Pf-HaploAtlas

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  Working at the Sanger Institute is truly unique. We put collaboration, innovation and support for people as individuals at the centre of everything we do. Join us to help shape the future by delivering life-changing science with the reach, scale, and creativity to solve some of humanity’s greatest challenges.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
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  - Careers
    Join our community of world class thinkers and professionals at the Sanger Institute located in Cambridge. Together we achieve life-changing science.
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    We are committed to training the next generation of pioneering genome scientists and clinicians. At the Wellome Sanger Institute we give PhD students and postdocs all the tools they need to succeed in the field of genomics research.
- Who we are
  Who we are
  Our vision and mission is to deliver world-leading genomics research in collaboration with research partners across the globe. Discover how our funding gives our leadership the independence to conduct bold, ambitious science that pioneers new fields in health, disease and conservation.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
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  - Our Vision
    By focusing on fundamental discovery research led by our faculty and employing our unique scale in cutting-edge data generation and analysis, we deliver discoveries not easily made elsewhere.
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    From providing fundamental resources for understanding biology to exploring cancer genomes and the effects of variation in human genomes, our work lays the foundations for personalised medicine. We also reveal the secrets of human development and how infectious diseases evolve and spread.
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    Discover how our leadership and structures are designed to enable holistic and effective decision making, with transparency and accountability woven into their make up.
  - Strategy and Funding
    Read how our strategy informs our research focus and how our unique funding enables our scientists to take scientific risks to pioneer new approaches.
- Equality, Diversity and Inclusion
  Equality, Diversity and Inclusion
  The diversity in skills and knowledge that we all bring make our Institute the thriving ideas factory that it is. Discover how we support each other to reach our full potential and thrive. We celebrate diversity and seek to ensure that everyone has equal access to professional and career development opportunities.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
- Policies
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  We play a pivotal role in helping to shape Government and International research policies. We also lead the way in developing guidance to support our scientists to carry out their research ethically, equitably and responsibly.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
  - Influencing Policy
    We advise all levels of government both in the UK and across the world on the the role, impact and importance of genomic and life science research.
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    Our policies help our researchers carry out their science collaboratively, equitably, ethically and responsibly.
- Admin Groups
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  Browse our management and support operations teams that facilitate the Sanger Institute’s science.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
- Campus Connections
  Campus Connections
  We are sited on the Wellcome Genome Campus at the very heart of a global hub of fundamental and applied genomic research, education and engagement. It is home to some of the world’s foremost institutes and organisations using genomes and biodata to deliver science with the reach, scale and imagination to solve some of humanity’s greatest challenges and maximise societal benefit.
  About Us
  We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
  Read more
About
We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
About Us
We tackle some of the most difficult challenges in genomic research. This demands science at scale; a visionary and creative approach to research that pushes the boundaries of our understanding in ever new and exciting ways.
Read more
Science
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  Our research is organised into six primary Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus. In addition, our Associate Research programmes pioneer new approaches to studying health and disease.
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  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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  Browse the research, scientific and support teams in the Sanger Institute.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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  Explore the national, international and global research projects and collaborations we either lead or actively contribute to.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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- Data
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  Browse our genomic and genetic data resources and repositories.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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- Software and Resources
  Software and Resources
  We freely and openly provide the global research community with a wide range of genomics software, protocols, and platforms.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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  The Sanger Institute has published papers in some of the most prestigious scientific journals. We aim to publish research that will transform biology and improve healthcare.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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- Research Policies
  Research Policies
  Sanger Institute’s Research Policies are designed to provide guidance to help researchers navigate the legislation relating to their research and to ensure that research is ethical and legal.
  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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  Science & technology
  Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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  - COVID-19
    The Sanger Institute played a major role in the genomic surveillance of the COVID-19 pandemic, providing large-scale high-throughput sequencing of the SARS-CoV-2 virus and analysis of its evolution and spread in the UK.
  - Sanger Seminar Series
    Throughout the COVID-19 lockdown of 2020-2021 we hosted a series of monthly freely available and open virtual seminars. From using genomic approaches to map all cell types in the human body, understand how cancer develops, and track the evolution and spread of global diseases, our senior scientists and faculty presented the latest developments in their field.
Science
Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease or analytic focus. In all cases, the studies provide insights into human, pathogen, cellular evolution, the phenotypic and hence biological consequences of genome variation and the processes which cause mutations.
Science & technology
Our science is organised into six Scientific Programmes, each defining a major area of research with a particular biological, disease, analytic or generative focus.
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People
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  Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
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  - Sanger Leadership Team
    The Sanger Leadership Team is an Executive Committee that enables holistic and effective decision making, with transparency and accountability woven into its make up.
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    How we are organised to enable transparent, open, responsive leadership.
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    We draw on a number of experienced and internationally recognised scientists to provide independent scientific support, advice and challenge to help us maintain our scientific excellence.
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  Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
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  - Faculty
    Our Faculty conceive and deliver our science. Within our strategic framework the Institute’s scientific aspirations are driven by their vision, imagination and intellectual energy.
  - Associate Faculty
    Our Associate Faculty combine their skills and knowledge with the Sanger Institute’s unique abilities to conduct data generation and analysis at scale to pioneer genomic research in new areas.
  - International Fellows
    Our International Fellows Programme empowers early-career researchers with resources, mentorship, and funding to advance genomic research globally.
  - Honorary Faculty
    Our Honorary Faculty contribute to our research by providing insights and knowledge and collaborating on important research projects.
- All Sanger Staff
  All Sanger Staff
  Almost 1,000 scientists, developers, engineers and skilled professionals work together to deliver the Sanger Institute’s cutting-edge genomic research.
  Join us
  Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
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    From PhD students and Postdoctoral Fellows, bioinformaticians and laboratory managers, search for our staff who the support the delivery of pioneering science.
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    Look up our management and support staff that facilitate the Sanger Institute’s science.
People
Almost 1,000 scientists, developers, engineers and skilled professionals work together to deliver the Sanger Institute’s cutting-edge genomic research.
Join us
Our science is founded on the talents, imagination and curiosity of our people. Our wet-lab scientists, bioinformaticians, developers, engineers and skilled administrators work together to deliver cutting-edge research. Join us
Read more
Innovation
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  Innovation at the Institute
  We deliver therapeutic, diagnostic and production benefits in areas as diverse as cancer, immunology, public health and personalised treatment.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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  Find out how our translation team maximises the socioeconomic impact of the Sanger Institute’s discoveries by translating our science into products, services and technologies that benefit patients in a variety of settings.
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  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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  For Researchers
  Read how we benefit society by buiding on the innovative capabilities of our people by engaging with businesses and creating commercial opportunities. We also develop a unique and vibrant ecosystem to establish and grow innovative genomics and biodata businesses.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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- Case Studies
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  Read examples of how we engage with funding, R&D, service and clinical communities to promote real-world utilisation of the Sanger Institute’s technologies and resources.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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- Our Spin-Outs
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  We have a culture and history of scaling technologies. Some have become spin-out companies that positively impact today’s healthcare sector.
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  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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  Browse our technology and therapy opportunities.
  Sanger Innovation
  We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
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Innovation
We deliver therapeutic, diagnostic and production benefits in areas as diverse as cancer, immunology, public health and personalised treatment.
Sanger Innovation
We apply our science to benefit society by empowering innovators and engaging with businesses and investors - driven by Sanger Genomics Innovation
Read more
News
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  News and stories Announcements, articles and blogs from the cutting edge of genomic research.
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Latest News

