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1. Optimizing the Diagnosis of Rare Genomic Disease in the UK and Ireland

Author

Wright, Caroline F, Campbell, Patrick, Eberhardt, Ruth Y., Aitken, Stuart, Perrett, Daniel, Brent, Simon, Danecek, Petr, Gardner, Eugene J., Chundru, V Kartik, Lindsay, Sarah J, Andrews, Katrina A, Hampstead, Juliet, Kaplanis, Joanna, Samocha, Kaitlin E., Middleton, Anna, Foreman, Julia, Hobson, Rachel J., Parker, Michael J., Martin, Hilary C, FitzPatrick, David R, Hurles, Matthew E, and Firth, Helen V.

Published
2023

2. Epidemiology of emergency ambulance service calls related to COVID-19 in Scotland: a national record linkage study

Author

Fitzpatrick, David, Duncan, Edward A S, Moore, Matthew, Best, Catherine, Andreis, Federico, Esposito, Martin, Dobbie, Richard, Corfield, Alasdair R, and Lowe, David J

Subjects
Cohort Studies, Scotland, RC86-88.9, SARS-CoV-2, Ambulances, Emergency Medicine, COVID-19, Humans, Medical emergencies. Critical care. Intensive care. First aid, Critical Care and Intensive Care Medicine, Retrospective Studies, Original Research
Abstract

Background COVID-19 has overwhelmed health services across the world; its global death toll has exceeded 5.3 million and continues to grow. There have been almost 15 million cases of COVID-19 in the UK. The need for rapid accurate identification, appropriate clinical care and decision making, remains a priority for UK ambulance service. To support identification and conveyance decisions of patients presenting with COVID-19 symptoms the Scottish Ambulance Service introduced the revised Medical Priority Dispatch System Protocol 36, enhanced physician led decision support and prehospital clinical guidelines. This study aimed to characterise the impact of these changes on the pathways and outcomes of people attended by the SAS) with potential COVID-19. Methods A retrospective record linkage cohort study using National Data collected from NHS Scotland over a 5 month period (April–August 2020). Results The SAS responded to 214,082 emergency calls during the study time period. The positive predictive value of the Protocol 36 to identify potentially COVID-19 positive patients was low (17%). Approximately 60% of those identified by Protocol 36 as potentially COVID-19 positive were conveyed. The relationship between conveyance and mortality differed between Protocol 36 Covid-19 positive calls and those that were not. In those identified by Protocol 36 as Covid-19 negative, 30 day mortality was higher in those not conveyed (not conveyed 9.2%; conveyed 6.6%) but in the Protocol 36 Covid-19 positive calls, mortality was higher in those conveyed (not conveyed 4.3% conveyed 8.8%). Thirty-day mortality rates of those with COVID-19 diagnosed through virology was between 28.8 and 30.2%. Conclusion The low positive predictive value (17%) of Protocol 36 in identifying potential COVID-19 in patients emphasises the importance of ambulance clinicians approaching each call as involving COVID-19, reinforcing the importance of adhering to existing policy and continued use of PPE at all calls. The non-conveyance rate of people that were categorised as COVID-19 negative was higher than in the preceding year in the same service. The reasons for the higher rates of non-conveyance and the relationship between non conveyance rates and death at 3 and 30 days post index call are unknown and would benefit from further study.

Published
2022

4. Additional file 2 of Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Author

Ellingford, Jamie M., Ahn, Joo Wook, Bagnall, Richard D., Baralle, Diana, Barton, Stephanie, Campbell, Chris, Downes, Kate, Ellard, Sian, Duff-Farrier, Celia, FitzPatrick, David R., Greally, John M., Ingles, Jodie, Krishnan, Neesha, Lord, Jenny, Martin, Hilary C., Newman, William G., O’Donnell-Luria, Anne, Ramsden, Simon C., Rehm, Heidi L., Richardson, Ebony, Singer-Berk, Moriel, Taylor, Jenny C., Williams, Maggie, Wood, Jordan C., Wright, Caroline F., Harrison, Steven M., and Whiffin, Nicola

Abstract

Additional file 2: Fig S1. Identifying regulatory variants in trans with pLoF variants in GEL.

Published
2022
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5. Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens

Author

Daly, Paul, Zhou, Dongmei, Shen, Danyu, Chen, Yifan, Xue, Taiqiang, Chen, Siqiao, Zhang, Qimeng, Zhang, Jinfeng, McGowan, Jamie, Cai, Feng, Pang, Guan, Wang, Nan, Sheikh, Taha Majid Mahmood, Deng, Sheng, Li, Jingjing, Soykam, Hüseyin Okan, Kara, Irem, Fitzpatrick, David A, Druzhinina, Irina S., Bayram Akcapinar, Günseli, Wei, Lihui, Burbank, Lindsey Price, Matson, Michael, and Acibadem University Dspace

Subjects
Microbiology (medical), Infectious Diseases, General Immunology and Microbiology, Ecology, ginger, Physiology, virulence factors, Genetics, Pythium myriotylum, Cell Biology, genome dynamics
Abstract

The Pythium (Peronosporales, Oomycota) genus includes devastating plant pathogens that cause widespread diseases and severe crop losses. Here, we have uncovered a far greater arsenal of virulence factor-related genes in the necrotrophic Pythium myriotylum than in other Pythium plant pathogens. The genome of a plant-virulent P. myriotylum strain (similar to 70 Mb and 19,878 genes) isolated from a diseased rhizome of ginger (Zingiber officinale) encodes the largest repertoire of putative effectors, proteases, and plant cell wall-degrading enzymes (PCWDEs) among the studied species. P. myriotylum has twice as many predicted secreted proteins than any other Pythium plant pathogen. Arrays of tandem duplications appear to be a key factor of the enrichment of the virulence factor-related genes in P. myriotylum. The transcriptomic analysis performed on two P. myriotylum isolates infecting ginger leaves showed that proteases were a major part of the upregulated genes along with PCWDEs, Nep1-like proteins (NLPs), and elicitin-like proteins. A subset of P. myriotylum NLPs were analyzed and found to have necrosis-inducing ability from agroinfiltration of tobacco (Nicotiana benthamiana) leaves. One of the heterologously produced infection-upregulated putative cutinases found in a tandem array showed esterase activity with preferences for longer-chain-length substrates and neutral to alkaline pH levels. Our results allow the development of science-based targets for the management of P. myriotylum-caused disease, as insights from the genome and transcriptome show that gene expansion of virulence factor-related genes play a bigger role in the plant parasitism of Pythium spp. than previously thought. IMPORTANCE Pythium species are oomycetes, an evolutionarily distinct group of filamentous fungus-like stramenopiles. The Pythium genus includes several pathogens of important crop species, e.g., the spice ginger. Analysis of our genome from the plant pathogen Pythium myriotylum uncovered a far larger arsenal of virulence factor-related genes than found in other Pythium plant pathogens, and these genes contribute to the infection of the plant host. The increase in the number of virulence factor-related genes appears to have occurred through the mechanism of tandem gene duplication events. Genes from particular virulence factor-related categories that were increased in number and switched on during infection of ginger leaves had their activities tested. These genes have toxic activities toward plant cells or activities to hydrolyze polymeric components of the plant. The research suggests targets to better manage diseases caused by P. myriotylum and prompts renewed attention to the genomics of Pythium plant pathogens.

Published
2022

6. F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans

Author

Freitag, Michael, Sarikaya Bayram, Özlem, Bayram, Ozgur, Karahoda, Betim, Meister, Cindy, Köhler, Anna M., Thieme, Sabine, Elramli, Nadia, Frawley, Dean, McGowan, Jamie, Fitzpatrick, David A., Schmitt, Kerstin, de Assis, Leandro Jose, Valerius, Oliver, Goldman, Gustavo H., and Braus, Gerhard H.

Subjects
Cancer Research, SKP Cullin F-Box Protein Ligases, F-Box Proteins, Ubiquitin-Protein Ligases, Genetics, Ubiquitination, Methyltransferases, Molecular Biology, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Aspergillus nidulans
Abstract

Fungal growth and development are coordinated with specific secondary metabolism. This coordination requires 8 of 74 F-box proteins of the filamentous fungus Aspergillus nidulans. F-box proteins recognize primed substrates for ubiquitination by Skp1-Cul1-Fbx (SCF) E3 ubiquitin RING ligases and degradation by the 26S proteasome. 24 F-box proteins are found in the nuclear fraction as part of SCFs during vegetative growth. 43 F-box proteins interact with SCF proteins during growth, development or stress. 45 F-box proteins are associated with more than 700 proteins that have mainly regulatory roles. This corroborates that accurate surveillance of protein stability is prerequisite for organizing multicellular fungal development. Fbx23 combines subcellular location and protein stability control, illustrating the complexity of F-box mediated regulation during fungal development. Fbx23 interacts with epigenetic methyltransferase VipC which interacts with fungal NF-κB-like velvet domain regulator VeA that coordinates fungal development with secondary metabolism. Fbx23 prevents nuclear accumulation of methyltransferase VipC during early development. These results suggest that in addition to their role in protein degradation, F-box proteins also control subcellular accumulations of key regulatory proteins for fungal development.

Published
2022

9. Coordinating Development of the SWARM-EX CubeSat Swarm Across Multiple Institutions

Author

Agarwal, Rohil, Oh, Braden, Fitzpatrick, David, Buynovskiy, Anton, Lowe, Shane, Lisy, Celvi, Kriezis, Anargyros, Lan, Berwin, Lee, Zoe, Thomas, Austen, Wallace, Brodie, Costantino, Emanuele, Miner, Grant, Thayer, Jeffrey, D'Amico, Simone, Lemmer, Kristina, Lohmeyer, Whitney, and Palo, Scott

Subjects
SWARM-EX, swarm, CubeSat, university institutions
Abstract

The Space Weather Atmospheric Reconfigurable Multiscale Experiment (SWARM-EX) is a National Science Foundation (NSF) sponsored CubeSat mission distributed across six colleges and universities in the United States. The project has three primary goals: (1) contributing to aeronomy and space weather knowledge, (2) demonstrating novel engineering technology, and (3) advancing higher education. The scientific focus of SWARM-EX is to study the spatial and temporal variability of ion-neutral interactions in the equatorial Ionosphere-Thermosphere (I-T) region. Since the mission consists of three spacecraft operating in a swarm, SWARM-EX will take in-situ measurements of the neutral and ion composition on timescales of less than an orbital period to study the persistence and correlation between different phenomena in the I-T region. The engineering objectives of SWARM-EX are focused on advancing the state of the art in spacecraft formation flying. In addition to being the first passively safe, autonomous formation of more than two spacecraft, SWARM-EX will demonstrate several other key innovations. These include a novel hybrid propulsive/differential drag control scheme and the realization of a distributed aeronomy sensor. Asa project selected by the NSF for its broader impacts as well as its intellectual merit, SWARM-EX aims to use CubeSat development as a vehicle for education. The six collaborating institutions have varying levels of CubeSat experience and involve students who range from first-year undergraduates to Ph.D. candidates. These differences in knowledge, as well as the distributed nature of the program, present a tremendous educational opportunity, but also raise challenges such as cross-institutional communication and coordination, document sharing and file management, and hardware development. By detailing its procedures for overcoming these challenges, the SWARM-EX team believes that it may serve as a case study for the coordination of a successful CubeSat program distributed across multiple institutions.

