Ag1000G
Ag1000G is an international collaboration using whole genome deep sequencing to provide a high-resolution view of genetic variation in natural populations of Anopheles gambiae, the principal vector of Plasmodium falciparum malaria in Africa.
Objectives & Coordination
We have three core objectives:
- Discovering natural genetic variation – We're using high-throughput sequencing of a large number of wild-caught mosquitoes sampled from across Africa to build a comprehensive catalogue of genetic variation in natural vector populations. Our primary focus is on A. gambiae sensu strictu and A. coluzzii, but we will be expanding to include A. arabiensis in the future.
- Describing the structure and history of vector populations – We're analysing genetic variation data to characterise key features of natural vector populations, such as patterns of diversity, linkage disequilibrium and recombination, population structure and gene flow, signals of recent selection, and demographic history.
- Connecting genetic variation and population biology with ecology and malaria epidemiology – We aim to study associations between genotype and broad phenotypes such as ecological specialisation and differences in local malaria epidemiology.
Our work is coordinated by two working groups:
- Partner Working Group (led by Martin Donnelly) is comprised of the investigators contributing samples or other significant resources and/or strategic guidance
- Data Analysis Group (led by Dominic Kwiatkowski) is undertaking core project analyses
Sampling locations
To date, we've collected and sequenced mosquitoes from 13 countries:
Partner studies
The Ag1000G project is coordinated by a consortium of partners from a range of different research institutions and countries. This includes consortium members who are carrying out independent research studies in malaria endemic regions, and who have contributed mosquito specimens or mosquito DNA samples collected in the course of their own research. The pages below describe the studies that have contributed samples to the Ag1000G project, which includes wild-caught samples from 19 African countries. They also provide information about the collection locations and methods, the people involved in the studies, and references to any published articles providing further information about the studies.
We use species nomenclature following (1). Unless otherwise stated, the DNA extraction method used for the collections described below was Qiagen DNeasy Blood and Tissue Kit (Qiagen Science, MD, USA).
1. Maureen Coetzee, Richard H. Hunt, Richard Wilkerson, Alessandra Della Torre, Mamadou B. Coulibaly, and Nora J. Besansky. Anopheles coluzzii and anopheles amharicus, new members of the anopheles gambiae complex. Zootaxa, 3619(3):246–274, February 2013. doi:10.11646/zootaxa.3619.3.2.
Data
Ag1000G samples are sequenced by the Wellcome Trust Sanger Institute Parasites and Microbes Programme using Illumina high-throughput technology. The sequence data are then used to discover genetic variation between samples and to make genotype calls. Raw sequence reads are deposited into the European Nucleotide Archive (ENA). The variant call data generated by the project is publicly released on a regular basis.
Any use of Ag1000G data is subject to the Terms of Use.
People
The Ag1000G Consortium involves researchers from several institutions around the world, including experts in Anopheles genomics, population genetics, epidemiology, and vector biology. The Ag1000G Consortium comprises members of two working groups, as well as affiliates involved in data production and analysis.
The Partner Working Group (PWG) is comprised of the investigators contributing samples or other significant resources / strategic guidance to the Project.
Alessandra della Torre
Andrew Kern
Beniamino Caputo
Bilali Kabula
Bradley White
Prof Charles Godfray
Constant Edi
Dr Craig Wilding
Dr Daniel Neafsey
Daniel Schrider
Prof David Conway
Projects
Partner studies
- 1006 Genome-wide analysis of genetic variation in The Gambia
- 1026 Effects of transmission intensity on population structure and signatures of selection in Guinea
- 1083 Alternative molecular mechanisms for erythrocyte invasion by Plasmodium falciparum in Ghana
- 1134 Population genetics of Plasmodium falciparum in West Africa
- 1135 Parasite adaption in Senegal at molecular, functional and population level
- 1147 Population genetics of Plasmodium falciparum parasites in Mauritania
- 1183 Alternative mechanisms for erythrocyte invasion by Plasmodium falciparum
- Human genetic determinants of severe malaria in The Gambia
Dr David Weetman
Diego Ayala
Prof Dominic Kwiatkowski
Prof Igor Sharakhov
Dr Janet Midega
Dr Jiannong (John) Xu
Dr João Pinto
John Essandoh
Johnson Matowo
Dr Ken Vernick
Dr Luc S. Djogbenou
Mamadou Coulibaly
Dr Mara Lawniczak
Prof Martin Donnelly
Prof Matthew Hahn
Dr Michaël Fontaine
Dr Michelle Riehle
Prof Nora Besansky
Dr Omar Cornejo
Robert McCann
Dr Sam O’Loughlin
Projects
Vincent Robert
The Data Analysis Group (DAG) is undertaking core project analyses and includes members of both the PWG and PMG, alongside additional members of the Ag1000G Consortium.
Alexander Xue
Alistair Miles
Dr Chris Clarkson
CJ Battey
Cody Champion
Daniel Schrider
Prof Dominic Kwiatkowski
Dr Frederic Labbe
Giordano Bottà
Dr Janet Midega
Jeffrey Adrion
Projects
Dr Jiannong (John) Xu
Joel Nelson
Projects
Dr Mara Lawniczak
Prof Martin Donnelly
Prof Matthew Hahn
Dr Michaël Fontaine
Dr Nick Harding
Dr Richard Wang
Projects
Dr Sam O’Loughlin
Projects
Dr Scott T Small
Dr Seth Redmond
Projects
Dr Tiago Antão
Projects
