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 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.

Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

MANGANO, VALENTINA;
2012-01-01

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(1,2). 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
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; Mangano, Valentina; 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
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11568/839784
Citazioni
  • ???jsp.display-item.citation.pmc??? 277
  • Scopus 371
  • ???jsp.display-item.citation.isi??? 357
social impact