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Articles by Cas Simons

Automated reanalysis of genomic data for rare disease diagnostics at scale

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By Matthew Welland, K. D. Ahlquist, Paul De Fazio, Christina A. Austin-Tse, Samantha J. Bryen, Rocio Rius, Michael Franklin, Caitlin Morrison, Giles Hall, Laura Gauthier, Alex Bloemendal, David Francis, Andrew Mallett, Amali Mallawaarachchi, Paul J. Lockhart, Richard J. Leventer, Ingrid E. Scheffer, Katherine Howell, Karin S. Kassahn, Hamish S. Scott, Julie McGaughran, John Christodoulou, David Thorburn, Bryony Thompson, Chirag Patel, Greg Smith, Anne H. O’Donnell-Luria, Simon Sadedin, Heidi Rehm, Sebastian Lunke, Jeremiah D. Wander, Kaitlin E. Samocha, Cas Simons, Daniel MacArthur, Zornitza Stark, Laura Wedd
| Nature Verified
Abstract Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necessary to ensure scalability, adoption and sustainability of iterative reanalysis.
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Author Correction: Biallelic variants in the noncoding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes

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By Rocio Rius, Alexander Blakes, Yuyang Chen, Joachim De Jonghe, François Lecoquierre, Ruebena Dawes, Benjamin Cogné, Hyung Chul Kim, Javeria R. Alvi, Florence Amblard, Morad Ansari, Annabelle Arlt, Christina A. Austin-Tse, Sarah I. Baer, Meena Balasubramanian, Elsa V. Balton, Giulia Barcia, Jonathan Bernstein, Jasmin Beygo, Pierre Blanc, Nuria C. Bramswig, Frederik Braun, Daniel G. Calame, Jamie Campbell, Charles Coutton, Chloe Cunningham, Nitsuh Dargie, Christel Depienne, Katrina M. Dipple, Abhijit Dixit, Lauren Dreyer, Haowei Du, Salima El Chehadeh, Lisa J. Ewans, Vanessa Geiger, Richard Gibbs, Ian Glass, Olivier GRUNEWALD, Paul Gueguen, Tobias B. Haack, Radu Harbuz, Ingo Helbig, Judit M. Horváth, Alexander Hustinx, Bertrand Isidor, Marie-Line Jacquemont, Médéric Jeanne, Riley Kessler, Hannah Klinkhammer, G. Christoph Korenke, Peter Krawitz, Steven S. Laurie, Richard J. Leventer, Rebecca J. Levy, James R. Lupski, Pierre Marijon, Kaitlin McGinnis, Rodrigo Mendez Verified, Rodrigo Matías Méndez, Olfa Messaoud, Caroline Nava, Anne H. O’Donnell-Luria, Melanie O’Leary, Simone Olivieri, Amitav Parida, Davut Pehlivan, Jennifer E. Posey, Chloe Reuter, Véronique Satre, Caroline Schluth-Bolard, Thomas Smol, Tipu Sultan, John Taylor, Christel Thauvin-Robinet, Julien Thevenon, Eloise Uebergang, Catherine Vincent-Delorme, Evangeline Wassmer, Matthew Wheeler, Elif Güleç, Adeline Vanderver, Arastoo Vossough, Stephan Sanders, Siddharth Banka, Gregory M. Findlay, Daniel MacArthur, Cas Simons, Nicola Whiffin, Ana Beleza-Meireles, Daniel Buchzik, Anne Dieux, Fraser Jamie, Urania Kotzaeridou, Mevyn Nizard, Anna Jenne Prentice, Sandra Ueberberg
| Nature Verified
Correction to: Nature Genetics https://doi.org/10.1038/s41588-026-02554-6, published online 8 April 2026. In the version of this article initially published, the last name of Christel Thauvin-Robinet was misspelled (Thauvin-Robinetvin) and is now amended in the HTML and PDF versions of the article.
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Saturation editing of RNU4-2 reveals distinct dominant and recessive disorders

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By Joachim De Jonghe, Hyung Chul Kim, Elsa Leitão, Ruebena Dawes, Christina M. Kajba, Benjamin Cogné, Yuyang Chen, Alexander Blakes, Cas Simons, Rocio Rius, Javeria R. Alvi, Christina A. Austin-Tse, Sarah I. Baer, Pierre Blanc, Daniel G. Calame, Charles Coutton, Chloe Cunningham, Katrina M. Dipple, Haowei Du, Salima El Chehadeh, Ian Glass, Joseph G. Gleeson, Olivier GRUNEWALD, Paul Gueguen, Marie-Line Jacquemont, Richard J. Leventer, Pierre Marijon, Olfa Messaoud, Tipu Sultan, Catherine Vincent-Delorme, Elif Güleç, Julien Thevenon, Rodrigo Mendez Verified, Rodrigo Matías Méndez, Daniel MacArthur, Christel Depienne, Caroline Nava, Nicola Whiffin, Gregory M. Findlay, Ayanfeoluwa Adedeji, Florence Amblard, Elsa V. Balton, Nitsuh Dargie, Radu Harbuz, Christel Thauvin
| Nature Verified
Abstract Recently, de novo variants in an 18-nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder that is predicted to affect tens of thousands of individuals worldwide1,2. RNU4-2 is a non-protein-coding gene that is transcribed into the U4 small nuclear RNA component of the major spliceosome3. ReNU syndrome variants disrupt spliceosome function and alter 5′ splice site selection1,4.
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Biallelic variants in RNU2-2 cause a remarkably frequent developmental and epileptic encephalopathy

