NDLI: Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

Content Provider	PubMed Central
Author	Manske, Magnus Miotto, Olivo Campino, Susana Auburn, Sarah Jacob, Almagro-garcia Maslen, Gareth O’brien, Jack Abdoulaye, Djimde Doumbo, Ogobara Zongo, Issaka Ouedraogo, Jean-bosco Michon, Pascal Mueller, Ivo Peter, Siba Nzila, Alexis Borrmann, Steffen Kiara, Steven M. Marsh, Kevin Jiang, Hongying Su, Xin-zhuan Amaratunga, Chanaki Fairhurst, Rick Duong, Socheat Francois, Nosten Mallika, Imwong White, Nicholas J. Sanders, Mandy Anastasi, Elisa Alcock, Dan Drury, Eleanor Oyola, Samuel Quail, Michael A. Turner, Daniel J. Rubio, Valentin Ruano Jyothi, Dushyanth Amenga-etego, Lucas Hubbart, Christina Jeffreys, Anna Rowlands, Kate Sutherland, Colin Roper, Cally Mangano, Valentina Modiano, David Tan, John C. Ferdig, Michael T. Alfred, Amambua-ngwa Conway, David J. Shannon, Takala-harrison Plowe, Christopher V. Rayner, Julian C. Rockett, Kirk A. Clark, Taane G. Newbold, Chris I. Berriman, Matthew Macinnis, Bronwyn Kwiatkowski, Dominic P.
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 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 SNPs 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 exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.
Related Links	http://dx.doi.org/10.1038/nature11174
Ending Page	379
Page Count	5
Starting Page	375
File Format	PDF
ISSN	00280836
e-ISSN	14764687
Journal	Nature
Issue Number	7407
Volume Number	487
Language	English
Publisher Date	2012-06-01
Access Restriction	Open
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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