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CiliaCarta: an integrated and validated compendium of ciliary genes

View ORCID ProfileTeunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michel R. Leroux, Rim Hjeij, Nicola Horn, Yves Texier, Yasmin Wissinger, Jeroen van Reeuwijk, Gabrielle Wheway, Barbara Knapp, Jan F. Scheel, Brunella Franco, Dorus A. Mans, Erwin van Wijk, François Képès, Gisela G. Slaats, Grischa Toedt, Hannie Kremer, Heymut Omran, Katarzyna Szymanska, Konstantinos Koutroumpas, Marius Ueffing, Thanh-Minh T. Nguyen, Stef J.F. Letteboer, Machteld M. Oud, Sylvia E. C. van Beersum, Miriam Schmidts, Philip L. Beales, Qianhao Lu, Rachel H. Giles, Radek Szklarczyk, Robert B. Russell, Toby J. Gibson, Colin A. Johnson, Oliver E. Blacque, Uwe Wolfrum, Karsten Boldt, Ronald Roepman, Victor Hernandez-Hernandez, Martijn A. Huynen
doi: https://doi.org/10.1101/123455
Teunis J. P. van Dam
1Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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  • ORCID record for Teunis J. P. van Dam
  • For correspondence: t.j.p.vandam@uu.nl martijn.huijnen@radboudnumc.nl
Julie Kennedy
2School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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Robin van der Lee
1Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Erik de Vrieze
3Department of Otorhinolaryngology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
4Donders Centre for Cognitive Neurosciences, 6525 AJ Nijmegen, the Netherlands
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Kirsten A. Wunderlich
5Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, Mainz, Germany
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Suzanne Rix
6Institute of Child Health, University College London, London, UK
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Gerard W. Dougherty
7Department of General Pediatrics, University Hospital Muenster, Muenster, Germany 48149
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Nils J. Lambacher
2School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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Chunmei Li
8Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
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Victor L. Jensen
8Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
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Michel R. Leroux
8Department of Molecular Biology and Biochemistry and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
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Rim Hjeij
7Department of General Pediatrics, University Hospital Muenster, Muenster, Germany 48149
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Nicola Horn
9Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 7207 Tuebingen, Germany
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Yves Texier
9Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 7207 Tuebingen, Germany
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Yasmin Wissinger
9Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 7207 Tuebingen, Germany
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Jeroen van Reeuwijk
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Gabrielle Wheway
11Section of Ophthalmology & Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
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Barbara Knapp
5Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, Mainz, Germany
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Jan F. Scheel
5Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, Mainz, Germany
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Brunella Franco
12Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
13Medical Genetics, Department of Translational Medicine, Federico II University of Naples, Naples, Italy
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Dorus A. Mans
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Erwin van Wijk
3Department of Otorhinolaryngology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
4Donders Centre for Cognitive Neurosciences, 6525 AJ Nijmegen, the Netherlands
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François Képès
14Institute of Systems and Synthetic Biology (iSSB), Genopole, CNRS, Univ. Evry, France
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Gisela G. Slaats
15Dept. Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 6, 3584CT Utrecht, the Netherlands
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Grischa Toedt
16Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
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Hannie Kremer
3Department of Otorhinolaryngology, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
4Donders Centre for Cognitive Neurosciences, 6525 AJ Nijmegen, the Netherlands
17Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Heymut Omran
7Department of General Pediatrics, University Hospital Muenster, Muenster, Germany 48149
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Katarzyna Szymanska
11Section of Ophthalmology & Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
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Konstantinos Koutroumpas
14Institute of Systems and Synthetic Biology (iSSB), Genopole, CNRS, Univ. Evry, France
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Marius Ueffing
9Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 7207 Tuebingen, Germany
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Thanh-Minh T. Nguyen
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Stef J.F. Letteboer
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Machteld M. Oud
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Sylvia E. C. van Beersum
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Miriam Schmidts
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
18Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Mathildenstrasse 1, 79106 Freiburg, Germany
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Philip L. Beales
6Institute of Child Health, University College London, London, UK
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Qianhao Lu
19Biochemie Zentrum Heidelberg (BZH), Ruprecht-Karls Universitaet Heidelberg, Im Neuenheimer Feld 328, Heidelberg, Germany
20Bioquant/Cell Networks, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
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Rachel H. Giles
15Dept. Nephrology and Hypertension, Regenerative Medicine Center, University Medical Center Utrecht, Uppsalalaan 6, 3584CT Utrecht, the Netherlands
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Radek Szklarczyk
1Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Robert B. Russell
19Biochemie Zentrum Heidelberg (BZH), Ruprecht-Karls Universitaet Heidelberg, Im Neuenheimer Feld 328, Heidelberg, Germany
20Bioquant/Cell Networks, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
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Toby J. Gibson
16Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
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Colin A. Johnson
11Section of Ophthalmology & Neurosciences, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, LS9 7TF, UK.
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Oliver E. Blacque
2School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
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Uwe Wolfrum
5Department of Cell and Matrix Biology, Institute of Zoology, Johannes Gutenberg University of Mainz, Mainz, Germany
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Karsten Boldt
9Medical Proteome Center, Institute for Ophthalmic Research, University of Tuebingen, 7207 Tuebingen, Germany
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Ronald Roepman
10Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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Victor Hernandez-Hernandez
6Institute of Child Health, University College London, London, UK
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Martijn A. Huynen
1Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
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  • For correspondence: t.j.p.vandam@uu.nl martijn.huijnen@radboudnumc.nl
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Abstract