20 Nov 2024

Early skeleton map reveals how bones form in humans
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20 Nov 2024

Human immune system is ‘ready to go’ long before birth
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20 Nov 2024

Mapping 1.6 million gut cells to find new ways to treat disease
Read more

News and Blogs
News and stories Announcements, articles and blogs from the cutting edge of genomic research.
Read more

Pf-HaploAtlas

The Plasmodium falciparum Haplotype Atlas allows anyone with an internet connection to study and track genetic variation in any gene in the P. falciparum genome

Try Pf-HaploAtlas

The Pf-HaploAtlas app allows you to explore and interpret malaria genomic data.

This app provides visualisations of haplotypes for all 5,102 core genes of malaria parasite Plasmodium falciparum by using data from 16,203 samples, from 33 countries, and spread between the years 1984 and 2018. It facilitates comprehensive spatial and temporal analyses of genes and variants of interest.

How to use the app

Learn to use the Pf-HaploAtlas with this demonstration, created by the app’s developers.

Further information

Data Use Statement

When publishing work that uses data and/or plots from the Pf-HaploAtlas, please cite the following:

Lee C, Ünlü ES, White NFD, Almagro-Garcia J, Ariani C, Pearson RD. Pf-HaploAtlas: An interactive web app for spatiotemporal analysis of P. falciparum genes. BioRxiv 603783 [Preprint] July 16, 2024. Available from: https://doi.org/10.1101/2024.07.16.603783.

Sanger Institute Contributors

Photo of Dr Jacob Almagro-Garcia

Dr Jacob Almagro-Garcia

Translational Research Lead

Photo of Dr Cristina Ariani

Dr Cristina Ariani

Malaria Parasite Surveillance Lead

Photo of Chiyun Lee

Chiyun Lee

Senior Data Scientist

Photo of Dr Richard Pearson

Dr Richard Pearson

Parasite Data Lead

Photo of Dr Eyyub Unlu

Dr Eyyub Unlu

Data Scientist

Photo of Dr Nina White

Dr Nina White

Senior Data Scientist

Related groups

Science group

Malaria Parasite Genomic Surveillance

Genomic Surveillance Unit

We generate and curate genomic public health data on the parasites that cause malaria. We also develop new scientific and bioinformatic ...

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Publications

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Related

Collaboration

Genomic Surveillance Unit

The Genomic Surveillance Unit (GSU) improves global human health by accelerating the use and impact of genomic surveillance. We deliver products, ...

Collaboration

MalariaGEN (Malaria Genomic Epidemiology Network)

MalariaGEN is a data-sharing community that creates genetic data resources to support the control and elimination of malaria.