Ag1000G

 

 

 

Started 2014

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:

  • Angola (AO)
  • Bioko Island, Equatorial Guinea (GQ)
  • Burkina Faso (BF)
  • Cameroon (CM)
  • Gabon (GA)
  • Ghana (GH)
  • Guinea-Bissau (GW)
  • Guinea (GN)
  • Ivory Coast (CI)
  • Kenya (KE)
  • Mayotte Island (YT)
  • The Gambia (GM)
  • Uganda (UG)

Data

Ag1000G samples are sequenced by the Wellcome Trust Sanger Institute Malaria 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.

Current

6 Nov 2017

Ag1000G phase 2 AR1 data release

Species: A. gambiae sensu lato

Sample set: 1,142 wild-caught specimens from 13 countries and 234 specimens comprising parents and progeny of 11 crosses.

21 Dec 2016

Ag1000G phase 1 AR3.1 data release

Species: A. gambiae sensu lato

Sample set: 765 wild-caught specimens from 8 countries and 80 specimens comprising parents and progeny of four crosses.

22 Jul 2015

Ag1000G phase 1 AR3 data release

Species: A. gambiae sensu lato

Sample set: 765 wild-caught specimens from 8 countries and 80 specimens comprising parents and progeny of four crosses

Archive

8 Dec 2014

Ag1000G phase 1 AR2 data release

Species: A. gambiae sensu lato

Sample set: 765 wild-caught specimens from 8 countries

21 May 2014

Ag1000G phase 1 preview data release

Species: A. gambiae sensu lato

Sample set: 103 wild-caught specimens from Uganda

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.

Partner Working Group

The Partner Working Group (PWG) is comprised of the investigators contributing samples or other significant resources / strategic guidance to the Project.

Alessandra della Torre
Sapienza University of Rome, Italy
Projects
Andrew Kern
Assistant Professor of Genetics
Rutgers University, New Jersey, USA
Beniamino Caputo
Sapienza University of Rome, Italy
Projects
Bradley White
Assistant Professor of Entomology
University of California, Riverside, USA
Prof Charles Godfray
Hope Professor and Fellow of Jesus College
Department of Zoology, University of Oxford, UK
Director
Oxford Martin School, University of Oxford, UK
Honorary Principal Research Fellow
Imperial College London, UK
Dr Craig Wilding
Lecturer in Evolutionary Genetics
Liverpool John Moores University, UK
Dr Dan Neafsey
Associate Director, Genomic Center of Infectious Disease
Broad Institute, USA
Visiting Scientist
Harvard T. H. Chan School of Public Health
Dr David Weetman
Liverpool School of Tropical Medicine, UK
Projects
Diego Ayala
Research Scientist
Institute of Research for Development (IRD), France
International Center for Medical Research (CIRMF)
Prof Dominic Kwiatkowski
Professor of Genomics and Global Health
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Head of Malaria Programme
Wellcome Trust Sanger Institute, UK
Director of Centre for Genomics and Global Health
Big Data Institute, University of Oxford
Prof Igor Sharakhov
Associate Professor Entomology
Virginia Tech, USA
Lead Research Scientist
Tomsk State University, Russia
Dr Janet Midega
Research Scientist
KEMRI Wellcome Trust Research Programme, Kenya
Research Associate
University of Oxford, UK
Visiting Research Scientist
Imperial College London, UK
Dr Jiannong (John) Xu
Associate Professor
New Mexico State University, USA
Dr João Pinto
Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
Projects
Dr Ken Vernick
University of Minnesota, USA
Projects
Dr Luc S. Djogbenou
Senior Lecturer
Université d’Abomey–Calavi, Benin
Research Associate
Liverpool School of Tropical Medicine
Dr Mara Lawniczak
Group Leader
Wellcome Trust Sanger Institute, UK
Prof Martin Donnelly
Professor of Evolutionary Genetics
Liverpool School of Tropical Medicine, UK
Honorary Faculty Member
Wellcome Trust Sanger Institute, UK
Prof Matthew Hahn
Professor of Biology and Informatics
Department of Biology, Indiana University Bloomington, USA
Dr Michelle Riehle
University of Minnesota, USA
Projects
Prof Nora Besansky
Professor
University of Notre Dame, USA
Dr Omar Cornejo
Assistant Professor
Washington State University, USA
Dr Sam O’Loughlin
Imperial College London, UK
Projects
Data Analysis Working Group

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.

Alistair Miles
Head of Epidemiological Informatics
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Dr Chris Clarkson
Postdoctoral Fellow
Wellcome Trust Sanger Institute, UK
Daniel Schrider
Rutgers University, New Jersey, USA
Projects
Prof Dominic Kwiatkowski
Professor of Genomics and Global Health
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Head of Malaria Programme
Wellcome Trust Sanger Institute, UK
Director of Centre for Genomics and Global Health
Big Data Institute, University of Oxford
Dr Frederic Labbe
Postdoctoral Research Associate
University of Notre Dame, USA
Postdoctoral Research Associate
Groningen Institute for Evolutionary Life Sciences (GELIFES), Genomics Research in Ecology & Evolution in Nature, University of Groningen, The Netherlands
Giordano Bottà
PhD student
Sapienza University of Rome, Italy
Visiting PhD Student
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Projects
Dr Janet Midega
Research Scientist
KEMRI Wellcome Trust Research Programme, Kenya
Research Associate
University of Oxford, UK
Visiting Research Scientist
Imperial College London, UK
Jeffrey Adrion
Graduate Student
Department of Biology, Indiana University, Bloomington, USA
Dr Jiannong (John) Xu
Associate Professor
New Mexico State University, USA
Joel Nelson
PhD Student
Washington State University, USA
Dr Mara Lawniczak
Group Leader
Wellcome Trust Sanger Institute, UK
Prof Martin Donnelly
Professor of Evolutionary Genetics
Liverpool School of Tropical Medicine, UK
Honorary Faculty Member
Wellcome Trust Sanger Institute, UK
Prof Matthew Hahn
Professor of Biology and Informatics
Department of Biology, Indiana University Bloomington, USA
Dr Michaël Fontaine
Assistant Professor
Groningen Institute for Evolutionary Life Sciences (GELIFES), Genomics Research in Ecology & Evolution in Nature, University of Groningen, The Netherlands
Dr Nick Harding
Principal Bioinformatician
Wellcome Trust Centre for Human Genetics, University of Oxford, UK
Dr Richard Wang
Department of Biology, Indiana University Bloomington, USA
Projects
Dr Sam O’Loughlin
Imperial College London, UK
Projects
Dr Scott T Small
Research Assistant Professor
University of Notre Dame, USA
Dr Seth Redmond
Postdoctoral Associate
Broad Institute, USA
Visiting Scientist
Harvard T. H. Chan School of Public Health
Dr Tiago Antão
University of Montana, USA
Projects