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The status of the human gene catalogue

Nature volume 622, pages 41–47 (2023)Cite this article

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Abstract

Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.

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Fig. 1: A major challenge for gene annotation is how to capture the diversity of gene products deriving from each gene locus.
Fig. 2: Predicted and observed human gene counts over time.

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Acknowledgements

We thank the staff at the Banbury Center at Cold Spring Harbor Laboratory and the Cold Spring Harbor Laboratory Corporate Sponsor Program for supporting a workshop that all authors of this work attended. This work was supported in part by the US National Institutes of Health (NIH) under grants R01-HG006677 (to M.P., S.L.S. and A.V.), R01-MH123567 (to M.P. and S.L.S.), R35-GM130151 (to S.L.S.), U41-HG007234 (to A.F.) and U24-HG007234 (to R.G. and S.C.-S.); the Wellcome Trust under grant WT222155/Z/20/Z (to A.F.); the European Molecular Biology Laboratory (to A.F.); the US National Science Foundation under grant DBI-1759518 (to M.P.); the European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under grant T2EDK-00391 (to A.G.H.); Science Foundation Ireland through Future Research Leaders award 18/FRL/6194 and the Irish Research Council through Consolidator Laureate award (IRCLA/2022/2500; to R.J.); the National Center for Biotechnology Information of the National Library of Medicine, NIH (to T.D.M., K.D.P. and S.P.); the National Health and Medical Research Council (NHMRC) APP1186371 (to C.A.W.); the Center for Genomic Medicine at the University of Utah Health, and the H.A. & Edna Benning Foundation (to M.Y.); the Spanish Ministry of Science and Innovation to the EMBL partnership, Centro de Excelencia Severo Ochoa and CERCA Programme/Generalitat de Catalunya (to R.G. and S.C.-S.); the RIKEN Center for Integrative Medical Sciences (to P.C. and H.T.); and Human Technopole (to P.C.).

Author information

Authors and Affiliations

  1. INSPER Institute of Education and Research, Sao Paulo, Brazil

    Paulo Amaral

  2. Centre for Genomic Regulation (CRG), Barcelona, Spain

    Silvia Carbonell-Sala & Roderic Guigo

  3. Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA

    Francisco M. De La Vega

  4. Tempus Labs, Chicago, IL, USA

    Francisco M. De La Vega

  5. Nature Genetics, San Francisco, CA, USA

    Tiago Faial

  6. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK

    Adam Frankish

  7. Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Thomas Gingeras

  8. Universitat Pompeu Fabra (UPF), Barcelona, Spain

    Roderic Guigo

  9. Centre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK

    Jennifer L. Harrow

  10. Department of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece

    Artemis G. Hatzigeorgiou

  11. Hellenic Pasteur Institute, Athens, Greece

    Artemis G. Hatzigeorgiou

  12. School of Biology and Environmental Science, University College Dublin, Dublin, Ireland

    Rory Johnson

  13. Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland

    Rory Johnson

  14. Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland

    Rory Johnson

  15. Department for BioMedical Research, University of Bern, Bern, Switzerland

    Rory Johnson

  16. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

    Terence D. Murphy, Kim D. Pruitt & Shashikant Pujar

  17. Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA

    Mihaela Pertea, Ales Varabyou & Steven L. Salzberg

  18. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA

    Mihaela Pertea & Steven L. Salzberg

  19. Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA

    Mihaela Pertea, Ales Varabyou & Steven L. Salzberg

  20. Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

    Hazuki Takahashi & Piero Carninci

  21. Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel

    Igor Ulitsky

  22. Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel

    Igor Ulitsky

  23. Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia

    Christine A. Wells

  24. Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA

    Mark Yandell

  25. Human Technopole, Milan, Italy

    Piero Carninci

  26. Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA

    Steven L. Salzberg

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  1. Paulo Amaral
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Contributions

P.A., S.C.-S., F.M.D.L.V., T.F., A.F., T.G., R.G., J.L.H., A.G.H., R.J., T.D.M., M.P., K.D.P., S.P., H.T., I.U., A.V., C.A.W., M.Y., P.C. and S.L.S. participated in discussions at a Banbury Conference at Cold Spring Harbor Laboratory, providing the source material for this paper. All authors contributed to writing, editing and reviewing the paper.

Corresponding authors

Correspondence to Piero Carninci or Steven L. Salzberg.

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T.F. is chief editor at Nature Genetics, a Nature Portfolio journal. T.F. was not involved in the editorial handling of this Nature paper (journals within the Nature Portfolio are editorially independent). The other authors declare no competing interests.

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Amaral, P., Carbonell-Sala, S., De La Vega, F.M. et al. The status of the human gene catalogue. Nature 622, 41–47 (2023). https://doi.org/10.1038/s41586-023-06490-x

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