Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.
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 par...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
2012
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| _version_ | 1826267610120978432 |
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| author | Manske, M Miotto, O Campino, S Auburn, S Almagro-Garcia, J Maslen, G O'Brien, J Djimde, A Doumbo, O Zongo, I Ouedraogo, J Michon, P Mueller, I Siba, P Nzila, A Borrmann, S Kiara, S Marsh, K Jiang, H Su, X Amaratunga, C Fairhurst, R Socheat, D Nosten, F Imwong, M |
| author_facet | Manske, M Miotto, O Campino, S Auburn, S Almagro-Garcia, J Maslen, G O'Brien, J Djimde, A Doumbo, O Zongo, I Ouedraogo, J Michon, P Mueller, I Siba, P Nzila, A Borrmann, S Kiara, S Marsh, K Jiang, H Su, X Amaratunga, C Fairhurst, R Socheat, D Nosten, F Imwong, M |
| author_sort | Manske, M |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T20:56:49Z |
| format | Journal article |
| id | oxford-uuid:398b526d-1ff9-4b93-95a4-caea3a746679 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T20:56:49Z |
| publishDate | 2012 |
| record_format | dspace |
| spelling | oxford-uuid:398b526d-1ff9-4b93-95a4-caea3a7466792022-03-26T13:56:19ZAnalysis of Plasmodium falciparum diversity in natural infections by deep sequencing.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:398b526d-1ff9-4b93-95a4-caea3a746679EnglishSymplectic Elements at Oxford2012Manske, MMiotto, OCampino, SAuburn, SAlmagro-Garcia, JMaslen, GO'Brien, JDjimde, ADoumbo, OZongo, IOuedraogo, JMichon, PMueller, ISiba, PNzila, ABorrmann, SKiara, SMarsh, KJiang, HSu, XAmaratunga, CFairhurst, RSocheat, DNosten, FImwong, MMalaria 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. |
| spellingShingle | Manske, M Miotto, O Campino, S Auburn, S Almagro-Garcia, J Maslen, G O'Brien, J Djimde, A Doumbo, O Zongo, I Ouedraogo, J Michon, P Mueller, I Siba, P Nzila, A Borrmann, S Kiara, S Marsh, K Jiang, H Su, X Amaratunga, C Fairhurst, R Socheat, D Nosten, F Imwong, M Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. |
| title | Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. |
| title_full | Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. |
| title_fullStr | Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. |
| title_full_unstemmed | Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. |
| title_short | Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. |
| title_sort | analysis of plasmodium falciparum diversity in natural infections by deep sequencing |
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