Published
2021

10. Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex

Author

Hanson, Sara J, Cinnéide, Eoin Ó, Salzberg, Letal I, Wolfe, Kenneth H, McGowan, Jamie, Fitzpatrick, David A, Matlin, Kate, and Berman, J

Subjects
AcademicSubjects/SCI01140, Species complex, population genomics, AcademicSubjects/SCI00010, QH426-470, Biology, AcademicSubjects/SCI01180, Loss of heterozygosity, Population genomics, 03 medical and health sciences, 0302 clinical medicine, mating-type switching, Peroxisomes, Genetics, Molecular Biology, chromosomal rearrangements, Genetics (clinical), 030304 developmental biology, Investigation, 0303 health sciences, Ogataea, Nucleic acid sequence, Genomics, biology.organism_classification, Yeast, Mating of yeast, Saccharomycetales, AcademicSubjects/SCI00960, interspecies hybridization, Ogataea polymorpha, 030217 neurology & neurosurgery, Biogenesis
Abstract

The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the O. polymorpha species complex, including representatives of the species O. polymorpha, Ogataea parapolymorpha, Ogataea haglerorum, and Ogataea angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.

Published
2021

11. Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language

Author

Snijders Blok, Lot, Rousseau, Justine, Twist, Joanna, Ehresmann, Sophie, Takaku, Motoki, Venselaar, Hanka, Rodan, Lance H., Nowak, Catherine B., Douglas, Jessica, Swoboda, Kathryn J., Steeves, Marcie A., Sahai, Inderneel, Stumpel, Connie T. R. M., Stegmann, Alexander P. A., Wheeler, Patricia, Willing, Marcia, Fiala, Elise, Kochhar, Aaina, Gibson, William T., Cohen, Ana S. A., Agbahovbe, Ruky, Innes, A. Micheil, Au, P. Y. Billie, Rankin, Julia, Anderson, Ilse J., Skinner, Steven A., Louie, Raymond J., Warren, Hannah E., Afenjar, Alexandra, Keren, Boris, Nava, Caroline, Buratti, Julien, Isapof, Arnaud, Rodriguez, Diana, Lewandowski, Raymond, Propst, Jennifer, van Essen, Ton, Choi, Murim, Lee, Sangmoon, Chae, Jong H., Price, Susan, Schnur, Rhonda E., Douglas, Ganka, Wentzensen, Ingrid M., Zweier, Christiane, Reis, André, Bialer, Martin G., Moore, Christine, Koopmans, Marije, Brilstra, Eva H., Monroe, Glen R., van Gassen, Koen L. I., van Binsbergen, Ellen, Newbury-Ecob, Ruth, Bownass, Lucy, Bader, Ingrid, Mayr, Johannes A., Wortmann, Saskia B., Jakielski, Kathy J., Strand, Edythe A., Kloth, Katja, Bierhals, Tatjana, McRae, Jeremy F., Clayton, Stephen, Fitzgerald, Tomas W., Kaplanis, Joanna, Prigmore, Elena, Rajan, Diana, Sifrim, Alejandro, Aitken, Stuart, Akawi, Nadia, Alvi, Mohsan, Ambridge, Kirsty, Barrett, Daniel M., Bayzetinova, Tanya, Jones, Philip, Jones, Wendy D., King, Daniel, Krishnappa, Netravathi, Mason, Laura E., Singh, Tarjinder, Tivey, Adrian R., Ahmed, Munaza, Anjum, Uruj, Archer, Hayley, Armstrong, Ruth, Awada, Jana, Balasubramanian, Meena, Banka, Siddharth, Baralle, Diana, Barnicoat, Angela, Batstone, Paul, Baty, David, Bennett, Chris, Berg, Jonathan, Bernhard, Birgitta, Bevan, A. Paul, Bitner-Glindzicz, Maria, Blair, Edward, Blyth, Moira, Bohanna, David, Bourdon, Louise, Bourn, David, Bradley, Lisa, Brady, Angela, Brent, Simon, Brewer, Carole, Brunstrom, Kate, Bunyan, David J., Burn, John, Canham, Natalie, Castle, Bruce, Chandler, Kate, Chatzimichali, Elena, Cilliers, Deirdre, Clarke, Angus, Clasper, Susan, Clayton-Smith, Jill, Clowes, Virginia, Coates, Andrea, Cole, Trevor, Colgiu, Irina, Collins, Amanda, Collinson, Morag N., Connell, Fiona, Cooper, Nicola, Cox, Helen, Cresswell, Lara, Cross, Gareth, Crow, Yanick, D’Alessandro, Mariella, Dabir, Tabib, Davidson, Rosemarie, Davies, Sally, de Vries, Dylan, Dean, John, Deshpande, Charu, Devlin, Gemma, Dixit, Abhijit, Dobbie, Angus, Donaldson, Alan, Donnai, Dian, Donnelly, Deirdre, Donnelly, Carina, Douglas, Angela, Douzgou, Sofia, Duncan, Alexis, Eason, Jacqueline, Ellard, Sian, Ellis, Ian, Elmslie, Frances, Evans, Karenza, Everest, Sarah, Fendick, Tina, Fisher, Richard, Flinter, Frances, Foulds, Nicola, Fry, Andrew, Fryer, Alan, Gardiner, Carol, Gaunt, Lorraine, Ghali, Neeti, Gibbons, Richard, Gill, Harinder, Goodship, Judith, Goudie, David, Gray, Emma, Green, Andrew, Greene, Philip, Greenhalgh, Lynn, Gribble, Susan, Harrison, Rachel, Harrison, Lucy, Harrison, Victoria, Hawkins, Rose, He, Liu, Hellens, Stephen, Henderson, Alex, Hewitt, Sarah, Hildyard, Lucy, Hobson, Emma, Holden, Simon, Holder, Muriel, Holder, Susan, Hollingsworth, Georgina, Homfray, Tessa, Humphreys, Mervyn, Hurst, Jane, Hutton, Ben, Ingram, Stuart, Irving, Melita, Islam, Lily, Jackson, Andrew, Jarvis, Joanna, Jenkins, Lucy, Johnson, Diana, Jones, Elizabeth, Josifova, Dragana, Joss, Shelagh, Kaemba, Beckie, Kazembe, Sandra, Kelsell, Rosemary, Kerr, Bronwyn, Kingston, Helen, Kini, Usha, Kinning, Esther, Kirby, Gail, Kirk, Claire, Kivuva, Emma, Kraus, Alison, Kumar, Dhavendra, Kumar, V. K. Ajith, Lachlan, Katherine, Lam, Wayne, Lampe, Anne, Langman, Caroline, Lees, Melissa, Lim, Derek, Longman, Cheryl, Lowther, Gordon, Lynch, Sally A., Magee, Alex, Maher, Eddy, Male, Alison, Mansour, Sahar, Marks, Karen, Martin, Katherine, Maye, Una, McCann, Emma, McConnell, Vivienne, McEntagart, Meriel, McGowan, Ruth, McKay, Kirsten, McKee, Shane, McMullan, Dominic J., McNerlan, Susan, McWilliam, Catherine, Mehta, Sarju, Metcalfe, Kay, Middleton, Anna, Miedzybrodzka, Zosia, Miles, Emma, Mohammed, Shehla, Montgomery, Tara, Moore, David, Morgan, Sian, Morton, Jenny, Mugalaasi, Hood, Murday, Victoria, Murphy, Helen, Naik, Swati, Nemeth, Andrea, Nevitt, Louise, Norman, Andrew, O’Shea, Rosie, Ogilvie, Caroline, Ong, Kai-Ren, Park, Soo-Mi, Parker, Michael J., Patel, Chirag, Paterson, Joan, Payne, Stewart, Perrett, Daniel, Phipps, Julie, Pilz, Daniela T., Pollard, Martin, Pottinger, Caroline, Poulton, Joanna, Pratt, Norman, Prescott, Katrina, Pridham, Abigail, Procter, Annie, Purnell, Hellen, Quarrell, Oliver, Ragge, Nicola, Rahbari, Raheleh, Randall, Josh, Raymond, Lucy, Rice, Debbie, Robert, Leema, Roberts, Eileen, Roberts, Jonathan, Roberts, Paul, Roberts, Gillian, Ross, Alison, Rosser, Elisabeth, Saggar, Anand, Samant, Shalaka, Sampson, Julian, Sandford, Richard, Sarkar, Ajoy, Schweiger, Susann, Scott, Richard, Scurr, Ingrid, Selby, Ann, Seller, Anneke, Sequeira, Cheryl, Shannon, Nora, Sharif, Saba, Shaw-Smith, Charles, Shearing, Emma, Shears, Debbie, Sheridan, Eamonn, Simonic, Ingrid, Singzon, Roldan, Skitt, Zara, Smith, Audrey, Smith, Kath, Smithson, Sarah, Sneddon, Linda, Splitt, Miranda, Squires, Miranda, Stewart, Fiona, Stewart, Helen, Straub, Volker, Suri, Mohnish, Sutton, Vivienne, Swaminathan, Ganesh Jawahar, Sweeney, Elizabeth, Tatton-Brown, Kate, Taylor, Cat, Taylor, Rohan, Tein, Mark, Temple, I. Karen, Thomson, Jenny, Tischkowitz, Marc, Tomkins, Susan, Torokwa, Audrey, Treacy, Becky, Turner, Claire, Turnpenny, Peter, Tysoe, Carolyn, Vandersteen, Anthony, Varghese, Vinod, Vasudevan, Pradeep, Vijayarangakannan, Parthiban, Vogt, Julie, Wakeling, Emma, Wallwark, Sarah, Waters, Jonathon, Weber, Astrid, Wellesley, Diana, Whiteford, Margo, Widaa, Sara, Wilcox, Sarah, Wilkinson, Emily, Williams, Denise, Williams, Nicola, Wilson, Louise, Woods, Geoff, Wragg, Christopher, Wright, Michael, Yates, Laura, Yau, Michael, Nellåker, Chris, Parker, Michael, Firth, Helen V., Wright, Caroline F., FitzPatrick, David R., Barrett, Jeffrey C., Hurles, Matthew E., Roberts, John D., Petrovich, Robert M., Machida, Shinichi, Kurumizaka, Hitoshi, Lelieveld, Stefan, Pfundt, Rolph, Jansen, Sandra, Deriziotis, Pelagia, Faivre, Laurence, Thevenon, Julien, Assoum, Mirna, Shriberg, Lawrence, Kleefstra, Tjitske, Brunner, Han G., Wade, Paul A., Fisher, Simon E., and Campeau, Philippe M.

