Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 375-379 |
| Number of pages | 5 |
| Journal | Nature |
| Volume | 487 |
| DOIs | |
| Publication status | Published - 19 Jul 2012 |
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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 journal › Article › Research › peer-review
TY - JOUR
T1 - Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
AU - Manske, Magnus
AU - Miotto, Olivo
AU - Campino, Susana
AU - Auburn, Sarah
AU - Almagro-Gracia, Jacob
AU - Maslen, Gareth
AU - O'Brien, J
AU - Djimde, Abdoulaye
AU - Doumbo, Ogobara
AU - Zongo, Issaka
AU - Ouedraogo, Jean
AU - Michon, Pascal
AU - Mueller, Ivo
AU - Siba, Peter
AU - Nzila, Alexis
AU - Borrman, Steffen
AU - Kiara, Steven
AU - Marsh, Kevin
AU - Jiang, Hongying
AU - Su, Xin-Zhuan
AU - Amaratunga, Chanaki
AU - Fairhurst, Rick
AU - Socheat, Duong
AU - Nosten, François
AU - Imwong, Mallika
AU - White, Nicholas J
AU - Sanders, Mandy
AU - Anastasi, Elisa
AU - Alcock, Daniel
AU - Drury, Eleanor
AU - Oyola, S
AU - Quail, Michael
AU - Turner, Daniel
AU - Ruano-Rubio, V
AU - Jyothi, D
AU - Amenga-Etego, Lucas
AU - Hubbart, C
AU - Jeffreys, A
AU - Rowlands, Kate
AU - Sutherland, Colin
AU - Roper, C
AU - Mangano, Valentina
AU - Modiano, David
AU - Tan, J
AU - Ferdig, M
AU - Amambua-Ngwa, A
AU - Conway, D
AU - Takala-Harrison, Shannon
AU - Plowe, C
AU - Rayner, J
AU - Rockett, Kirk
AU - Clark, Taane
AU - Newbold, Christopher
AU - Berriman, M
AU - MacInnis, Bronwyn
AU - Kwiatkowski, Dominic
PY - 2012/7/19
Y1 - 2012/7/19
N2 - 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.
AB - 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.
KW - protozoal DNA
KW - allele
KW - blood
KW - drug resistance
KW - genetic variation
KW - genome
KW - inbreeding
KW - infectious disease
KW - malaria
KW - polymorphism
KW - population structure
KW - protozoan
KW - public health
KW - quality control
KW - Africa
KW - article
KW - Asia
KW - DNA determination
KW - exon
KW - gene frequency
KW - gene linkage disequilibrium
KW - gene locus
KW - gene sequence
KW - genetic variability
KW - genotype
KW - heterozygosity
KW - host range
KW - malaria falciparum
KW - nonhuman
KW - Pacific islands
KW - Plasmodium falciparum
KW - priority journal
KW - single nucleotide polymorphism
KW - Alleles
KW - Biodiversity
KW - Genome, Protozoan
KW - Genotype
KW - High-Throughput Nucleotide Sequencing
KW - Humans
KW - Malaria, Falciparum
KW - Phylogeny
KW - Polymorphism, Single Nucleotide
KW - Principal Component Analysis
KW - Australia
KW - Pacific Ocean
UR - http://www.scopus.com/inward/record.url?scp=84863982076&partnerID=8YFLogxK
U2 - 10.1038/nature11174
DO - 10.1038/nature11174
M3 - Article
VL - 487
SP - 375
EP - 379
JO - Nature
JF - Nature
SN - 0028-0836
ER -