Standardized annotation of translated open reading frames

Jonathan M Mudge^#¹, Jorge Ruiz-Orera^#², John R Prensner^#^{3

4

5}, Marie A Brunet⁶, Ferriol Calvet⁷, Irwin Jungreis^{8

9}, Jose Manuel Gonzalez⁷, Michele Magrane⁷, Thomas F Martinez^{10

11}, Jana Felicitas Schulz¹², Yucheng T Yang^{13

14}, M Mar Albà^{15

16}, Julie L Aspden^{17

18}, Pavel V Baranov¹⁹, Ariel A Bazzini^{20

21}, Elspeth Bruford^{7

22}, Maria Jesus Martin⁷, Lorenzo Calviello^{23

24}, Anne-Ruxandra Carvunis^{25

26}, Jin Chen²⁷, Juan Pablo Couso²⁸, Eric W Deutsch²⁹, Paul Flicek⁷, Adam Frankish⁷, Mark Gerstein^{13

30

31

32}, Norbert Hubner^{12

33

34}, Nicholas T Ingolia³⁵, Manolis Kellis^{8

9}, Gerben Menschaert³⁶, Robert L Moritz²⁹, Uwe Ohler^{37

38

39}, Xavier Roucou⁴⁰, Alan Saghatelian¹⁰, Jonathan S Weissman^{41

42

43}, Sebastiaan van Heesch^#⁴⁴

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. jmudge@ebi.ac.uk.
² Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. jorge.ruizorera@mdc-berlin.de.
³ Broad Institute of MIT and Harvard, Cambridge, MA, USA. prensner@broadinstitute.org.
⁴ Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. prensner@broadinstitute.org.
⁵ Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. prensner@broadinstitute.org.
⁶ Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
⁷ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
⁸ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁹ MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
¹⁰ Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
¹¹ Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.
¹² Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
¹³ Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.
¹⁴ Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
¹⁵ Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain.
¹⁶ Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
¹⁷ School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
¹⁸ LeedsOmics, University of Leeds, Leeds, UK.
¹⁹ School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
²⁰ Stowers Institute for Medical Research, Kansas City, MO, USA.
²¹ Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
²² Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.
²³ Functional Genomics Centre, Human Technopole, Milan, Italy.
²⁴ Computational Biology Centre, Human Technopole, Milan, Italy.
²⁵ Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
²⁶ Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
²⁷ Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
²⁸ Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain.
²⁹ Institute for Systems Biology, Seattle, WA, USA.
³⁰ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
³¹ Department of Computer Science, Yale University, New Haven, CT, USA.
³² Department of Statistics & Data Science, Yale University, New Haven, CT, USA.
³³ Charité-Universitätsmedizin, Berlin, Germany.
³⁴ DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.
³⁵ Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
³⁶ Biobix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
³⁷ Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
³⁸ Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
³⁹ Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany.
⁴⁰ Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada.
⁴¹ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴² Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
⁴³ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴⁴ Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. S.vanHeesch@prinsesmaximacentrum.nl.

^# Contributed equally.

PMID: 35831657
PMCID: PMC9757701
DOI: 10.1038/s41587-022-01369-0

Standardized annotation of translated open reading frames

Jonathan M Mudge et al. Nat Biotechnol. 2022 Jul.

. 2022 Jul;40(7):994-999.

doi: 10.1038/s41587-022-01369-0.

Authors

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. jmudge@ebi.ac.uk.
² Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. jorge.ruizorera@mdc-berlin.de.
³ Broad Institute of MIT and Harvard, Cambridge, MA, USA. prensner@broadinstitute.org.
⁴ Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. prensner@broadinstitute.org.
⁵ Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. prensner@broadinstitute.org.
⁶ Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, Quebec, Canada.
⁷ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
⁸ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁹ MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA.
¹⁰ Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
¹¹ Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.
¹² Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
¹³ Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA.
¹⁴ Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
¹⁵ Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain.
¹⁶ Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
¹⁷ School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
¹⁸ LeedsOmics, University of Leeds, Leeds, UK.
¹⁹ School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
²⁰ Stowers Institute for Medical Research, Kansas City, MO, USA.
²¹ Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
²² Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.
²³ Functional Genomics Centre, Human Technopole, Milan, Italy.
²⁴ Computational Biology Centre, Human Technopole, Milan, Italy.
²⁵ Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
²⁶ Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
²⁷ Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
²⁸ Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain.
²⁹ Institute for Systems Biology, Seattle, WA, USA.
³⁰ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
³¹ Department of Computer Science, Yale University, New Haven, CT, USA.
³² Department of Statistics & Data Science, Yale University, New Haven, CT, USA.
³³ Charité-Universitätsmedizin, Berlin, Germany.
³⁴ DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.
³⁵ Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
³⁶ Biobix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium.
³⁷ Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
³⁸ Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
³⁹ Department of Computer Science, Humboldt-Universität zu Berlin, Berlin, Germany.
⁴⁰ Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada.
⁴¹ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴² Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
⁴³ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁴⁴ Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. S.vanHeesch@prinsesmaximacentrum.nl.

^# Contributed equally.

PMID: 35831657
PMCID: PMC9757701
DOI: 10.1038/s41587-022-01369-0

No abstract available

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Conflict of interest statement

Competing interests

P.V.B. is a co-founder of RiboMaps Ltd., which provides Ribo-seq analysis as a commercial service, including identification of translated ORFs. A.R.C. is a member of the scientific advisory board for Flagship Labs 69, Inc. P.F. is a member of the scientific advisory boards of Fabric Genomics, Inc., and Eagle Genomics, Ltd. The other authors declare no competing interests.

Figures

**Fig. 1 |. Characterization of a consensus set of Ribo-seq ORFs for annotation by GENCODE.**
a, Schematic of the main steps and goals for this consortium effort. b, Map showing the participating institutions included in this effort. c, Schematic overview of filtering steps used to create the consensus set of ribosome profiling (Ribo-seq) ORFs. d, Diagrammatic representation of all Ribo-seq ORFs according to ORF type (see Table 2 for more information).

See this image and copyright information in PMC

References

1. Ingolia NT, Ghaemmaghami S, Newman JRS & Weissman JS Science 324,218–223 (2009). - PMC - PubMed
1. van Heesch S et al. Cell 178, 242–260.e29 (2019). - PubMed
1. Ji Z, Song R, Regev A, & Struhl K eLife 4, e08890 (2015). - PMC - PubMed
1. Cahviello L et al. Nat. Methods 13, 165–170 (2016). - PubMed
1. Martinez TF et al. Nat. Chem. Biol 16, 458–468 (2020). - PMC - PubMed

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Standardized annotation of translated open reading frames

Affiliations

Standardized annotation of translated open reading frames

Authors

Affiliations

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

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