Subjects
Male, Models, Molecular, Developmental Disabilities, Gene Expression, General Physics and Astronomy, 02 engineering and technology, Chromatin remodelling, Sociology, lcsh:Science, Independent research, Adenosine Triphosphatases, 0303 health sciences, Multidisciplinary, biology, Health innovation, Disease genetics, Published Erratum, Neurodevelopmental disorders, 021001 nanoscience & nanotechnology, Spelling, 3. Good health, Phenotype, General partnership, Child, Preschool, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Female, medicine.symptom, Construct (philosophy), 0210 nano-technology, Psychology, Mi-2 Nucleosome Remodeling and Deacetylase Complex, Clinical epigenetics, Genotype, Science, Mutation, Missense, Library science, Child health, Speech Disorders, General Biochemistry, Genetics and Molecular Biology, Domain (software engineering), 03 medical and health sciences, Protein Domains, Intellectual Disability, medicine, Humans, Author Correction, 030304 developmental biology, Research ethics, Language Disorders, Whole Genome Sequencing, Core Grant, Macrocephaly, DNA Helicases, Helicase, General Chemistry, Chromatin Assembly and Disassembly, Megalencephaly, HEK293 Cells, biology.protein, lcsh:Q, Neuroscience, Impaired speech
Abstract

An Author Correction to this article was published on 15 February 2019 An Author Correction to this article was published on 02 May 2019 We thank all individuals and families for their contribution. We thank Amaia Carrion Castillo and Else Eising for assistance with the WGS analysis of the index individual, and Sarah Graham and Elliot Sollis for cloning the wild-type CHD3 construct for immunofluorescence. This work was supported by the Netherlands Organization for Scientific Research (NWO) Gravitation Grant 24.001.006 to the Language in Interaction Consortium (L.S.B., S.E.F., and H.G.B.), the Max Planck Society (S.E.F.), the National Institute on Deafness and Other Communication Disorders Grant DC000496 (L.Sh.) and a core grant to the Waisman Center from the National Institute of Child Health and Human Development (Grant U54 HD090256) to L.Sh., the Canadian Institutes of Health Research Grants MOP-119595 and PJT-148830 to W.T.G. Individuals 11, 16, 24, and 28 were part of The DDD Study cohort. The DDD Study presents independent research commissioned by the Health Innovation Challenge Fund [Grant number HICF-1009-003], a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute [Grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of the Wellcome Trust or the Department of Health. The DDD study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12, granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network.

Published
2019

12. Evaluating variants classified as pathogenic in ClinVar in the DDD Study

Author

Wright, Caroline F, Eberhardt, Ruth Y, Constantinou, Panayiotis, Hurles, Matthew E, FitzPatrick, David R, Firth, Helen V, DDD Study, Wright, Caroline F [0000-0003-2958-5076], and Apollo - University of Cambridge Repository

Subjects
genomic medicine, Gene Frequency, variant interpretation, Databases, Genetic, Exome Sequencing, reanalysis, Humans, developmental disorders, Exome
Abstract

PURPOSE: Automated variant filtering is an essential part of diagnostic genome-wide sequencing but may generate false negative results. We sought to investigate whether some previously identified pathogenic variants may be being routinely excluded by standard variant filtering pipelines. METHODS: We evaluated variants that were previously classified as pathogenic or likely pathogenic in ClinVar in known developmental disorder genes using exome sequence data from the Deciphering Developmental Disorders (DDD) study. RESULTS: Of these ClinVar pathogenic variants, 3.6% were identified among 13,462 DDD probands, and 1134/1352 (83.9%) had already been independently communicated to clinicians using DDD variant filtering pipelines as plausibly pathogenic. The remaining 218 variants failed consequence, inheritance, or other automated variant filters. Following clinical review of these additional variants, we were able to identify 112 variants in 107 (0.8%) DDD probands as potential diagnoses. CONCLUSION: Lower minor allele frequency (1 star) are good predictors of a previously identified variant being plausibly diagnostic for developmental disorders. However, around half of previously identified pathogenic variants excluded by automated variant filtering did not appear to be disease-causing, underlining the continued need for clinical evaluation of candidate variants as part of the diagnostic process.

Published
2021
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13. The contribution of X-linked coding variation to severe developmental disorders

Author

Martin, Hilary C., Gardner, Eugene J., Samocha, Kaitlin E., Kaplanis, Joanna, Akawi, Nadia, Sifrim, Alejandro, Eberhardt, Ruth Y., Tavares, Ana Lisa Taylor, Neville, Matthew D. C., Niemi, Mari E. K., Gallone, Giuseppe, McRae, Jeremy, Wright, Caroline F., FitzPatrick, David R., Firth, Helen V., Hurles, Matthew E., Borras, Silvia, Clark, Caroline, Dean, John, Miedzybrodzka, Zosia, Ross, Alison, Tennant, Stephen, Dabir, Tabib, Donnelly, Deirdre, Humphreys, Mervyn, Magee, Alex, McConnell, Vivienne, McKee, Shane, McNerlan, Susan, Morrison, Patrick J., Rea, Gillian, Stewart, Fiona, Cole, Trevor, Cooper, Nicola, Cooper-Charles, Lisa, Cox, Helen, Islam, Lily, Jarvis, Joanna, Keelagher, Rebecca, Lim, Derek, McMullan, Dominic, Morton, Jenny, Naik, Swati, O’Driscoll, Mary, Ong, Kai-Ren, Osio, Deborah, Ragge, Nicola, Turton, Sarah, Vogt, Julie, Williams, Denise, Bodek, Simon, Donaldson, Alan, Hills, Alison, Low, Karen, Newbury-Ecob, Ruth, Norman, Andrew M., Roberts, Eileen, Scurr, Ingrid, Smithson, Sarah, Tooley, Madeleine, Abbs, Steve, Armstrong, Ruth, Dunn, Carolyn, Holden, Simon, Park, Soo-Mi, Paterson, Joan, Raymond, Lucy, Reid, Evan, Sandford, Richard, Simonic, Ingrid, Tischkowitz, Marc, Woods, Geoff, Bradley, Lisa, Comerford, Joanne, Green, Andrew, Lynch, Sally, McQuaid, Shirley, Mullaney, Brendan, Berg, Jonathan, Goudie, David, Mavrak, Eleni, McLean, Joanne, McWilliam, Catherine, Reavey, Eleanor, Azam, Tara, Cleary, Elaine, Jackson, Andrew, Lam, Wayne, Lampe, Anne, Moore, David, Porteous, Mary, Baple, Emma, Baptista, Júlia, Brewer, Carole, Castle, Bruce, Kivuva, Emma, Owens, Martina, Rankin, Julia, Shaw-Smith, Charles, Turner, Claire, Turnpenny, Peter, Tysoe, Carolyn, Bradley, Therese, Davidson, Rosemarie, Gardiner, Carol, Joss, Shelagh, Kinning, Esther, Longman, Cheryl, McGowan, Ruth, Murday, Victoria, Pilz, Daniela, Tobias, Edward, Whiteford, Margo, Williams, Nicola, Barnicoat, Angela, Clement, Emma, Faravelli, Francesca, Hurst, Jane, Jenkins, Lucy, Jones, Wendy, Kumar, V.K.Ajith, Lees, Melissa, Loughlin, Sam, Male, Alison, Morrogh, Deborah, Rosser, Elisabeth, Scott, Richard, Wilson, Louise, Beleza, Ana, Deshpande, Charu, Flinter, Frances, Holder, Muriel, Irving, Melita, Izatt, Louise, Josifova, Dragana, Mohammed, Shehla, Molenda, Aneta, Robert, Leema, Roworth, Wendy, Ruddy, Deborah, Ryten, Mina, Yau, Shu, Bennett, Christopher, Blyth, Moira, Campbell, Jennifer, Coates, Andrea, Dobbie, Angus, Hewitt, Sarah, Hobson, Emma, Jackson, Eilidh, Jewell, Rosalyn, Kraus, Alison, Prescott, Katrina, Sheridan, Eamonn, Thomson, Jenny, Bradshaw, Kirsty, Dixit, Abhijit, Eason, Jacqueline, Haines, Rebecca, Harrison, Rachel, Mutch, Stacey, Sarkar, Ajoy, Searle, Claire, Shannon, Nora, Sharif, Abid, Suri, Mohnish, Vasudevan, Pradeep, Canham, Natalie, Ellis, Ian, Greenhalgh, Lynn, Howard, Emma, Stinton, Victoria, Swale, Andrew, Weber, Astrid, Banka, Siddharth, Breen, Catherine, Briggs, Tracy, Burkitt-Wright, Emma, Chandler, Kate, Clayton-Smith, Jill, Donnai, Dian, Douzgou, Sofia, Gaunt, Lorraine, Jones, Elizabeth, Kerr, Bronwyn, Langley, Claire, Metcalfe, Kay, Smith, Audrey, Wright, Ronnie, Bourn, David, Burn, John, Fisher, Richard, Hellens, Steve, Henderson, Alex, Montgomery, Tara, Splitt, Miranda, Straub, Volker, Wright, Michael, Zwolinski, Simon, Allen, Zoe, Bernhard, Birgitta, Brady, Angela, Brooks, Claire, Busby, Louise, Clowes, Virginia, Ghali, Neeti, Holder, Susan, Ibitoye, Rita, Wakeling, Emma, Blair, Edward, Carmichael, Jenny, Cilliers, Deirdre, Clasper, Susan, Gibbons, Richard, Kini, Usha, Lester, Tracy, Nemeth, Andrea, Poulton, Joanna, Price, Sue, Shears, Debbie, Stewart, Helen, Wilkie, Andrew, Albaba, Shadi, Baker, Duncan, Balasubramanian, Meena, Johnson, Diana, Parker, Michael, Quarrell, Oliver, Stewart, Alison, Willoughby, Josh, Crosby, Charlene, Elmslie, Frances, Homfray, Tessa, Jin, Huilin, Lahiri, Nayana, Mansour, Sahar, Marks, Karen, McEntagart, Meriel, Saggar, Anand, Tatton-Brown, Kate, Butler, Rachel, Clarke, Angus, Corrin, Sian, Fry, Andrew, Kamath, Arveen, McCann, Emma, Mugalaasi, Hood, Pottinger, Caroline, Procter, Annie, Sampson, Julian, Sansbury, Francis, Varghese, Vinod, Baralle, Diana, Callaway, Alison, Cassidy, Emma J., Daniels, Stacey, Douglas, Andrew, Foulds, Nicola, Hunt, David, Kharbanda, Mira, Lachlan, Katherine, Mercer, Catherine, Side, Lucy, Temple, I. Karen, Wellesley, Diana, Martin, Hilary C. [0000-0002-4454-9084], Gardner, Eugene J. [0000-0001-9671-1533], Samocha, Kaitlin E. [0000-0002-1704-3352], Eberhardt, Ruth Y. [0000-0001-6152-1369], Tavares, Ana Lisa Taylor [0000-0001-7089-0502], Neville, Matthew D. C. [0000-0001-5816-7936], Niemi, Mari E. K. [0000-0003-0696-6175], Wright, Caroline F. [0000-0003-2958-5076], Hurles, Matthew E. [0000-0002-2333-7015], and Apollo - University of Cambridge Repository

Subjects
631/208/366, 49/23, article, 631/208/1516, 631/208/205
Abstract

Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.

