Human Cell Atlas takes first steps towards understanding human development: First 250 thousand developmental cells sequenced

The Human Developmental Cell Atlas programme will create genomic reference maps of all the cells that are important for human development

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Researchers from the global Human Cell Atlas Consortium are taking the first steps towards using powerful single-cell genome analysis tools to understand early human development and how this can affect health or lead to disease. Preliminary projects for the Human Developmental Cell Atlas (HDCA) have sequenced a quarter of a million separate cells so far and the first tranche of data analysis is underway.

The HDCA programme will create genomic reference maps of all the cells that are important for human development, which will revolutionise our understanding of health and disease, from miscarriages and children’s developmental disorders, through to cancer and ageing.

The HDCA is one part of the ambitious Human Cell Atlas (HCA), a global consortium that aims to transform biological research and medicine by mapping every cell in the human body. Progress on the HDCA and other aspects of the Human Cell Atlas will be discussed at the international HCA meeting at the Wellcome Genome Campus, Cambridge on 8 March 2018.

Many diseases have their origin in early human development, and a detailed understanding of development is key to explaining human health and disease. Researchers at the Wellcome Sanger Institute and Newcastle University have collected genomic data from over 250 thousand cells from a range of donated developing human tissues including liver, skin, kidney and placenta. This data will show which genes are switched on in each individual cell, and help explain vital processes in development.

“Our understanding of human development will be transformed by the HDCA project and could lead to significant advances in biology and medicine. We expect this fundamental research to deliver a wide range of important insights – from a better understanding of why miscarriages and genetic developmental disorders happen, through to understanding childhood cancers that have their root in development and the developmental pathways that cancer cells take advantage of in adults.”

Dr Sarah Teichmann Co-chair of the HCA Organising Committee and Head of Cellular Genetics at the Wellcome Sanger Institute

Other primary areas of focus for the HDCA include an improved understanding of how blood cells form and how the immune system functions. In addition, further understanding of the processes during human development will shed light on the processes of ageing and how tissues repair themselves, which could lead to advances in regenerative medicine.

“This research is possible due to the Human Developmental Biology Resource, which provides human embryonic and fetal tissues to ethically approved scientific studies such as the HDCA. Funded by Wellcome and the MRC, this well established tissue bank provides vital materials to enable research into understanding human development to help improve health.”

Prof Muzlifah Haniffa From Newcastle University

Outside the UK, other HDCA projects are underway and researchers in Sweden are focusing on the development of the brain, lung and heart, and on first trimester development. Scientists from Karolinska Institute, Stockholm University, KTH Royal Institute of Technology and Science for Life Laboratory are collaborating to discover how these organs develop in order to understand normal human development and shed light on developmental disorders.

“About a third of neurological disorders are developmental in origin, including autism, schizophrenia and intellectual disability. Developmental heart disorders are the most common complication in newborns, and incomplete lung development is the most common cause of death in extremely premature babies. Learning about how these organs develop will help us make progress on disorders that severely affect large numbers of babies and children.”

Professor Sten Linnarsson from the Karolinska Institut in Sweden

The March 2018 international HCA community meeting in Hinxton is the first time that members have come together to discuss details of the HDCA. The meeting will also feature other aspects of the Human Cell Atlas initiative Including updates on progress so far towards atlases of tumour, lung, gut, kidney and immune system cells.

“The Human Cell Atlas initiative is growing fast, and with more than 480 scientists now registered with the initiative from 44 countries around the world, it is a truly global collaboration. As we will hear in the opening session, in the 18 months since the initiative planning process was launched, more than 1.5 million cells have been sequenced from various tissues including the immune system and the gut, working towards our ambitious aim of creating an open and accessible reference map of every type of cell in the human body.”

Prof Aviv Regev, co-chair of the HCA Organising Committee, a core member, chair of faculty, and director of the Klarman Cell Observatory and Cell Circuits Program at the Broad Institute of MIT and Harvard; an HHMI Investigator; and Professor of Biology at Massachusetts Institute of Technology

The Human Cell Atlas. Image credit: Wellcome Sanger Institute, Genome Research Limited

More information

• A recent overview of the Human Cell Atlas is published in eLife: Aviv Regev, Sarah A. Teichmann, Eric S. Lander (2017) Science Forum: The Human Cell Atlas. eLife 2017; 6: e27041 DOI: 10.7554/eLife.27041

• A recent review of the ambitious aims of the HDCA is published in Development: Sam Behjati, Susan Lindsay, Sarah A. Teichmann, Muzlifah Haniffa (2018) Mapping human development at single cell resolution. Development DOI: 10.1242/dev.152561


Various government and philanthropic organizations around the world have supported HCA and HCA-related scientific activities. Since 2015, the U.S. National Institutes of Health has supported more than $200 million in HCA-related activities, including pilot and foundational projects. Additional supporters include: the Chan-Zuckerberg Initiative, which has provided key support for the HCA’s Data Coordination Platform; Wellcome, The Manton Foundation, The Kavli Foundation, and others.

Selected websites

  • About the Human Cell Atlas

    The Human Cell Atlas (HCA) is an international collaborative consortium, which aims to create comprehensive reference maps of all human cells—the fundamental units of life—as a basis for both understanding human health and diagnosing, monitoring, and treating disease. The HCA is a foundational, open resource charting cells, tissues, organs and systems throughout the body. The HCA will impact every aspect of biology and medicine, propelling translational discoveries and applications and ultimately leading to a new era of precision medicine. The HCA is steered and governed by an Organizing Committee, spanning 27 scientists from 10 countries and diverse areas of expertise. The HCA Organizing Committee is currently co-chaired by Dr. Aviv Regev of the Broad Institute of MIT and Harvard (USA) and Dr. Sarah Teichmann of the Wellcome Sanger Institute (UK). For more information about The Human Cell Atlas, visit