PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation

PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation

Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic va...

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Main Authors: Preston, Mark D., Assefa, Samuel A., Ocholla, Harold, Sutherland, Colin J., Borrmann, Steffen, Nzila, Alexis, Michon, Pascal, Hien, Tran Tinh, Bousema, Teun, Drakeley, Christopher J., Zongo, Issaka, Ouédraogo, Jean-Bosco, Djimde, Abdoulaye A., Doumbo, Ogobara K., Nosten, Francois, Fairhurst, Rick M., Conway, David J., Roper, Cally, Clark, Taane G.
Format: Online
Language:English
Published: Oxford University Press 2014
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017360/
id pubmed-4017360
recordtype oai_dc
spelling pubmed-40173602014-05-12 PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation Preston, Mark D. Assefa, Samuel A. Ocholla, Harold Sutherland, Colin J. Borrmann, Steffen Nzila, Alexis Michon, Pascal Hien, Tran Tinh Bousema, Teun Drakeley, Christopher J. Zongo, Issaka Ouédraogo, Jean-Bosco Djimde, Abdoulaye A. Doumbo, Ogobara K. Nosten, Francois Fairhurst, Rick M. Conway, David J. Roper, Cally Clark, Taane G. Major Articles and Brief Reports Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600 000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania). Oxford University Press 2014-06-01 2013-12-12 /pmc/articles/PMC4017360/ /pubmed/24338354 http://dx.doi.org/10.1093/infdis/jit812 Text en © The Author 2013. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Preston, Mark D.
Assefa, Samuel A.
Ocholla, Harold
Sutherland, Colin J.
Borrmann, Steffen
Nzila, Alexis
Michon, Pascal
Hien, Tran Tinh
Bousema, Teun
Drakeley, Christopher J.
Zongo, Issaka
Ouédraogo, Jean-Bosco
Djimde, Abdoulaye A.
Doumbo, Ogobara K.
Nosten, Francois
Fairhurst, Rick M.
Conway, David J.
Roper, Cally
Clark, Taane G.
spellingShingle Preston, Mark D.
Assefa, Samuel A.
Ocholla, Harold
Sutherland, Colin J.
Borrmann, Steffen
Nzila, Alexis
Michon, Pascal
Hien, Tran Tinh
Bousema, Teun
Drakeley, Christopher J.
Zongo, Issaka
Ouédraogo, Jean-Bosco
Djimde, Abdoulaye A.
Doumbo, Ogobara K.
Nosten, Francois
Fairhurst, Rick M.
Conway, David J.
Roper, Cally
Clark, Taane G.
PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
author_facet Preston, Mark D.
Assefa, Samuel A.
Ocholla, Harold
Sutherland, Colin J.
Borrmann, Steffen
Nzila, Alexis
Michon, Pascal
Hien, Tran Tinh
Bousema, Teun
Drakeley, Christopher J.
Zongo, Issaka
Ouédraogo, Jean-Bosco
Djimde, Abdoulaye A.
Doumbo, Ogobara K.
Nosten, Francois
Fairhurst, Rick M.
Conway, David J.
Roper, Cally
Clark, Taane G.
author_sort Preston, Mark D.
title PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
title_short PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
title_full PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
title_fullStr PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
title_full_unstemmed PlasmoView: A Web-based Resource to Visualise Global Plasmodium falciparum Genomic Variation
title_sort plasmoview: a web-based resource to visualise global plasmodium falciparum genomic variation
description Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600 000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania).
publisher Oxford University Press
publishDate 2014
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017360/
_version_ 1612087845510447104

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