Published
2021
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15. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder

Author

Shieh, Christine, Jones, Natasha, Vanle, Brigitte, Au, Margaret, Huang, Alden Y, Silva, Ana PG, Lee, Hane, Douine, Emilie D, Otero, Maria G, Choi, Andrew, Grand, Katheryn, Taff, Ingrid P, Delgado, Mauricio R, Hajianpour, MJ, Seeley, Andrea, Rohena, Luis, Vernon, Hilary, Gripp, Karen W, Vergano, Samantha A, Mahida, Sonal, Naidu, Sakkubai, Sousa, Ana Berta, Wain, Karen E, Challman, Thomas D, Beek, Geoffrey, Basel, Donald, Ranells, Judith, Smith, Rosemarie, Yusupov, Roman, Freckmann, Mary-Louise, Ohden, Lisa, Davis-Keppen, Laura, Chitayat, David, Dowling, James J, Finkel, Richard, Dauber, Andrew, Spillmann, Rebecca, Pena, Loren DM, Undiagnosed Diseases Network, Metcalfe, Kay, Splitt, Miranda, Lachlan, Katherine, McKee, Shane A, Hurst, Jane, Fitzpatrick, David R, Morton, Jenny EV, Cox, Helen, Venkateswaran, Sunita, Young, Juan I, Marsh, Eric D, Nelson, Stanley F, Martinez, Julian A, Graham, John M, Kini, Usha, Mackay, Joel P, and Pierson, Tyler Mark

Subjects
Intellectual and Developmental Disabilities (IDD), Clinical Sciences, apraxia of speech, NuRD complex, macrocephaly, GATA Transcription Factors, chromatin remodeling, GATAD2B, Pregnancy, Clinical Research, Intellectual Disability, Genetics, Humans, 2.1 Biological and endogenous factors, Aetiology, Child, Pediatric, Genetics & Heredity, Undiagnosed Diseases Network, Megalencephaly, Nucleosomes, Brain Disorders, Repressor Proteins, Phenotype, Neurodevelopmental Disorders, Congenital Structural Anomalies, Female
Abstract

PurposeDetermination of genotypic/phenotypic features of GATAD2B-associated neurodevelopmental disorder (GAND).MethodsFifty GAND subjects were evaluated to determine consistent genotypic/phenotypic features. Immunoprecipitation assays utilizing in vitro transcription-translation products were used to evaluate GATAD2B missense variants' ability to interact with binding partners within the nucleosome remodeling and deacetylase (NuRD) complex.ResultsSubjects had clinical findings that included macrocephaly, hypotonia, intellectual disability, neonatal feeding issues, polyhydramnios, apraxia of speech, epilepsy, and bicuspid aortic valves. Forty-one novelGATAD2B variants were identified with multiple variant types (nonsense, truncating frameshift, splice-site variants, deletions, and missense). Seven subjects were identified with missense variants that localized within two conserved region domains (CR1 or CR2) of the GATAD2B protein. Immunoprecipitation assays revealed several of these missense variants disrupted GATAD2B interactions with its NuRD complex binding partners.ConclusionsA consistent GAND phenotype was caused by a range of genetic variants in GATAD2B that include loss-of-function and missense subtypes. Missense variants were present in conserved region domains that disrupted assembly of NuRD complex proteins. GAND's clinical phenotype had substantial clinical overlap with other disorders associated with the NuRD complex that involve CHD3 and CHD4, with clinical features of hypotonia, intellectual disability, cardiac defects, childhood apraxia of speech, and macrocephaly.

Published
2020

16. Electronic health records in ambulances: the ERA multiple-methods study

Author

Porter, Alison, Badshah, Anisha, Black, Sarah, Fitzpatrick, David, Harris-Mayes, Robert, Islam, Saiful, Jones, Matthew, Kingston, Mark, LaFlamme-Williams, Yvette, Mason, Suzanne, McNee, Katherine, Morgan, Heather, Morrison, Zoe, Mountain, Pauline, and Potts, Henry

Abstract

Ambulance services have a vital role in the shift towards the delivery of health care out of hospitals, when this is better for patients, by offering alternatives to transfer to the emergency department (ED). For this to happen safely and effectively, ambulance clinicians must be able to decide which patients will benefit from being treated at scene or left at home, and ensure that patient information, including details of 999 assessment and care, is passed to community based care providers. The introduction of information technology (IT) in ambulance services, to electronically capture and store patient data, can support out of hospital care, and has been encouraged by national policy across the UK, but roll-out has proved complex, with major workforce implications. There is considerable variation across services in terms of implementation and the degree to which electronic records are integrated with other IT. We aim to examine how electronic records in ambulance services can support community-based care in a number of ways: by acting as a base to which other electronic resources (e.g. decision support software, referral tools or 'apps') are attached; by facilitating transfer of patient information to or from other providers; by allowing services to identify and manage repeat service users; and by making data readily available for research and evaluation. We aim to investigate and describe the opportunities and challenges of implementing electronic records and associated technology in ambulances to support a safe and effective shift to out of hospital care, including the implications for workforce in terms of training, role and clinical decision making skills. Lessons learned from the experience of implementing electronic records so far should inform future development of IT in ambulance services, and help service providers to understand how best to maximise the opportunities offered by electronic records to redesign care. Our study will include a baseline assessment of progress in all UK ambulance services in implementing electronic records and other technologies to support care delivery and decision-making. We will review and build on what is already known about implementation of technology in health care to inform four in-depth case studies of services at different stages of implementation. Across the case studies, we will assess current usage, and examine the role of context and time in shaping implementation and service change. We will take a whole systems approach, looking at the recursive relationship between technology and the ambulance workforce. Our working methods are participatory, built on a close relationship between the research team, ambulance services and other stakeholders, and using research paramedics as field researchers. In the final phase of our research, we will work with all UK ambulance services and other stakeholders to assess the potential for further development of electronic records, electronic decision support and referral tools to maximise their potential to support the shift of care from hospital to community based services. We will develop and build on existing theory about the implementation of IT in health care, developing the research base in the field of pre-hospital care and across care settings, and examining how implementation of electronic records takes place in relation to the implementation of other IT developments to support alternative care pathways.

Published
2020

17. Adaptive County Level COVID-19 Forecast Models: Analysis and Improvement

Author

Doe, Stewart W, Seekins, Tyler Russell, Fitzpatrick, David, Blanchard, Dawsin, and Sekeh, Salimeh Yasaei

Subjects
FOS: Computer and information sciences, Computer Science - Machine Learning, Physics - Physics and Society, Statistics - Machine Learning, FOS: Biological sciences, Populations and Evolution (q-bio.PE), FOS: Physical sciences, Machine Learning (stat.ML), Physics and Society (physics.soc-ph), Quantitative Biology - Populations and Evolution, Machine Learning (cs.LG)
Abstract

Accurately forecasting county level COVID-19 confirmed cases is crucial to optimizing medical resources. Forecasting emerging outbreaks pose a particular challenge because many existing forecasting techniques learn from historical seasons trends. Recurrent neural networks (RNNs) with LSTM-based cells are a logical choice of model due to their ability to learn temporal dynamics. In this paper, we adapt the state and county level influenza model, TDEFSI-LONLY, proposed in Wang et a. [l2020] to national and county level COVID-19 data. We show that this model poorly forecasts the current pandemic. We analyze the two week ahead forecasting capabilities of the TDEFSI-LONLY model with combinations of regularization techniques. Effective training of the TDEFSI-LONLY model requires data augmentation, to overcome this challenge we utilize an SEIR model and present an inter-county mixing extension to this model to simulate sufficient training data. Further, we propose an alternate forecast model, {\it County Level Epidemiological Inference Recurrent Network} (\alg{}) that trains an LSTM backbone on national confirmed cases to learn a low dimensional time pattern and utilizes a time distributed dense layer to learn individual county confirmed case changes each day for a two weeks forecast. We show that the best, worst, and median state forecasts made using CLEIR-Net model are respectively New York, South Carolina, and Montana., Comment: 18 pages, 9 Figures, 3 Tables

Published
2020
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18. Distance problems for planar hypercomplex numbers

Author

FitzPatrick, David

Subjects
Mathematics - Metric Geometry, FOS: Mathematics, Mathematics - Combinatorics, Metric Geometry (math.MG), Combinatorics (math.CO)
Abstract

We study the unit distance and distinct distances problems over the planar hypercomplex numbers: the dual numbers $\mathbb{D}$ and the double numbers $\mathbb{S}$. We show that the distinct distances problem in $\mathbb{S}^2$ behaves similarly to the original problem in $\mathbb{R}^2$. The other three problems behave rather differently from their real analogs. We study those three problems by introducing various notions of multiplicity of a point set. Our analysis is based on studying the geometry of the dual plane and of the double plane. We also rely on classical results from discrete geometry, such as the Szemer\'edi-Trotter theorem., Comment: 20 pages

Published
2020
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19. The genetic architecture of aniridia and Gillespie syndrome

Author

Hall, Hildegard Nikki, Williamson, Kathleen A., and FitzPatrick, David R.

