Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Magnus Manske, Olivo Miotto, Susana Campino, Sarah Auburn, Jacob Almagro-Gracia, Gareth Maslen, J O'Brien, Abdoulaye Djimde, Ogobara Doumbo, Issaka Zongo, Jean Ouedraogo, Pascal Michon, Ivo Mueller, Peter Siba, Alexis Nzila, Steffen Borrman, Steven Kiara, Kevin Marsh, Hongying Jiang, Xin-Zhuan Su & 36 others Chanaki Amaratunga, Rick Fairhurst, Duong Socheat, François Nosten, Mallika Imwong, Nicholas J White, Mandy Sanders, Elisa Anastasi, Daniel Alcock, Eleanor Drury, S Oyola, Michael Quail, Daniel Turner, V Ruano-Rubio, D Jyothi, Lucas Amenga-Etego, C Hubbart, A Jeffreys, Kate Rowlands, Colin Sutherland, C Roper, Valentina Mangano, David Modiano, J Tan, M Ferdig, A Amambua-Ngwa, D Conway, Shannon Takala-Harrison, C Plowe, J Rayner, Kirk Rockett, Taane Clark, Christopher Newbold, M Berriman, Bronwyn MacInnis, Dominic Kwiatkowski

    Research output: Contribution to journalArticleResearchpeer-review

    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.
    Original languageEnglish
    Pages (from-to)375-379
    Number of pages5
    JournalNature
    Volume487
    DOIs
    Publication statusPublished - 19 Jul 2012

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    Genes
    Population distribution
    Public health
    Nucleotides
    Polymorphism
    Quality control
    DNA
    Blood
    Parasites

    Cite this

    Manske, M., Miotto, O., Campino, S., Auburn, S., Almagro-Gracia, J., Maslen, G., ... Kwiatkowski, D. (2012). Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature, 487, 375-379. https://doi.org/10.1038/nature11174
    Manske, Magnus ; Miotto, Olivo ; Campino, Susana ; Auburn, Sarah ; Almagro-Gracia, Jacob ; Maslen, Gareth ; O'Brien, J ; Djimde, Abdoulaye ; Doumbo, Ogobara ; Zongo, Issaka ; Ouedraogo, Jean ; Michon, Pascal ; Mueller, Ivo ; Siba, Peter ; Nzila, Alexis ; Borrman, Steffen ; Kiara, Steven ; Marsh, Kevin ; Jiang, Hongying ; Su, Xin-Zhuan ; Amaratunga, Chanaki ; Fairhurst, Rick ; Socheat, Duong ; Nosten, François ; Imwong, Mallika ; White, Nicholas J ; Sanders, Mandy ; Anastasi, Elisa ; Alcock, Daniel ; Drury, Eleanor ; Oyola, S ; Quail, Michael ; Turner, Daniel ; Ruano-Rubio, V ; Jyothi, D ; Amenga-Etego, Lucas ; Hubbart, C ; Jeffreys, A ; Rowlands, Kate ; Sutherland, Colin ; Roper, C ; Mangano, Valentina ; Modiano, David ; Tan, J ; Ferdig, M ; Amambua-Ngwa, A ; Conway, D ; Takala-Harrison, Shannon ; Plowe, C ; Rayner, J ; Rockett, Kirk ; Clark, Taane ; Newbold, Christopher ; Berriman, M ; MacInnis, Bronwyn ; Kwiatkowski, Dominic. / Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. In: Nature. 2012 ; Vol. 487. pp. 375-379.
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    Manske, M, Miotto, O, Campino, S, Auburn, S, Almagro-Gracia, J, Maslen, G, O'Brien, J, Djimde, A, Doumbo, O, Zongo, I, Ouedraogo, J, Michon, P, Mueller, I, Siba, P, Nzila, A, Borrman, S, Kiara, S, Marsh, K, Jiang, H, Su, X-Z, Amaratunga, C, Fairhurst, R, Socheat, D, Nosten, F, Imwong, M, White, NJ, Sanders, M, Anastasi, E, Alcock, D, Drury, E, Oyola, S, Quail, M, Turner, D, Ruano-Rubio, V, Jyothi, D, Amenga-Etego, L, Hubbart, C, Jeffreys, A, Rowlands, K, Sutherland, C, Roper, C, Mangano, V, Modiano, D, Tan, J, Ferdig, M, Amambua-Ngwa, A, Conway, D, Takala-Harrison, S, Plowe, C, Rayner, J, Rockett, K, Clark, T, Newbold, C, Berriman, M, MacInnis, B & Kwiatkowski, D 2012, 'Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing', Nature, vol. 487, pp. 375-379. https://doi.org/10.1038/nature11174

    Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. / Manske, Magnus; Miotto, Olivo; Campino, Susana; Auburn, Sarah; Almagro-Gracia, Jacob; Maslen, Gareth; O'Brien, J; Djimde, Abdoulaye; Doumbo, Ogobara; Zongo, Issaka; Ouedraogo, Jean; Michon, Pascal; Mueller, Ivo; Siba, Peter; Nzila, Alexis; Borrman, Steffen; Kiara, Steven; Marsh, Kevin; Jiang, Hongying; Su, Xin-Zhuan; Amaratunga, Chanaki; Fairhurst, Rick; Socheat, Duong; Nosten, François; Imwong, Mallika; White, Nicholas J; Sanders, Mandy; Anastasi, Elisa; Alcock, Daniel; Drury, Eleanor; Oyola, S; Quail, Michael; Turner, Daniel; Ruano-Rubio, V; Jyothi, D; Amenga-Etego, Lucas; Hubbart, C; Jeffreys, A; Rowlands, Kate; Sutherland, Colin; Roper, C; Mangano, Valentina; Modiano, David; Tan, J; Ferdig, M; Amambua-Ngwa, A; Conway, D; Takala-Harrison, Shannon; Plowe, C; Rayner, J; Rockett, Kirk; Clark, Taane; Newbold, Christopher; Berriman, M; MacInnis, Bronwyn; Kwiatkowski, Dominic.

    In: Nature, Vol. 487, 19.07.2012, p. 375-379.

    Research output: Contribution to journalArticleResearchpeer-review

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    Manske M, Miotto O, Campino S, Auburn S, Almagro-Gracia J, Maslen G et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012 Jul 19;487:375-379. https://doi.org/10.1038/nature11174