Human Cell Atlas (IRAS 260474)

We are building a detailed map of human cells by analysing single cells and their location within tissues using donated blood and tissue samples from people of all ages, both healthy and diseased. We combine advanced genomic technologies with powerful computing to reveal how cells work in health and illness. Our work will provide a valuable resource that could improve biological research, support better healthcare, and guide future discoveries for patients.

Cell atlasing is a quantitative approach to characterising cells within tissues at the molecular level. The international Human Cell Atlas consortium brings together expertise from biology, clinical medicine, technology, physics, computational science, software engineering and mathematics to generate a comprehensive reference map of human cell states. Unlike conventional tissue-based methods, such as microarray and standard RNA sequencing, which average gene activity across millions of cells, single-cell approaches capture the diversity of cell populations that is essential for understanding normal tissue function and disease.

The Sanger Human Cell Atlasing programme uses single-cell genomics, highly multiplex spatial gene expression profiling and advanced computational analysis to generate genome-wide molecular information from individual cells. Blood and tissue samples are obtained retrospectively from established tissue banks and ethically approved research studies in the UK and internationally, with appropriate consent for future research. Samples include healthy and diseased donors, both living and deceased, across all age groups. Prospective sample collection may be incorporated through the substantial amendment process. The resulting reference map will provide a foundational resource for basic biological research and future clinical applications.

Rationale

Cell atlasing has already shown its value: Sanger researchers used scRNA-seq to redefine the mononuclear phagocyte compartment of the immune system, identifying new dendritic cell and monocyte populations with distinct secretory profiles—work with direct implications for vaccine design and tumour biology.

Building a comprehensive reference map of human cells, their locations, and gene expression will advance understanding of health and disease, underpinning improved diagnosis, monitoring, and treatment.

This atlas requires a developmental axis—collecting fetal, post-natal, paediatric, and adult tissue data—to identify novel cell types across development and serve as a reference for studying developmental disease.

For selected tissues, comparing diseased samples (immune disorders, infections, non-immune conditions) against healthy reference data will validate the atlas as a tool for understanding disease mechanisms. Characterising cell viability and maturation state may also inform improvements in cryopreservation.

Together, these aims support the need for a comprehensive, developmentally-inclusive cell atlas as a foundation for basic and translational research.

Aims

The study aims to use state of the art and emerging molecular and immune technologies, and cutting-edge biological approaches to define all human cell types in terms of their distinctive patterns of gene expression, physiological states, developmental trajectories, and location.

Primary Outcome

Scaled up single cell genomics and high-throughput highly multiplex spatial gene expression profiling approaches. Coupled with powerful computational methods, this strategy will produce a comprehensive and systematic reference map of human cells, providing a fundamental blueprint of cell states for both basic biological research and clinical practice.

Key Secondary outcome(s)

None

Study Type

Observational

Participant and Sample Information

Populations involved:

Living and deceased donors, ages 0 to 99+, healthy and diseased individuals.

Countries of recruitment:

International

Approximate participant or sample numbers (if applicable):

4000

Key inclusion criteria:

Living and the deceased age 0 to 99+ from healthy and diseased individuals.

Key exclusion criteria:

None

Recruitment status:

Recruiting by invitation only.

Governance and Ethical Approval

Governance and oversight:

Study Sponsor: Wellcome Sanger Institute

All work conducted at the Wellcome Sanger Institute is reviewed and overseen by institutional Research Governance processes, ensuring compliance with ethical, legal, and regulatory requirements.

Ethical approval:

This study has been reviewed by the Yorkshire & the Humber – Leeds East NHS Research Ethics Committee. The study received REC approval on 16 December 2019.

IRAS 260474

REC reference: 19/YH/0441

Data and Sample Use

Data sharing:

Anonymised DNA sequence data are stored in the European Genome-Phenome Archive (EGA) and made available to bonafide researchers via managed access, subject to data access agreements. Anonymised samples and cultured cells may also be shared with other legitimate research organisations under appropriate legal agreements.

IPD sharing statement

Deidentified individual participant-level data (IPD) will not be shared as part of this study.

Completion date

Ongoing

Further Information

For enquiries about the scientific aims of this study or potential collaboration, please contact the relevant scientific programme at https://www.sanger.ac.uk/group/vento-tormo-group/.

For enquiries relating to research governance, ethics, or regulatory oversight, please contact the Research Governance team at researchgovernance@sanger.ac.uk.