The cilium is an essential organelle at the surface of most mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We found experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins. In addition, we show that OSCP1, which has previously been implicated in two distinct non-ciliary functions, causes a cilium dysfunction phenotype when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 836 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/.

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CiliaCarta: an integrated and validated compendium of ciliary genes
Teunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michel R. Leroux, Rim Hjeij, Nicola Horn, Yves Texier, Yasmin Wissinger, Jeroen van Reeuwijk, Gabrielle Wheway, Barbara Knapp, Jan F. Scheel, Brunella Franco, Dorus A. Mans, Erwin van Wijk, François Képès, Gisela G. Slaats, Grischa Toedt, Hannie Kremer, Heymut Omran, Katarzyna Szymanska, Konstantinos Koutroumpas, Marius Ueffing, Thanh-Minh T. Nguyen, Stef J.F. Letteboer, Machteld M. Oud, Sylvia E. C. van Beersum, Miriam Schmidts, Philip L. Beales, Qianhao Lu, Rachel H. Giles, Radek Szklarczyk, Robert B. Russell, Toby J. Gibson, Colin A. Johnson, Oliver E. Blacque, Uwe Wolfrum, Karsten Boldt, Ronald Roepman, Victor Hernandez-Hernandez, Martijn A. Huynen
bioRxiv 123455; doi: https://doi.org/10.1101/123455
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CiliaCarta: an integrated and validated compendium of ciliary genes
Teunis J. P. van Dam, Julie Kennedy, Robin van der Lee, Erik de Vrieze, Kirsten A. Wunderlich, Suzanne Rix, Gerard W. Dougherty, Nils J. Lambacher, Chunmei Li, Victor L. Jensen, Michel R. Leroux, Rim Hjeij, Nicola Horn, Yves Texier, Yasmin Wissinger, Jeroen van Reeuwijk, Gabrielle Wheway, Barbara Knapp, Jan F. Scheel, Brunella Franco, Dorus A. Mans, Erwin van Wijk, François Képès, Gisela G. Slaats, Grischa Toedt, Hannie Kremer, Heymut Omran, Katarzyna Szymanska, Konstantinos Koutroumpas, Marius Ueffing, Thanh-Minh T. Nguyen, Stef J.F. Letteboer, Machteld M. Oud, Sylvia E. C. van Beersum, Miriam Schmidts, Philip L. Beales, Qianhao Lu, Rachel H. Giles, Radek Szklarczyk, Robert B. Russell, Toby J. Gibson, Colin A. Johnson, Oliver E. Blacque, Uwe Wolfrum, Karsten Boldt, Ronald Roepman, Victor Hernandez-Hernandez, Martijn A. Huynen
bioRxiv 123455; doi: https://doi.org/10.1101/123455

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