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By Adam Jackson, Alexander Blakes, Bader Alhaddad, Olivia Henry, Elizabeth 'Ebbie' Wall, Ola A. Abdelhadi, Khadijah Bakur, Edward D Blair, Angela Brady, Helen K Brittain, Kate Chandler, Natasha Clarke, Irene Duba, Frances Elmslie, Jamie M. Ellingford, Lisa J. Ewans, Andrew Fennell, Simon Heller, Anna Hammarsjö, Nicole Lesko, Anna Lindstrand, Rebecca Macintosh, Sahar Mahmoud Mansour, Lara Menzies, Kay Metcalfe, Lina Nashef, Raymond T. O’Keefe, Elizabeth Palmer, Amitav Parida, Melody Redman, Alessandra Renieri, Chiara Fallerini, Caterina Rizzo, Rani Sachdev, Cas Simons, Sanjay M Sisodiya, Helen Stewart, Tommy Stödberg, Benito Banos-Pinero, Fulya Taylan, Huw Thomas Verified, Samuel Wiafe, Anna Wedell, Nicola Whiffin, Susan Walker, Rocio Rius, Ann Nordgren, Fowzan S. Alkuraya, Jenny Lord, Siddharth Banka, Angelica M. Delgado-Vega, Shakti Agrawal, Miriana Danelli, Nicholas Drinkall, Gabriella Gazdagh, Kristina Karrman, Usha Kini, Alison Milhench, Nadja Pekkola Pacheco, Katrina Prescott, Flavia Tinella, Jong Hee Chae
| Nature Verified
Abstract Neurodevelopmental disorders (NDDs) affect 2–4% of the population, are predominantly genetic and remain unsolved in ~50% of individuals. We show that rare biallelic variants in RNU2-2 are enriched and over-transmitted in individuals with unresolved NDDs. We define a recessive RNU2-2 syndrome, delineate its unique genetic architecture and show that it manifests clinically as a severe developmental and epileptic encephalopathy.
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Non-coding structural variants disrupting conserved PITX2 enhancer loci in Axenfeld–Rieger syndrome

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By Lucas A. Mitchell, Joshua Schmidt, Emmanuelle Souzeau, Lachlan Knight, Giorgina Maxwell, Andrew Dubowsky, Ridia Lim, Matthew Welland, Cas Simons, Daniel MacArthur, Janey L. Wiggs, Jamie Craig, Owen M. Siggs, Edward Formaini
| Nature Verified
Abstract Axenfeld–Rieger Syndrome (ARS) is an autosomal dominant condition with both ocular and non-ocular manifestations. ARS is primarily caused by coding variants at the PITX2 or FOXC1 loci, yet many cases still remain undiagnosed.
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De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome - Nature

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By Yuyang Chen, Ruebena Dawes, Hyung Chul Kim, Sarah Stenton, Susan Walker, Jenny Lord, Alexandra Martin-Geary, Erwan Delage, Elston N. D’Souza, Seth Berger, Jonathan Bernstein, David J. Coman, Alison G. Compton, Kerith-Rae Dias, Frances Elmslie, Jamie Fraser, Lyndon Gallacher, Anne Goriely, Christina L. Grant, Tobias B. Haack, Anjali G. Hinch, Matthew E Hurles, Elsa Leitão, Anna Le Fevre, Sarah J Lindsay, Paul J. Lockhart, Taylor Maurer, Hector Mendez, Stephen Montgomery, Serena M. Neumann, Melanie O’Leary, Nikhil Pattani, Nicole Revencu, Rocio Rius, Jill A. Rosenfeld, Cas Simons, Penny Snell, David Thorburn, Eloise Uebergang, Pradeep Vasudevan, Matthew Wheeler, Zoe Wolfenson, Caroline Wright, Sebastian M. Fica, Christel Depienne, Joanna M. M. Howson, Stephan Sanders, Anne H. O’Donnell-Luria
| Nature Verified
Abstract Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2.
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TEFM variants impair mitochondrial transcription causing childhood-onset neurological disease - Nature Communications

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By Lindsey Van Haute, Daniella H. Hock, Nicola Brunetti-Pierri, Nikeisha Caruana, Guy Helman, Henry Houlden, Guy Lenaers, Pedro Rebelo-Guiomar, Maha S. Zaki, David Thorburn, David Stroud, John Christodoulou, Claes Gustafsson, Michal Minczuk, Kiran Polavarapu, Mainak Bardhan, Rocio Rius, Cas Simons, Seena Vengalil
| Nature Verified
Abstract Mutations in the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA biology. The TEFM gene encodes the mitochondrial transcription elongation factor responsible for enhancing the processivity of mitochondrial RNA polymerase, POLRMT.
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