Subjects
congenital, hereditary, and neonatal diseases and abnormalities, Cerebellar Ataxia, Iris, WAGR syndrome, Review, Biology, Gillespie syndrome, 03 medical and health sciences, Intellectual Disability, Genetics, medicine, Animals, Humans, Eye Proteins, Aniridia, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Cerebellar ataxia, 030305 genetics & heredity, Partial aniridia, Aplasia, medicine.disease, eye diseases, Human genetics, 3. Good health, Mutation, sense organs, PAX6, medicine.symptom
Abstract

Absence of part or all of the iris, aniridia, is a feature of several genetically distinct conditions. This review focuses on iris development and then the clinical features and molecular genetics of these iris malformations. Classical aniridia, a panocular eye malformation including foveal hypoplasia, is the archetypal phenotype associated with heterozygous PAX6 loss-of-function mutations. Since this was identified in 1991, many genetic mechanisms of PAX6 inactivation have been elucidated, the commonest alleles being intragenic mutations causing premature stop codons, followed by those causing C-terminal extensions. Rarely, aniridia cases are associated with FOXC1, PITX2 and/or their regulatory regions. Aniridia can also occur as a component of many severe global eye malformations. Gillespie syndrome—a triad of partial aniridia, non-progressive cerebellar ataxia and intellectual disability—is phenotypically and genotypically distinct from classical aniridia. The causative gene has recently been identified as ITPR1. The same characteristic Gillespie syndrome-like iris, with aplasia of the pupillary sphincter and a scalloped margin, is seen in ACTA2-related multisystemic smooth muscle dysfunction syndrome. WAGR syndrome (Wilms tumour, aniridia, genitourinary anomalies and mental retardation/intellectual disability), is caused by contiguous deletion of PAX6 and WT1 on chromosome 11p. Deletions encompassing BDNF have been causally implicated in the obesity and intellectual disability associated with the condition. Lastly, we outline a genetic investigation strategy for aniridia in light of recent developments, suggesting an approach based principally on chromosomal array and gene panel testing. This strategy aims to test all known aniridia loci—including the rarer, life-limiting causes—whilst remaining simple and practical.

Published
2018

20. Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity

Author

Hendricks, Audrey E., Bochukova, Elena G., Marenne, Gaëlle, Keogh, Julia M., Atanassova, Neli, Bounds, Rebecca, Wheeler, Eleanor, Mistry, Vanisha, Henning, Elana, Körner, Antje, Muddyman, Dawn, McCarthy, Shane, Hinney, Anke, Hebebrand, Johannes, Scott, Robert A., Langenberg, Claudia, Wareham, Nick J., Surendran, Praveen, Howson, Joanna M M, Butterworth, Adam S., Danesh, John, Nordestgaard, Børge G., Nielsen, Sune F., Afzal, Shoaib, Papadia, Sofia, Ashford, Sofie, Garg, Sumedha, Millhauser, Glenn L., Palomino, Rafael I., Kwasniewska, Alexandra, Tachmazidou, Ioanna, O'Rahilly, Stephen, Zeggini, Eleftheria, Barroso, Inês, Farooqi, I. Sadaf, Benzeval, Michaela, Burton, Jonathan, Buck, Nicholas, Jäckle, Annette, Kumari, Meena, Laurie, Heather, Lynn, Peter, Pudney, Stephen, Rabe, Birgitta, Wolke, Dieter, Overvad, Kim, Tjønneland, Anne, Clavel-Chapelon, Francoise, Kaaks, Rudolf, Boeing, Heiner, Trichopoulou, Antonia, Ferrari, Pietro, Palli, Domenico, Krogha, Vittorio, Panico, Salvatore, Tuminoa, Rosario, Matullo, Giuseppe, Boer, Jolanda Ma, Van Der Schouw, Yvonne, Weiderpass, Elisabete, Quiros, J. Ramon, Sánchez, María José, Navarro, Carmen, Moreno-Iribas, Conchi, Arriola, Larraitz, Melander, Olle, Wennberg, Patrik, Key, Timothy J., Riboli, Elio, Al-Turki, Saeed, Anderson, Carl A, Anney, Richard, Antony, Dinu, Soler Artigas, María, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C, Beales, Phil, Bentham, Jamie, Bhattacharyaa, Shoumo, Birney, Ewan, Blackwooda, Douglas, Bobrow, Martin, Bolton, Patrick F., Boustred, Chris, Breen, Gerome, Calissanoa, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampia, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Coccaa, Massimiliano, Collier, David A, Cosgrove, Catherine, Coxa, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N M, Day-Williams, Aaron G, Dominiczak, Anna, Down, Thomas, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evansa, David M., FitzPatrick, David R., Flicek, Paul, Floyd, James S., Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthias, Geschwind, Daniel H., Greenwood, Celia M.T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah J., Holmans, Peter A, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro G., Iotchkova, Valentina, Jackson, David K., Jamshidi, Yalda, Joyce, Chris, Karczewski, Konrad J., Kaye, Jane, Keane, Thomas, Kemp, John P., Kennedy, Karen, Kent, Alastair, Khawaja, Farrah, Van Kogelenberg, Margriet, Kolb-Kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lönnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, MacArthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Maslen, John, Mathieson, Iain, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Min, Josine L., Mitchison, Hannah M, Moayyeri, Alireza, Morris, Andrew D., Morris, James, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., Onoufriadis, Alexandros, Oualkacha, Karim, Owen, Michael J, Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnström, Karola, Richards, J Brent, Ridout, Cheryl K., Ring, Susan M., Ritchie, Graham R.S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So Youn, Skuse, David, Small, Kerrin S, Smee, Carol, Smith, Blair H., Davey Smith, George, Soranzo, Nicole, Southam, Lorraine, Spasic-Boskovic, Olivera, Spector, Timothy D, St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela L, Suvisaari, Jaana, Syrris, Petros, Taylor, Rohan, Tian, Jing, Timpson, Nicholas J., Tobin, Martin D, Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Walters, James T.R., Wang, Guangbiao, Wang, Jun, Wang, Nai-Yu, Ward, Kirsten, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, Zheng, Hou Feng, Hendricks, Audrey E., Bochukova, Elena G., Marenne, Gaã«lle, Keogh, Julia M., Atanassova, Neli, Bounds, Rebecca, Wheeler, Eleanor, Mistry, Vanisha, Henning, Elana, Kã¶rner, Antje, Muddyman, Dawn, Mccarthy, Shane, Hinney, Anke, Hebebrand, Johanne, Scott, Robert A., Langenberg, Claudia, Wareham, Nick J., Surendran, Praveen, Howson, Joanna M., Butterworth, Adam S., Danesh, John, Nordestgaard, Bã¸rge G, Nielsen, Sune F, Afzal, Shoaib, Papadia, Sofia, Ashford, Sofie, Garg, Sumedha, Millhauser, Glenn L., Palomino, Rafael I., Kwasniewska, Alexandra, Tachmazidou, Ioanna, O'Rahilly, Stephen, Zeggini, Eleftheria, Barroso, Inãª, Farooqi, I. Sadaf, Benzeval, Michaela, Burton, Jonathan, Buck, Nichola, Jã¤ckle, Annette, Kumari, Meena, Laurie, Heather, Lynn, Peter, Pudney, Stephen, Rabe, Birgitta, Wolke, Dieter, Overvad, Kim, Tjã¸nneland, Anne, Clavel chapelon, Francoise, Kaaks, Rudolf, Boeing, Heiner, Trichopoulou, Antonia, Ferrari, Pietro, Palli, Domenico, Krogha, Vittorio, Panico, Salvatore, Tuminoa, Rosario, Matullo, Giuseppe, Boer, Jolanda, Van Der Schouw, Yvonne, Weiderpass, Elisabete, Quiros, J. Ramon, Sã¡nchez, Marã­a josã©, Navarro, Carmen, Moreno iribas, Conchi, Arriola, Larraitz, Melander, Olle, Wennberg, Patrik, Key, Timothy J., Riboli, Elio, Turki, Saeed Al, Anderson, Carl A., Anney, Richard, Antony, Dinu, Soler Artigas, Marã­a, Ayub, Muhammad, Bala, Senduran, Barrett, Jeffrey C., Beales, Phil, Bentham, Jamie, Bhattacharyaa, Shoumo, Birney, Ewan, Blackwooda, Dougla, Bobrow, Martin, Bolton, Patrick F., Boustred, Chri, Breen, Gerome, Calissanoa, Mattia, Carss, Keren, Charlton, Ruth, Chatterjee, Krishna, Chen, Lu, Ciampia, Antonio, Cirak, Sebahattin, Clapham, Peter, Clement, Gail, Coates, Guy, Coccaa, Massimiliano, Collier, David A., Cosgrove, Catherine, Coxa, Tony, Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Daly, Allan, Danecek, Petr, Day, Ian N. M., Day williams, Aaron, Dominiczak, Anna, Down, Thoma, Du, Yuanping, Dunham, Ian, Durbin, Richard, Edkins, Sarah, Ekong, Rosemary, Ellis, Peter, Evansa, David M., Fitzpatrick, David R., Flicek, Paul, Floyd, Jame, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Gallagher, Louise, Gaunt, Tom R., Geihs, Matthia, Geschwind, Daniel, Greenwood, Celia M. T., Griffin, Heather, Grozeva, Detelina, Guo, Xiaosen, Guo, Xueqin, Gurling, Hugh, Hart, Deborah, Holmans, Peter, Howie, Bryan, Huang, Jie, Huang, Liren, Hubbard, Tim, Humphries, Steve E., Hurles, Matthew E., Hysi, Pirro, Iotchkova, Valentina, Jackson, David K., Jamshidi, Yalda, Joyce, Chri, Karczewski, Konrad J., Kaye, Jane, Keane, Thoma, Kemp, John P., Kennedy, Karen, Kent, Alastair, Khawaja, Farrah, Van Kogelenberg, Margriet, Kolb kokocinski, Anja, Lachance, Genevieve, Langford, Cordelia, Lawson, Daniel, Lee, Irene, Lek, Monkol, Li, Rui, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Lã¶nnqvist, Jouko, Lopes, Luis R., Lopes, Margarida, Macarthur, Daniel G., Mangino, Massimo, Marchini, Jonathan, Maslen, John, Mathieson, Iain, Mcguffin, Peter, Mcintosh, Andrew M., Mckechanie, Andrew G., Mcquillin, Andrew, Memari, Yasin, Metrustry, Sarah, Migone, Nicola, Min, Josine L., Mitchison, Hannah M., Moayyeri, Alireza, Morris, Andrew, Morris, Jame, Muntoni, Francesco, Northstone, Kate, O'Donovan, Michael C., Onoufriadis, Alexandro, Oualkacha, Karim, Owen, Michael J., Palotie, Aarno, Panoutsopoulou, Kalliope, Parker, Victoria, Parr, Jeremy R., Paternoster, Lavinia, Paunio, Tiina, Payne, Felicity, Payne, Stewart J., Perry, John R. B., Pietilainen, Olli, Plagnol, Vincent, Pollitt, Rebecca C., Porteous, David J., Povey, Sue, Quail, Michael A., Quaye, Lydia, Raymond, F. Lucy, Rehnstrã¶m, Karola, Richards, J. Brent, Ridout, Cheryl K., Ring, Susan, Ritchie, Graham R. S., Roberts, Nicola, Robinson, Rachel L., Savage, David B., Scambler, Peter, Schiffels, Stephan, Schmidts, Miriam, Schoenmakers, Nadia, Scott, Richard H., Semple, Robert K., Serra, Eva, Sharp, Sally I., Shaw, Adam, Shihab, Hashem A., Shin, So youn, Skuse, David, Small, Kerrin S., Smee, Carol, Smith, Blair H., Davey Smith, George, Soranzo, Nicole, Southam, Lorraine, Spasic boskovic, Olivera, Spector, Timothy D., St Clair, David, St Pourcain, Beate, Stalker, Jim, Stevens, Elizabeth, Sun, Jianping, Surdulescu, Gabriela, Suvisaari, Jaana, Syrris, Petro, Taylor, Rohan, Tian, Jing, Timpson, Nicholas J., Tobin, Martin D., Valdes, Ana M., Vandersteen, Anthony M., Vijayarangakannan, Parthiban, Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Walters, James T. R., Wang, Guangbiao, Wang, Jun, Wang, Yu, Ward, Kirsten, Whyte, Tamieka, Williams, Hywel J., Williamson, Kathleen A., Wilson, Crispian, Wilson, Scott G., Wong, Kim, Xu, Changjiang, Yang, Jian, Zhang, Feng, Zhang, Pingbo, and Zheng, Hou feng

Subjects
Multidisciplinary, Journal Article, General
Abstract

Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as describedw previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6. The p.S284X variant in ANGPTL6 drives the association signal (rs201622589, MAF∼0.1%, odds ratio = 10.13, p-value = 0.042) and results in complete loss of secretion in cells. Further analysis including additional case-control studies and population controls (N = 260,642) did not support association of this variant with obesity (odds ratio = 2.34, p-value = 2.59 × 10-3), highlighting the challenges of testing rare variant associations and the need for very large sample sizes. Further validation in cohorts with severe obesity and engineering the variants in model organisms will be needed to explore whether human variants in ANGPTL6 and other genes that lead to obesity when deleted in mice, do contribute to obesity. Such studies may yield druggable targets for weight loss therapies.

