Literature DB >> 28389516

Malaria Genomics in the Era of Eradication.

Daniel E Neafsey1, Sarah K Volkman2,3,4.   

Abstract

The first reference genome assembly for the Plasmodium falciparum malaria parasite was completed over a decade ago, and the impact of this and other genomic resources on malaria research has been significant. Genomic resources for other malaria parasites are being established, even as P. falciparum continues to be the focus of development of new genomic methods and applications. Here we review the impact and applications of genomic data on malaria research, and discuss future needs and directions as genomic data generation becomes less expensive and more decentralized. Specifically, we focus on how population genomic strategies can be utilized to advance the malaria eradication agenda.
Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2017        PMID: 28389516      PMCID: PMC5538406          DOI: 10.1101/cshperspect.a025544

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Med        ISSN: 2157-1422            Impact factor:   6.915


  49 in total

Review 1.  A PCR method for molecular epidemiology of Plasmodium falciparum Msp-1.

Authors:  K Tanabe; N Sakihama; O Kaneko; A Saito-Ito; M Kimura
Journal:  Tokai J Exp Clin Med       Date:  1998-12

2.  A genome-wide map of diversity in Plasmodium falciparum.

Authors:  Sarah K Volkman; Pardis C Sabeti; David DeCaprio; Daniel E Neafsey; Stephen F Schaffner; Danny A Milner; Johanna P Daily; Ousmane Sarr; Daouda Ndiaye; Omar Ndir; Soulyemane Mboup; Manoj T Duraisingh; Amanda Lukens; Alan Derr; Nicole Stange-Thomann; Skye Waggoner; Robert Onofrio; Liuda Ziaugra; Evan Mauceli; Sante Gnerre; David B Jaffe; Joanne Zainoun; Roger C Wiegand; Bruce W Birren; Daniel L Hartl; James E Galagan; Eric S Lander; Dyann F Wirth
Journal:  Nat Genet       Date:  2006-12-10       Impact factor: 38.330

3.  Genome variation and evolution of the malaria parasite Plasmodium falciparum.

Authors:  Daniel C Jeffares; Arnab Pain; Andrew Berry; Anthony V Cox; James Stalker; Catherine E Ingle; Alan Thomas; Michael A Quail; Kyle Siebenthall; Anne-Catrin Uhlemann; Sue Kyes; Sanjeev Krishna; Chris Newbold; Emmanouil T Dermitzakis; Matthew Berriman
Journal:  Nat Genet       Date:  2006-12-10       Impact factor: 38.330

4.  Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome.

Authors:  Jianbing Mu; Philip Awadalla; Junhui Duan; Kate M McGee; Jon Keebler; Karl Seydel; Gilean A T McVean; Xin-zhuan Su
Journal:  Nat Genet       Date:  2006-12-10       Impact factor: 38.330

Review 5.  Genetic diversity and malaria vaccine design, testing and efficacy: preventing and overcoming 'vaccine resistant malaria'.

Authors:  S L Takala; C V Plowe
Journal:  Parasite Immunol       Date:  2009-09       Impact factor: 2.280

6.  Artemisinin resistance in Plasmodium falciparum malaria.

Authors:  Arjen M Dondorp; François Nosten; Poravuth Yi; Debashish Das; Aung Phae Phyo; Joel Tarning; Khin Maung Lwin; Frederic Ariey; Warunee Hanpithakpong; Sue J Lee; Pascal Ringwald; Kamolrat Silamut; Mallika Imwong; Kesinee Chotivanich; Pharath Lim; Trent Herdman; Sen Sam An; Shunmay Yeung; Pratap Singhasivanon; Nicholas P J Day; Niklas Lindegardh; Duong Socheat; Nicholas J White
Journal:  N Engl J Med       Date:  2009-07-30       Impact factor: 91.245

