Julian C. Rockett, Kirk A. Clark, Taane G. Newbold, Chris I. Berriman, Matthew MacInnis, Bronwyn Kwiatkowski, Dominic P.
spellingShingle	Manske, Magnus Miotto, Olivo Campino, Susana Auburn, Sarah Almagro-Garcia, Jacob Maslen, Gareth O’Brien, Jack Djimde, Abdoulaye Doumbo, Ogobara Zongo, Issaka Ouedraogo, Jean-Bosco Michon, Pascal Mueller, Ivo Siba, Peter Nzila, Alexis Borrmann, Steffen Kiara, Steven M. Marsh, Kevin Jiang, Hongying Su, Xin-Zhuan Amaratunga, Chanaki Fairhurst, Rick Socheat, Duong Nosten, Francois Imwong, Mallika White, Nicholas J. Sanders, Mandy Anastasi, Elisa Alcock, Dan Drury, Eleanor Oyola, Samuel Quail, Michael A. Turner, Daniel J. Rubio, Valentin Ruano Jyothi, Dushyanth Amenga-Etego, Lucas Hubbart, Christina Jeffreys, Anna Rowlands, Kate Sutherland, Colin Roper, Cally Mangano, Valentina Modiano, David Tan, John C. Ferdig, Michael T. Amambua-Ngwa, Alfred Conway, David J. Takala-Harrison, Shannon Plowe, Christopher V. Rayner, Julian C. Rockett, Kirk A. Clark, Taane G. Newbold, Chris I. Berriman, Matthew MacInnis, Bronwyn Kwiatkowski, Dominic P. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
author_facet	Manske, Magnus Miotto, Olivo Campino, Susana Auburn, Sarah Almagro-Garcia, Jacob Maslen, Gareth O’Brien, Jack Djimde, Abdoulaye Doumbo, Ogobara Zongo, Issaka Ouedraogo, Jean-Bosco Michon, Pascal Mueller, Ivo Siba, Peter Nzila, Alexis Borrmann, Steffen Kiara, Steven M. Marsh, Kevin Jiang, Hongying Su, Xin-Zhuan Amaratunga, Chanaki Fairhurst, Rick Socheat, Duong Nosten, Francois Imwong, Mallika White, Nicholas J. Sanders, Mandy Anastasi, Elisa Alcock, Dan Drury, Eleanor Oyola, Samuel Quail, Michael A. Turner, Daniel J. Rubio, Valentin Ruano Jyothi, Dushyanth Amenga-Etego, Lucas Hubbart, Christina Jeffreys, Anna Rowlands, Kate Sutherland, Colin Roper, Cally Mangano, Valentina Modiano, David Tan, John C. Ferdig, Michael T. Amambua-Ngwa, Alfred Conway, David J. Takala-Harrison, Shannon Plowe, Christopher V. Rayner, Julian C. Rockett, Kirk A. Clark, Taane G. Newbold, Chris I. Berriman, Matthew MacInnis, Bronwyn Kwiatkowski, Dominic P.
author_sort	Manske, Magnus
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
description	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. 1,2 Here we describe methods for 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 SNPs 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 exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738909/
_version_	1612001997758660608

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

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