Published
2017

21. Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data

Author

Aitken, Stuart, Firth, Helen V, McRae, Jeremy, Halachev, Mihail, Kini, Usha, Parker, Michael J, Lees, Melissa M, Lachlan, Katherine, Sarkar, Ajoy, Joss, Shelagh, Splitt, Miranda, McKee, Shane, Németh, Andrea H, Scott, Richard H, Wright, Caroline F, Marsh, Joseph A, Hurles, Matthew E, FitzPatrick, David R, DDD Study, Németh, Andrea H [0000-0002-2941-7657], Marsh, Joseph A [0000-0003-4132-0628], and Apollo - University of Cambridge Repository

Subjects
Male, Heterozygote, phenotype, genotype, Developmental Disabilities, Spectrin, Bayes Theorem, Dwarfism, naive Bayes, Repressor Proteins, Gene Frequency, developmental disease, Mutation, Exome Sequencing, tSNE, Humans, Exome, Female, Genetic Predisposition to Disease, Child
Abstract

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands.

Published
2019

22. Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders

Author

Kaplanis, Joanna, Samocha, Kaitlin E., Wiel, Laurens, Zhang, Zhancheng, Arvai, Kevin J., Eberhardt, Ruth Y., Gallone, Giuseppe, Lelieveld, Stefan H., Martin, Hilary C., McRae, Jeremy F., Short, Patrick J., Torene, Rebecca I., de Boer, Elke, Danecek, Petr, Gardner, Eugene J., Huang, Ni, Lord, Jenny, Martincorena, Iñigo, Pfundt, Rolph, Reijnders, Margot R. F., Yeung, Alison, Yntema, Helger G., Vissers, Lisenka E. L. M., Juusola, Jane, Wright, Caroline F., Brunner, Han G., Firth, Helen V., FitzPatrick, David R., Barrett, Jeffrey C., Hurles, Matthew E., Gilissen, Christian, and Retterer, Kyle

Abstract

Summary De novo mutations (DNMs) in protein-coding genes are a well-established cause of developmental disorders (DD). However, known DD-associated genes only account for a minority of the observed excess of such DNMs. To identify novel DD-associated genes, we integrated healthcare and research exome sequences on 31,058 DD parent-offspring trios, and developed a simulation-based statistical test to identify gene-specific enrichments of DNMs. We identified 299 significantly DD-associated genes, including 49 not previously robustly associated with DDs. Despite detecting more DD-associated genes than in any previous study, much of the excess of DNMs of protein-coding genes remains unaccounted for. Modelling suggests that over 500 novel DD-associated genes await discovery, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of dominant DDs.

Published
2019
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24. NAA10 polyadenylation signal variants cause syndromic microphthalmia

Author

Johnston, Jennifer J., Williamson, Kathleen A., Chou, Christopher M., Sapp, Julie C., Ansari, Morad, Chapman, Heather M., Cooper, David N., Dabir, Tabib, Dudley, Jeffrey N., Holt, Richard J., Ragge, Nicola K., Schäffer, Alejandro A., Sen, Shurjo K., Slavotinek, Anne M., Fitzpatrick, David R., Glaser, Thomas M., Stewart, Fiona, Black, Graeme C.M., and Biesecker, Leslie G.

Subjects
Male, Naa10, Genotype, Medical and Health Sciences, Article, X Chromosome Inactivation, Clinical Research, Genetics, Humans, Microphthalmos, 2.1 Biological and endogenous factors, Genetics(clinical), Genetic Predisposition to Disease, N-Terminal Acetyltransferase E, Aetiology, 3' Untranslated Regions, Alleles, Genetic Association Studies, N-Terminal Acetyltransferase A, Genetics & Heredity, polyadenylation signal, Human Genome, Anophthalmos, Genetic Variation, DNA, X-Linked, Biological Sciences, Pedigree, Brain Disorders, Good Health and Well Being, Genes, Female, Lod Score, Poly A, Sequence Analysis
Abstract

BACKGROUND: A single variant in NAA10 (c.471+2T>A), the gene encoding N-acetyltransferase 10, has been associated with Lenz microphthalmia syndrome. In this study, we aimed to identify causative variants in families with syndromic X-linked microphthalmia.METHODS: Three families, including 15 affected individuals with syndromic X-linked microphthalmia, underwent analyses including linkage analysis, exome sequencing and targeted gene sequencing. The consequences of two identified variants in NAA10 were evaluated using quantitative PCR and RNAseq.RESULTS: Genetic linkage analysis in family 1 supported a candidate region on Xq27-q28, which included NAA10. Exome sequencing identified a hemizygous NAA10 polyadenylation signal (PAS) variant, chrX:153,195,397T>C, c.*43A>G, which segregated with the disease. Targeted sequencing of affected males from families 2 and 3 identified distinct NAA10 PAS variants, chrX:g.153,195,401T>C, c.*39A>G and chrX:g.153,195,400T>C, c.*40A>G. All three variants were absent from gnomAD. Quantitative PCR and RNAseq showed reduced NAA10 mRNA levels and abnormal 3' UTRs in affected individuals. Targeted sequencing of NAA10 in 376 additional affected individuals failed to identify variants in the PAS.CONCLUSION: These data show that PAS variants are the most common variant type in NAA10-associated syndromic microphthalmia, suggesting reduced RNA is the molecular mechanism by which these alterations cause microphthalmia/anophthalmia. We reviewed recognised variants in PAS associated with Mendelian disorders and identified only 23 others, indicating that NAA10 harbours more than 10% of all known PAS variants. We hypothesise that PAS in other genes harbour unrecognised pathogenic variants associated with Mendelian disorders. The systematic interrogation of PAS could improve genetic testing yields.

Published
2019

25. ITPase Deficiency Causes a Martsolf-Like Syndrome With a Lethal Infantile Dilated Cardiomyopathy

Author

Handley, Mark T., Reddy, Kaalak, Wills, Jimi, Rosser, Elisabeth, Kamath, Archith, Halachev, Mihail, Falkous, Gavin, Williams, Denise, Cox, Phillip, Meynert, Alison, Raymond, Eleanor S., Morrison, Harris, Brown, Stephen, Allan, Emma, Aligianis, Irene, Jackson, Andrew P., Ramsahoye, Bernard H., von Kriegsheim, Alex, Taylor, Robert W., Finch, Andrew J., and FitzPatrick, David R.

Subjects
Male, Embryology, DNA Mutational Analysis, Glycobiology, Artificial Gene Amplification and Extension, QH426-470, Biochemistry, Polymerase Chain Reaction, Mice, Medicine and Health Sciences, Pyrophosphatases, Energy-Producing Organelles, Mice, Knockout, Mammalian Genomics, Homozygote, Nucleosides, Heart, Mouse Embryonic Stem Cells, Genomics, Glycosylamines, Mitochondrial DNA, Mitochondria, Pedigree, Nucleic acids, Child, Preschool, Female, Anatomy, Cellular Structures and Organelles, Transcriptome Analysis, Research Article, Cardiomyopathy, Dilated, Forms of DNA, Bioenergetics, Research and Analysis Methods, DNA, Mitochondrial, Cataract, Intellectual Disability, Exome Sequencing, Genetics, Animals, Humans, Molecular Biology Techniques, Molecular Biology, Base Sequence, Hypogonadism, Embryos, Biology and Life Sciences, Computational Biology, DNA, Cell Biology, Genome Analysis, Inosine, Animal Genomics, Mutation, Cardiovascular Anatomy, RNA, Metabolism, Inborn Errors, Developmental Biology
Abstract

Typical Martsolf syndrome is characterized by congenital cataracts, postnatal microcephaly, developmental delay, hypotonia, short stature and biallelic hypomorphic mutations in either RAB3GAP1 or RAB3GAP2. Genetic analysis of 85 unrelated “mutation negative” probands with Martsolf or Martsolf-like syndromes identified two individuals with different homozygous null mutations in ITPA, the gene encoding inosine triphosphate pyrophosphatase (ITPase). Both probands were from multiplex families with a consistent, lethal and highly distinctive disorder; a Martsolf-like syndrome with infantile-onset dilated cardiomyopathy. Severe ITPase-deficiency has been previously reported with infantile epileptic encephalopathy (MIM 616647). ITPase acts to prevent incorporation of inosine bases (rI/dI) into RNA and DNA. In Itpa-null cells dI was undetectable in genomic DNA. dI could be identified at a low level in mtDNA without detectable mitochondrial genome instability, mtDNA depletion or biochemical dysfunction of the mitochondria. rI accumulation was detectable in proband-derived lymphoblastoid RNA. In Itpa-null mouse embryos rI was detectable in the brain and kidney with the highest level seen in the embryonic heart (rI at 1 in 385 bases). Transcriptome and proteome analysis in mutant cells revealed no major differences with controls. The rate of transcription and the total amount of cellular RNA also appeared normal. rI accumulation in RNA–and by implication rI production—correlates with the severity of organ dysfunction in ITPase deficiency but the basis of the cellulopathy remains cryptic. While we cannot exclude cumulative minor effects, there are no major anomalies in the production, processing, stability and/or translation of mRNA., Author summary Nucleotide triphosphate bases containing inosine, ITP and dITP, are continually produced within the cell as a consequence of various essential biosynthetic reactions. The enzyme inosine triphosphate pyrophosphatase (ITPase) scavenges ITP and dITP to prevent their incorporation into RNA and DNA. Here we describe two unrelated families with complete loss of ITPase function as a consequence of disruptive mutations affecting both alleles of ITPA, the gene that encodes this protein. Both of the families have a very distinctive and severe combination of clinical problems, most notably a failure of heart muscle that was lethal in infancy or early childhood. They also have features that are reminiscent of another rare genetic disorder affecting the brain and the eyes called Martsolf syndrome. We could not detect any evidence of dITP accumulation in double-stranded DNA from the nucleus in cells from the affected individuals. A low but detectable level of inosine was present in the circular double-stranded DNA present in mitochondria but this did not have any obvious detrimental effect. The inosine accumulation in RNA was detectable in the patient cells. We made both cellular and animal models that were completely deficient in ITPase. Using these reagents we could show that the highest level of inosine accumulation into RNA was seen in the embryonic mouse heart. In this tissue more than 1 in 400 bases in all RNA in the cell was inosine. In normal tissues inosine is almost undetectable using very sensitive assays. The inosine accumulation did not seem to be having a global effect on the balance of RNA molecules or proteins.