7.  Genome sequence of the human malaria parasite Plasmodium falciparum.

Authors:  Malcolm J Gardner; Neil Hall; Eula Fung; Owen White; Matthew Berriman; Richard W Hyman; Jane M Carlton; Arnab Pain; Karen E Nelson; Sharen Bowman; Ian T Paulsen; Keith James; Jonathan A Eisen; Kim Rutherford; Steven L Salzberg; Alister Craig; Sue Kyes; Man-Suen Chan; Vishvanath Nene; Shamira J Shallom; Bernard Suh; Jeremy Peterson; Sam Angiuoli; Mihaela Pertea; Jonathan Allen; Jeremy Selengut; Daniel Haft; Michael W Mather; Akhil B Vaidya; David M A Martin; Alan H Fairlamb; Martin J Fraunholz; David S Roos; Stuart A Ralph; Geoffrey I McFadden; Leda M Cummings; G Mani Subramanian; Chris Mungall; J Craig Venter; Daniel J Carucci; Stephen L Hoffman; Chris Newbold; Ronald W Davis; Claire M Fraser; Bart Barrell
Journal:  Nature       Date:  2002-10-03       Impact factor: 49.962

8.  Dynamics of polymorphism in a malaria vaccine antigen at a vaccine-testing site in Mali.

Authors:  Shannon L Takala; Drissa Coulibaly; Mahamadou A Thera; Alassane Dicko; David L Smith; Ando B Guindo; Abdoulaye K Kone; Karim Traore; Amed Ouattara; Abdoulaye A Djimde; Paul S Sehdev; Kirsten E Lyke; Dapa A Diallo; Ogobara K Doumbo; Christopher V Plowe
Journal:  PLoS Med       Date:  2007-03       Impact factor: 11.069

9.  A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking.

Authors:  Rachel Daniels; Sarah K Volkman; Danny A Milner; Nira Mahesh; Daniel E Neafsey; Daniel J Park; David Rosen; Elaine Angelino; Pardis C Sabeti; Dyann F Wirth; Roger C Wiegand
Journal:  Malar J       Date:  2008-10-29       Impact factor: 2.979

10.  Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.

Authors:  Daniel E Neafsey; Stephen F Schaffner; Sarah K Volkman; Daniel Park; Philip Montgomery; Danny A Milner; Amanda Lukens; David Rosen; Rachel Daniels; Nathan Houde; Joseph F Cortese; Erin Tyndall; Casey Gates; Nicole Stange-Thomann; Ousmane Sarr; Daouda Ndiaye; Omar Ndir; Soulyemane Mboup; Marcelo U Ferreira; Sandra do Lago Moraes; Aditya P Dash; Chetan E Chitnis; Roger C Wiegand; Daniel L Hartl; Bruce W Birren; Eric S Lander; Pardis C Sabeti; Dyann F Wirth
Journal:  Genome Biol       Date:  2008-12-15       Impact factor: 13.583

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  18 in total

1.  R H: a genetic metric for measuring intrahost Plasmodium falciparum relatedness and distinguishing cotransmission from superinfection.

Authors:  Wesley Wong; Sarah Volkman; Rachel Daniels; Stephen Schaffner; Mouhamad Sy; Yaye Die Ndiaye; Aida S Badiane; Awa B Deme; Mamadou Alpha Diallo; Jules Gomis; Ngayo Sy; Daouda Ndiaye; Dyann F Wirth; Daniel L Hartl
Journal:  PNAS Nexus       Date:  2022-09-10

2.  Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol.

Authors:  Alfredo Mayor; Clemente da Silva; Eduard Rovira-Vallbona; Arantxa Roca-Feltrer; Craig Bonnington; Alexandra Wharton-Smith; Bryan Greenhouse; Caitlin Bever; Arlindo Chidimatembue; Caterina Guinovart; Joshua L Proctor; Maria Rodrigues; Neide Canana; Paulo Arnaldo; Simone Boene; Pedro Aide; Sonia Enosse; Francisco Saute; Baltazar Candrinho
Journal:  BMJ Open       Date:  2022-07-12       Impact factor: 3.006

3.  Evidence for Reduced Malaria Parasite Population after Application of Population-Level Antimalarial Drug Strategies in Southern Province, Zambia.

