This is a preprint.

It has not yet been peer reviewed by a journal.

The National Library of Medicine is running a pilot to include preprints that result from research funded by NIH in PMC and PubMed.

[Preprint]. 2023 Mar 24:arXiv:2303.13996v1.

The status of the human gene catalogue

Paulo Amaral¹, Silvia Carbonell-Sala², Francisco M De La Vega³, Tiago Faial⁴, Adam Frankish⁵, Thomas Gingeras⁶, Roderic Guigo^{2

7}, Jennifer L Harrow⁸, Artemis G Hatzigeorgiou⁹, Rory Johnson¹⁰, Terence D Murphy¹¹, Mihaela Pertea^{12

13}, Kim D Pruitt¹¹, Shashikant Pujar¹¹, Hazuki Takahashi¹⁴, Igor Ulitsky¹⁵, Ales Varabyou^{11

16}, Christine A Wells¹⁷, Mark Yandell¹⁸, Piero Carninci^{13

19}, Steven L Salzberg^{11

12

15

20}

Affiliations

¹ INSPER Institute of Education and Research, São Paulo, SP, Brasil.
² Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
³ Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA; Tempus Labs, Inc., Chicago, IL.
⁴ Nature Genetics, San Francisco, CA, USA.
⁵ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁶ Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
⁷ Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.
⁸ Centre for Genomics Research, Discovery Sciences, AstraZeneca, Da Vinci Building. Melbourn Science Park, Royston UK SG8 6HB.
⁹ Universithy of Thessaly, Department of Computer Science and Biomedical Informatics, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece.
¹⁰ School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland; Conway Institute of Biomedical and Biomolecular Research, University College Dublin, D04 V1W8 Dublin, Ireland; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.
¹¹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
¹² Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
¹³ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
¹⁴ Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama Kanagawa 230-0045 Japan.
¹⁵ Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
¹⁶ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
¹⁷ Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010 Vic Australia.
¹⁸ Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
¹⁹ Human Technopole, via Rita Levi Montalcini 1, Milan 20157 Italy.
²⁰ Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.

PMID: 36994150
PMCID: PMC10055485

The status of the human gene catalogue

Paulo Amaral et al. ArXiv. 2023.

[Preprint]. 2023 Mar 24:arXiv:2303.13996v1.

Authors

Affiliations

¹ INSPER Institute of Education and Research, São Paulo, SP, Brasil.
² Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.
³ Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA; Tempus Labs, Inc., Chicago, IL.
⁴ Nature Genetics, San Francisco, CA, USA.
⁵ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
⁶ Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
⁷ Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.
⁸ Centre for Genomics Research, Discovery Sciences, AstraZeneca, Da Vinci Building. Melbourn Science Park, Royston UK SG8 6HB.
⁹ Universithy of Thessaly, Department of Computer Science and Biomedical Informatics, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece.
¹⁰ School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland; Conway Institute of Biomedical and Biomolecular Research, University College Dublin, D04 V1W8 Dublin, Ireland; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland.
¹¹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
¹² Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
¹³ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
¹⁴ Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama Kanagawa 230-0045 Japan.
¹⁵ Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
¹⁶ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
¹⁷ Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010 Vic Australia.
¹⁸ Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA.
¹⁹ Human Technopole, via Rita Levi Montalcini 1, Milan 20157 Italy.
²⁰ Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.

PMID: 36994150
PMCID: PMC10055485

Update in

The status of the human gene catalogue.
Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. Amaral P, et al. Nature. 2023 Oct;622(7981):41-47. doi: 10.1038/s41586-023-06490-x. Epub 2023 Oct 4. Nature. 2023. PMID: 37794265 Free PMC article. Review.

Abstract

Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants.

PubMed Disclaimer

References

1. Understanding our genetic inheritance: The US Human Genome Project, the first five years 1991–1995. (U.S. Department of Health and Human Services and U.S. Department of Energy, 1990).
1. Nurk S. et al. The complete sequence of a human genome. Science 376, 44–53, doi:10.1126/science.abj6987 (2022). - DOI - PMC - PubMed
1. The Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74, doi:10.1038/nature11247 (2012). - DOI - PMC - PubMed
1. Kawaji H., Kasukawa T., Forrest A., Carninci P. & Hayashizaki Y. The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types. Sci Data 4, 170113, doi:10.1038/sdata.2017.113 (2017). - DOI - PMC - PubMed
1. Fields C., Adams M. D., White O. & Venter J. C. How many genes in the human genome? Nature Genetics 7, 345–346, doi:10.1038/ng0794-345 (1994). - DOI - PubMed

Publication types

Actions

Grants and funding

R01 MH123567/MH/NIMH NIH HHS/United States

LinkOut - more resources

Full Text Sources
- Europe PubMed Central
- PubMed Central

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

This is a preprint.

The status of the human gene catalogue

Affiliations

The status of the human gene catalogue

Authors

Affiliations

Update in

Abstract

References

Publication types

Grants and funding

LinkOut - more resources

Full Text Sources