Published
2019

26. Diagnosis and management of Cornelia de Lange Syndrome: First international consensus statement (Adapted for easy access and wider distribution)

Author

A D Kline, J F Selicorni, A Bisgaard, A Deardorff, M A Gillett, S L Kerr, L M Levin, A V Mulder, P A Ramos, P F Axtell, N Cereda, A Costantino, A Cormier-Daire, V Fitzpatrick, M Groves, L Guthrie, W Huisman, S Kaiser, F J Koekkoek, G Levis, M Mariani, J P Menke, L A Metrena, A O'connor, J Oliver, A L Quaglio, E Richman, C Shi, Balkom, Van, I D C Hennekam, Shelley, Lauren, Royston, Rachel, Oliver, Chris, Kline, Tonie, Fitzpatrick, David, Harris, Bjorn, Knight, Steve, Peaford, Alan, Harris, Jules, Axtell, David, Blockley, Charlie, Peaford, Sara, and Blockley, Natalie

Published
2019
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27. Steroid receptor coactivator-1 modulates the function of Pomc neurons and energy homeostasis

Author

Yang, Yongjie, van der Klaauw, Agatha A., Zhu, Liangru, Cacciottolo, Tessa M., He, Yanlin, Stadler, Lukas K. J., Wang, Chunmei, Xu, Pingwen, Saito, Kenji, Hinton, Antentor, Yan, Xiaofeng, Keogh, Julia M., Henning, Elana, Banton, Matthew C., Hendricks, Audrey E., Bochukova, Elena G., Mistry, Vanisha, Lawler, Katherine L., Liao, Lan, Xu, Jianming, O'Rahilly, Stephen, Tong, Qingchun, Barroso, Ines, O'Malley, Bert W., Farooqi, I. Sadaf, Xu, Yong, Balasubramanian, Senduran, Clapham, Peter, Coates, Guy, Cox, Tony, Daly, Allan, Danecek, Petr, Du, Yuanping, Durbin, Richard, Edkins, Sarah, Ellis, Peter, Flicek, Paul, Guo, Xiaosen, Guo, Xueqin, Huang, Liren, Jackson, David K., Joyce, Chris, Keane, Thomas, Kolb-Kokocinski, Anja, Langford, Cordelia, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Maslen, John, McCarthy, Shane, Muddyman, Dawn, Quail, Michael A., Stalker, Jim, Sun, Jianping, Tian, Jing, Wang, Guangbiao, Wang, Jun, Wang, Yu, Wong, Kim, Zhang, Pingbo, Birney, Ewan, Boustred, Chris, Brion, Marie-Jo, Chen, Lu, Clement, Gail, Smith, George Davey, Day, Ian N. M., Day-Williams, Aaron, Down, Thomas, Dunham, Ian, Evans, David M., Fatemifar, Ghazaleh, Gaunt, Tom R., Geihs, Matthias, Greenwood, Celia M. T., Hart, Deborah, Howie, Bryan, Huang, Jie, Hubbard, Tim, Hysi, Pirro, Iotchkova, Valentina, Jamshidi, Yalda, Kemp, John P., Lachance, Genevieve, Lawson, Daniel, Lek, Monkol, Lopes, Margarida, MacArthur, Daniel G., Marchini, Jonathan, Massimo, Mangino, Mathieson, Iain, Memari, Yasin, Metrustry, Sarah, Min, Josine L., Moayyeri, Alireza, Northstone, Kate, Panoutsopoulou, Kalliope, Paternoster, Lavinia, Perry, John R. B., Quaye, Lydia, Richards, J. Brent, Ring, Susan, Ritchie, Graham R. S., Schiffels, Stephan, Shihab, Hashem A., Shin, So-Youn, Small, Kerrin S., Artigas, Maria Soler, Soranzo, Nicole, Southam, Lorraine, Spector, Timothy D., St Pourcain, Beate, Surdulescu, Gabriela, Tachmazidou, Ioanna, Timpson, Nicholas J., Tobin, Martin D., Valdes, Ana M., Visscher, Peter M., Wain, Louise V., Walter, Klaudia, Ward, Kirsten, Wilson, Scott G., Yang, Jian, Zeggini, Eleftheria, Zhang, Feng, Zheng, Hou-Feng, Anney, Richard, Ayub, Muhammad, Barrett, Jeffrey C., Blackwood, Douglas, Bolton, Patrick F., Breen, Gerome, Collier, David A., Craddock, Nick, Crooks, Lucy, Curran, Sarah, Curtis, David, Gallagher, Louise, Geschwind, Daniel, Gurling, Hugh, Holmans, Peter, Lee, Irene, Lonnqvist, Jouko, McGuffin, Peter, McIntosh, Andrew M., McKechanie, Andrew G., McQuillin, Andrew, Morris, James, O'Donovan, Michael C., Owen, Michael J., Palotie, Aarno, Parr, Jeremy R., Paunio, Tiina, Pietilainen, Olli, Rehnstrom, Karola, Sharp, Sally I., Skuse, David, St Clair, David, Suvisaari, Jaana, Walters, James T. R., Williams, Hywel J., Bochukova, Elena, Bounds, Rebecca, Dominiczak, Anna, Keogh, Julia, Marenne, Gaelle, Morris, Andrew, Porteous, David J., Smith, Blair H., Wheeler, Eleanor, Al Turki, Saeed, Anderson, Carl A., Antony, Dinu, Beales, Phil, Bentham, Jamie, Bhattacharya, Shoumo, Calissano, Mattia, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Fitzpatrick, David R., Floyd, James, Foley, A. Reghan, Franklin, Christopher S., Futema, Marta, Grozeva, Detelina, Humphries, Steve E., Hurles, Matthew E., Mitchison, Hannah M., Muntoni, Francesco, Onoufriadis, Alexandros, Parker, Victoria, Payne, Felicity, Plagnol, Vincent, Raymond, F. Lucy, Roberts, Nicola, Savage, David B., Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert K., Serra, Eva, Spasic-Boskovic, Olivera, Stevens, Elizabeth, van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Williamson, Kathleen A., Wilson, Crispian, Whyte, Tamieka, Ciampi, Antonio, Li, Rui, Oualkacha, Karim, Xu, ChangJiang, Bobrow, Martin, Griffin, Heather, Kaye, Jane, Kennedy, Karen, Kent, Alastair, Smee, Carol, Charlton, Ruth, Ekong, Rosemary, Khawaja, Farrah, Lopes, Luis R., Migone, Nicola, Payne, Stewart J., Pollitt, Rebecca C., Povey, Sue, Ridout, Cheryl K., Robinson, Rachel L., Scott, Richard H., Shaw, Adam, Syrris, Petros, Taylor, Rohan, Vandersteen, Anthony M., Amuzu, Antoinette, Casas, Juan Pablo, Chambers, John C., Cocca, Massimiliano, Dedoussis, George, Gambaro, Giovanni, Gasparini, Paolo, Isaacs, Aaron, Johnson, Jon, Kleber, Marcus E., Kooner, Jaspal S., Langenberg, Claudia, Luan, Jian'an, Malerba, Giovanni, Marz, Winfried, Matchan, Angela, Morris, Richard, Nordestgaard, Børge G., Benn, Marianne, Scott, Robert A., Toniolo, Daniela, Traglia, Michela, Tybjaerg-Hansen, Anne, van Duijn, Cornelia M., van Leeuwen, Elisabeth M., Varbo, Anette, Whincup, Peter, Zaza, Gianluigi, and Zhang, Weihua

Published
2019

28. Clinical and molecular consequences of disease-associated de novo mutations in SATB2

Author

Bengani, Hemant, Handley, Mark, Alvi, Mohsan, Ibitoye, Rita, Lees, Melissa, Lynch, Sally Ann, Lam, Wayne, Fannemel, Madeleine, Nordgren, Ann, Malmgren, H, Kvarnung, M, Mehta, Sarju, McKee, Shane, Whiteford, Margo, Stewart, Fiona, Connell, Fiona, Clayton-Smith, Jill, Mansour, Sahar, Mohammed, Shehla, Fryer, Alan, Morton, Jenny, UK10K Consortium, Grozeva, Detelina, Asam, Tara, Moore, David, Sifrim, Alejandro, McRae, Jeremy, Hurles, Matthew E, Firth, Helen V, Raymond, F Lucy, Kini, Usha, Nellåker, Christoffer, Ddd Study, FitzPatrick, David R, Alvi, Mohsan [0000-0003-4331-7078], Ibitoye, Rita [0000-0002-2887-2068], Lynch, Sally Ann [0000-0003-0287-4134], Nordgren, Ann [0000-0003-3338-8382], Malmgren, H [0000-0003-3285-4281], McKee, Shane [0000-0003-0446-3435], Whiteford, Margo [0000-0002-1772-0106], Connell, Fiona [0000-0002-0444-8203], Mohammed, Shehla [0000-0001-6629-4118], Sifrim, Alejandro [0000-0001-9308-5741], McRae, Jeremy [0000-0001-8247-4020], Kini, Usha [0000-0003-2652-3355], FitzPatrick, David R [0000-0001-7609-3504], and Apollo - University of Cambridge Repository

Subjects
Cohort Studies, Whole Genome Sequencing, Loss of Function Mutation, Intellectual Disability, Mutation, Missense, Humans, Haploinsufficiency, Matrix Attachment Region Binding Proteins, Genetic Association Studies, Cell Line, HeLa Cells, Protein Binding, Transcription Factors
Abstract

PURPOSE: To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability. METHODS: Twenty previously unreported individuals with 19 different SATB2 mutations (11 loss-of-function and 8 missense variants) were studied. Fibroblasts were used to measure mutant protein production. Subcellular localization and mobility of wild-type and mutant SATB2 were assessed using fluorescently tagged protein. RESULTS: Recurrent clinical features included neurodevelopmental impairment (19/19), absent/near absent speech (16/19), normal somatic growth (17/19), cleft palate (9/19), drooling (12/19), and dental anomalies (8/19). Six of eight missense variants clustered in the first CUT domain. Sibling recurrence due to gonadal mosaicism was seen in one family. A nonsense mutation in the last exon resulted in production of a truncated protein retaining all three DNA-binding domains. SATB2 nuclear mobility was mutation-dependent; p.Arg389Cys in CUT1 increased mobility and both p.Gly515Ser in CUT2 and p.Gln566Lys between CUT2 and HOX reduced mobility. The clinical features in individuals with missense variants were indistinguishable from those with loss of function. CONCLUSION: SATB2 haploinsufficiency is a common cause of syndromic intellectual disability. When mutant SATB2 protein is produced, the protein appears functionally inactive with a disrupted pattern of chromatin or matrix association.Genet Med advance online publication 02 February 2017.