Authors:  Rachel F Daniels; Stephen F Schaffner; Adam Bennett; Travis R Porter; Joshua O Yukich; Conceptor Mulube; Brenda Mambwe; Mulenga C Mwenda; Sandra Chishimba; Daniel J Bridges; Hawela Moonga; Busiku Hamainza; Elizabeth Chizema Kawesha; John M Miller; Richard W Steketee; Dyann F Wirth; Thomas P Eisele; Daniel L Hartl; Sarah K Volkman
Journal:  Am J Trop Med Hyg       Date:  2020-08       Impact factor: 2.345

4.  High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo.

Authors:  Julia C Pringle; Amy Wesolowski; Sophie Berube; Tamaki Kobayashi; Mary E Gebhardt; Modest Mulenga; Mike Chaponda; Thierry Bobanga; Jonathan J Juliano; Steven Meshnick; William J Moss; Giovanna Carpi; Douglas E Norris
Journal:  Malar J       Date:  2019-12-04       Impact factor: 2.979

5.  Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago.

Authors:  Andrew P Morgan; Nicholas F Brazeau; Billy Ngasala; Lwidiko E Mhamilawa; Madeline Denton; Mwinyi Msellem; Ulrika Morris; Dayne L Filer; Ozkan Aydemir; Jeffrey A Bailey; Jonathan B Parr; Andreas Mårtensson; Anders Bjorkman; Jonathan J Juliano
Journal:  Malar J       Date:  2020-01-28       Impact factor: 2.979

Review 6.  Strengthening Surveillance Systems for Malaria Elimination by Integrating Molecular and Genomic Data.

Authors:  Christian Nsanzabana
Journal:  Trop Med Infect Dis       Date:  2019-12-03

7.  Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination.

Authors:  Lucas E Buyon; Ana Maria Santamaria; Angela M Early; Mario Quijada; Itza Barahona; Jose Lasso; Mario Avila; Sarah K Volkman; Matthias Marti; Daniel E Neafsey; Nicanor Obaldia Iii
Journal:  PLoS Negl Trop Dis       Date:  2020-12-14

8.  Microgeographic Epidemiology of Malaria Parasites in an Irrigated Area of Western Kenya by Deep Amplicon Sequencing.

Authors:  Elizabeth Hemming-Schroeder; Daibin Zhong; Solomon Kibret; Amanda Chie; Ming-Chieh Lee; Guofa Zhou; Harrysone Atieli; Andrew Githeko; James W Kazura; Guiyun Yan
Journal:  J Infect Dis       Date:  2021-04-23       Impact factor: 5.226

9.  Spatio-temporal dynamics of Plasmodium falciparum transmission within a spatial unit on the Colombian Pacific Coast.

Authors:  Angélica Knudson; Felipe González-Casabianca; Alejandro Feged-Rivadeneira; Maria Fernanda Pedreros; Samanda Aponte; Adriana Olaya; Carlos F Castillo; Elvira Mancilla; Anderson Piamba-Dorado; Ricardo Sanchez-Pedraza; Myriam Janeth Salazar-Terreros; Naomi Lucchi; Venkatachalam Udhayakumar; Chris Jacob; Alena Pance; Manuela Carrasquilla; Giovanni Apráez; Jairo Andrés Angel; Julian C Rayner; Vladimir Corredor
Journal:  Sci Rep       Date:  2020-02-28       Impact factor: 4.379

10.  SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics.

Authors:  Abebe A Fola; Eline Kattenberg; Zahra Razook; Dulcie Lautu-Gumal; Stuart Lee; Somya Mehra; Melanie Bahlo; James Kazura; Leanne J Robinson; Moses Laman; Ivo Mueller; Alyssa E Barry
Journal:  Malar J       Date:  2020-10-20       Impact factor: 2.979

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