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Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.

Publication ,  Journal Article
Manske, M; Miotto, O; Campino, S; Auburn, S; Almagro-Garcia, J; Maslen, G; O'Brien, J; Djimde, A; Doumbo, O; Zongo, I; Ouedraogo, J-B; Siba, P ...
Published in: Nature
July 2012

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.

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Published In

Nature

DOI

EISSN

1476-4687

ISSN

0028-0836

Publication Date

July 2012

Volume

487

Issue

7407

Start / End Page

375 / 379

Related Subject Headings

  • Principal Component Analysis
  • Polymorphism, Single Nucleotide
  • Plasmodium falciparum
  • Phylogeny
  • Malaria, Falciparum
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genotype
  • Genome, Protozoan
  • General Science & Technology
 

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Manske, M., Miotto, O., Campino, S., Auburn, S., Almagro-Garcia, J., Maslen, G., … Kwiatkowski, D. P. (2012). Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature, 487(7407), 375–379. https://doi.org/10.1038/nature11174
Manske, Magnus, Olivo Miotto, Susana Campino, Sarah Auburn, Jacob Almagro-Garcia, Gareth Maslen, Jack O’Brien, et al. “Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.Nature 487, no. 7407 (July 2012): 375–79. https://doi.org/10.1038/nature11174.
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012 Jul;487(7407):375–9.
Manske, Magnus, et al. “Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.Nature, vol. 487, no. 7407, July 2012, pp. 375–79. Epmc, doi:10.1038/nature11174.
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G, O’Brien J, Djimde A, Doumbo O, Zongo I, Ouedraogo J-B, Michon P, Mueller I, Siba P, Nzila A, Borrmann S, Kiara SM, 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 MA, Turner DJ, Ruano-Rubio V, Jyothi D, Amenga-Etego L, Hubbart C, Jeffreys A, Rowlands K, Sutherland C, Roper C, Mangano V, Modiano D, Tan JC, Ferdig MT, Amambua-Ngwa A, Conway DJ, Takala-Harrison S, Plowe CV, Rayner JC, Rockett KA, Clark TG, Newbold CI, Berriman M, MacInnis B, Kwiatkowski DP. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012 Jul;487(7407):375–379.
Journal cover image

Published In

Nature

DOI

EISSN

1476-4687

ISSN

0028-0836

Publication Date

July 2012

Volume

487

Issue

7407

Start / End Page

375 / 379

Related Subject Headings

  • Principal Component Analysis
  • Polymorphism, Single Nucleotide
  • Plasmodium falciparum
  • Phylogeny
  • Malaria, Falciparum
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genotype
  • Genome, Protozoan
  • General Science & Technology