Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

  title={Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing},
  author={Magnus Manske and Olivo Miotto and Susana G. Campino and Sarah Auburn and Jacob Almagro-Garcia and Gareth L. Maslen and Jack J. O’Brien and Abdoulaye A. Djimd{\'e} and Ogobara K. Doumbo and Issaka Zongo and Jean-Bosco Ou{\'e}draogo and Pascal Michon and Ivo Mueller and Peter Siba and Alexis M Nzila and Steffen Borrmann and Steven M. Kiara and Kevin Marsh and Hongying Jiang and Xin-Zhuan Su and Chanaki Amaratunga and Rick M. Fairhurst and Doung 7 Socheat and François H Nosten and Mallika Imwong and Nicholas J White and Mandy J. Sanders and Elisa Anastasi and Dan Alcock and Eleanor Drury and Samuel O. Oyola and Michael A. Quail and Daniel J Turner and Valentin Ruano Rubio and Dushyanth Jyothi and Lucas Amenga-Etego and Christina Hubbart and Anna E. Jeffreys and Kate Rowlands and Colin J. Sutherland and Cally Roper and Valentina Dianora Mangano and David Laurence Modiano and John Tan and Michael T. Ferdig and Alfred Amambua-Ngwa and David J Conway and Shannon L Takala-Harrison and Christopher V. Plowe and Julian C. Rayner and Kirk A. Rockett and Taane G. Clark and Chris I Newbold and Matthew Berriman and Bronwyn Macinnis and Dominic P Kwiatkowski},
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… CONTINUE READING