Human Cell Atlas


The cell is the core unit of the human body—the key to understanding the biology of health and the ways in which molecular dysfunction leads to disease. Yet our characterization of the hundreds of types and subtypes of cells in the human body is limited, based partly on techniques that have limited resolution and classifications that do not always map neatly to each other. Genomics has offered a systematic approach, but it has largely been applied in bulk to many cell types at once—masking critical differences between cells—and in isolation from other valuable sources of data.

Recent advances in single-cell genomic analysis of cells and tissues have put systematic, high-resolution and comprehensive reference maps of all human cells within reach. In other words, we can now realistically envision a human cell atlas to serve as a basis for both understanding human health and diagnosing, monitoring, and treating disease.

A White Paper, openly available for download, provides an overview of the effort; our framework for the first draft of the atlas; descriptions of the technology and data analysis tools available to build the atlas; an introduction to the Data Coordination Platform that will host the data for researchers worldwide; a deeper look at biological systems we plan to explore and map; and details on the organization and governance of the HCA consortium and its relationships to the public (including ethical considerations regarding organ and tissue donors) and to funding support.

At its core, a cell atlas would be a collection of cellular reference maps, characterizing each of the thousands of cell types in the human body and where they are found. It would be an extremely valuable resource to empower the global research community to systematically study the biological changes associated with different diseases, understand where genes associated with disease are active in our bodies, analyze the molecular mechanisms that govern the production and activity of different cell types, and sort out how different cell types combine and work together to form tissues.

More specifically, a human cell atlas could:

  • catalog all cell types (for example, immune cells, brain cells) and sub-types in the human body;
  • map cell types to their location within tissues and within the body;
  • distinguish cell states (for example, a naive immune cell that has not yet encountered a pathogen compared to the same immune cell type after it is activated by encountering a bacterium);
  • capture the key characteristics of cells during transitions, such as activation or differentiation (for example, from a stem cell); and
  • trace the history of cells through a lineage, such as from a predecessor stem cell in bone marrow to a functional red blood cell.

Building a human cell atlas would require a collaboration across the international scientific community.

Disparate fields of expertise in biology, medicine, genomics, technology development, and computation (including data analysis, software engineering, and visualization) would need to come together in a coherent, concerted way. Furthermore, an international effort must be able to compare across diverse cell types and tissue types in consistent ways, while studying samples from diverse human communities. This would likely require standardized methods and strategies.

Almost certainly. A human cell atlas would have immediate, tangible, and transformative benefits.

For example, a cell atlas could:

  • provide a reference map for comparing related cells and identifying new cell types;
  • help interpret genetic variants by determining the cells in which such genes are acting;
  • distinguish disease from healthy states;
  • determine markers and signatures for pathology, cell sorting, and other measurements and tests;
  • reformulate our fundamental definition of cell types, states and transitions;
  • provide a direct view of human biology in vivo, removing the distorting aspects of cell culture and facilitating better comparison with current models and analysis of legacy data;
  • identify the regulatory code that controls cell differentiation and cell–cell interactions and  maintains cell state;
  • discover targets for therapeutic intervention; and
  • drive the development of new technologies and advanced analysis techniques.

A human cell atlas would likely impact almost every aspect of biology and medicine, leading to a richer understanding of life's most fundamental units and principles.

We need to understand exactly what a potential project could look like and address critical questions.

Some of the important issues to be discussed include:

  • What are all of the potential benefits of a human cell atlas?
  • How to engage biological communities in specific areas?
  • What should the scope of a human cell atlas be?
  • From where and how should samples be sourced?
  • How and where should samples be processed?
  • Which technologies should be used, and which technologies must be developed further?
  • What computational strategies will be most appropriate?
  • How should activities toward a cell atlas be organized?
  • What new biological communities need to be created?
  • How should data be shared and disseminated?
  • How can it be ensured that the global research community benefits from a human cell atlas?

In London on 13 and 14 October, 2016, we will begin to address these questions and more, with the goal of building a framework from which a human cell atlas could take shape.

The Human Cell Atlas has the potential to transform our understanding of human health and disease and will impact almost every aspect of biology and medicine. This effort will require an international community of researchers contributing their diverse expertise. To read more about current efforts, you can browse the following documents, links and tools.

Previous meetings
Preliminary Meeting Questions

Meeting website

Meeting agenda

Science Philanthropy Alliance XO File

NHGRI Human Cell Atlas Presentation

NIH Request for Information (RFI)

Sanger Institute Response to NIH RFI

Broad Institute NIH Response

HCA Reading Biology

HCA International collaboration


Useful links
Wellcome Trust Sanger Institute

Wellcome Trust

Broad Institute

The European Bioinformatics Institute

Karolinska Institute


Teichmann Lab

Regev Lab

Klarman Cell Observatory

Sanger Institute-EBI Single-Cell Genomics Centre 


Single Cell Portal

Weizmann Institute