Published
2017

29. The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

Author

Rodor, Julie, FitzPatrick, David R., Eyras, Eduardo, and Cáceres, Javier F.

Subjects
Male, RBM10, iCLIP, Embryonic Development, RNA-binding proteins, Stem cells, Alternative splicing, mandibular cell line, stem cells, TARP syndrome, Gene Knockout Techniques, Mice, RNA, Small Nuclear, Animals, RNA, Messenger, Nucleotide Motifs, Embryonic Stem Cells, ICLIP, Binding Sites, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Alternative Splicing, Phenotype, Gene Expression Regulation, Spliceosomes, Mandibular cell line, Female, Research Paper, Genome-Wide Association Study, Protein Binding
Abstract

Mutations in the RNA-binding protein, RBM10, result in a human syndromic form of cleft palate, termed TARP syndrome. A role for RBM10 in alternative splicing regulation has been previously demonstrated in human cell lines. To uncover the cellular functions of RBM10 in a cell line that is relevant to the phenotype observed in TARP syndrome, we used iCLIP to identify its endogenous RNA targets in a mouse embryonic mandibular cell line. We observed that RBM10 binds to pre-mRNAs with significant enrichment in intronic regions, in agreement with a role for this protein in pre-mRNA splicing. In addition to protein-coding transcripts, RBM10 also binds to a variety of cellular RNAs, including non-coding RNAs, such as spliceosomal small nuclear RNAs, U2 and U12. RNA-seq was used to investigate changes in gene expression and alternative splicing in RBM10 KO mouse mandibular cells and also in mouse ES cells. We uncovered a role for RBM10 in the regulation of alternative splicing of common transcripts in both cell lines but also identified cell-type specific events. Importantly, those pre-mRNAs that display changes in alternative splicing also contain RBM10 iCLIP tags, suggesting a direct role of RBM10 in these events. Finally, we show that depletion of RBM10 in mouse ES cells leads to proliferation defects and to gross alterations in their differentiation potential. These results demonstrate a role for RBM10 in the regulation of alternative splicing in two cell models of mouse early development and suggests that mutations in RBM10 could lead to splicing changes that affect normal palate development and cause human disease. D.R.F. and J.F.C. were supported by Core funding from the Medical Research Council. J.F.C had also funding from the Wellcome Trust (Grant 095518/Z/11/Z). E.E. was supported by MINECO (Ministerio de Economía y Competitividad) and FEDER (Fondo Europeo de Desarrollo Regional) through grant BIO2014-52566-R, by Sandra Ibarra Foundation for Cancer and by AGAUR (Agència de Gestió d'Ajuts Universitaris i de Recerca) through grant 2014-SGR1121.

Published
2016

30. Novel de novo EEF1A2 missense mutations causing epilepsy and intellectual disability

Author

Lam, Wayne W.K., Millichap, John J., Soares, Dinesh C., Chin, Richard, McLellan, Ailsa, FitzPatrick, David R., Elmslie, Frances, Lees, Melissa M., Schaefer, G. Bradley, and Abbott, Catherine M.

Subjects
intellectual disability, Autism, EEF1A2, epilepsy, Original Article, Original Articles, translation elongation
Abstract

Background Exome sequencing has led to the discovery of mutations in novel causative genes for epilepsy. One such gene is EEF1A2, encoding a neuromuscular specific translation elongation factor, which has been found to be mutated de novo in five cases of severe epilepsy. We now report on a further seven cases, each with a different mutation, of which five are newly described. Methods New cases were identified and sequenced through the Deciphering Developmental Disabilities project, via direct contact with neurologists or geneticists, or recruited via our website. Results All the mutations cause epilepsy and intellectual disability, but with a much wider range of severity than previously identified. All new cases share specific subtle facial dysmorphic features. Each mutation occurs at an evolutionarily highly conserved amino acid position indicating strong structural or functional selective pressure. Conclusions EEF1A2 should be considered as a causative gene not only in cases of epileptic encephalopathy but also in children with less severe epilepsy and intellectual disability. The emergence of a possible discernible phenotype, a broad nasal bridge, tented upper lip, everted lower lip and downturned corners of the mouth may help in identifying patients with mutations in EEF1A2.

Published
2016

31. CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language

Author

Snijders Blok, Lot, Rousseau, Justine, Twist, Joanna, Ehresmann, Sophie, Takaku, Motoki, Venselaar, Hanka, Rodan, Lance H., Nowak, Catherine B., Douglas, Jessica, Swoboda, Kathryn J., Steeves, Marcie A., Sahai, Inderneel, Stumpel, Connie T. R. M., Stegmann, Alexander P. A., Wheeler, Patricia, Willing, Marcia, Fiala, Elise, Kochhar, Aaina, Gibson, William T., Cohen, Ana S. A., Agbahovbe, Ruky, Innes, A. Micheil, Au, P. Y. Billie, Rankin, Julia, Anderson, Ilse J., Skinner, Steven A., Louie, Raymond J., Warren, Hannah E., Afenjar, Alexandra, Keren, Boris, Nava, Caroline, Buratti, Julien, Isapof, Arnaud, Rodriguez, Diana, Lewandowski, Raymond, Propst, Jennifer, van Essen, Ton, Choi, Murim, Lee, Sangmoon, Chae, Jong H., Price, Susan, Schnur, Rhonda E., Douglas, Ganka, Wentzensen, Ingrid M., Zweier, Christiane, Reis, André, Bialer, Martin G., Moore, Christine, Koopmans, Marije, Brilstra, Eva H., Monroe, Glen R., van Gassen, Koen L. I., van Binsbergen, Ellen, Newbury-Ecob, Ruth, Bownass, Lucy, Bader, Ingrid, Mayr, Johannes A., Wortmann, Saskia B., Jakielski, Kathy J., Strand, Edythe A., Kloth, Katja, Bierhals, Tatjana, McRae, Jeremy F., Clayton, Stephen, Fitzgerald, Tomas W., Kaplanis, Joanna, Prigmore, Elena, Rajan, Diana, Sifrim, Alejandro, Aitken, Stuart, Akawi, Nadia, Alvi, Mohsan, Ambridge, Kirsty, Barrett, Daniel M., Bayzetinova, Tanya, Jones, Philip, Jones, Wendy D., King, Daniel, Krishnappa, Netravathi, Mason, Laura E., Singh, Tarjinder, Tivey, Adrian R., Ahmed, Munaza, Anjum, Uruj, Archer, Hayley, Armstrong, Ruth, Awada, Jana, Balasubramanian, Meena, Banka, Siddharth, Baralle, Diana, Barnicoat, Angela, Batstone, Paul, Baty, David, Bennett, Chris, Berg, Jonathan, Bernhard, Birgitta, Bevan, A. Paul, Bitner-Glindzicz, Maria, Blair, Edward, Blyth, Moira, Bohanna, David, Bourdon, Louise, Bourn, David, Bradley, Lisa, Brady, Angela, Brent, Simon, Brewer, Carole, Brunstrom, Kate, Bunyan, David J., Burn, John, Canham, Natalie, Castle, Bruce, Chandler, Kate, Chatzimichali, Elena, Cilliers, Deirdre, Clarke, Angus, Clasper, Susan, Clayton-Smith, Jill, Clowes, Virginia, Coates, Andrea, Cole, Trevor, Colgiu, Irina, Collins, Amanda, Collinson, Morag N., Connell, Fiona, Cooper, Nicola, Cox, Helen, Cresswell, Lara, Cross, Gareth, Crow, Yanick, D’Alessandro, Mariella, Dabir, Tabib, Davidson, Rosemarie, Davies, Sally, de Vries, Dylan, Dean, John, Deshpande, Charu, Devlin, Gemma, Dixit, Abhijit, Dobbie, Angus, Donaldson, Alan, Donnai, Dian, Donnelly, Deirdre, Donnelly, Carina, Douglas, Angela, Douzgou, Sofia, Duncan, Alexis, Eason, Jacqueline, Ellard, Sian, Ellis, Ian, Elmslie, Frances, Evans, Karenza, Everest, Sarah, Fendick, Tina, Fisher, Richard, Flinter, Frances, Foulds, Nicola, Fry, Andrew, Fryer, Alan, Gardiner, Carol, Gaunt, Lorraine, Ghali, Neeti, Gibbons, Richard, Gill, Harinder, Goodship, Judith, Goudie, David, Gray, Emma, Green, Andrew, Greene, Philip, Greenhalgh, Lynn, Gribble, Susan, Harrison, Rachel, Harrison, Lucy, Harrison, Victoria, Hawkins, Rose, He, Liu, Hellens, Stephen, Henderson, Alex, Hewitt, Sarah, Hildyard, Lucy, Hobson, Emma, Holden, Simon, Holder, Muriel, Holder, Susan, Hollingsworth, Georgina, Homfray, Tessa, Humphreys, Mervyn, Hurst, Jane, Hutton, Ben, Ingram, Stuart, Irving, Melita, Islam, Lily, Jackson, Andrew, Jarvis, Joanna, Jenkins, Lucy, Johnson, Diana, Jones, Elizabeth, Josifova, Dragana, Joss, Shelagh, Kaemba, Beckie, Kazembe, Sandra, Kelsell, Rosemary, Kerr, Bronwyn, Kingston, Helen, Kini, Usha, Kinning, Esther, Kirby, Gail, Kirk, Claire, Kivuva, Emma, Kraus, Alison, Kumar, Dhavendra, Kumar, V. K. Ajith, Lachlan, Katherine, Lam, Wayne, Lampe, Anne, Langman, Caroline, Lees, Melissa, Lim, Derek, Longman, Cheryl, Lowther, Gordon, Lynch, Sally A., Magee, Alex, Maher, Eddy, Male, Alison, Mansour, Sahar, Marks, Karen, Martin, Katherine, Maye, Una, McCann, Emma, McConnell, Vivienne, McEntagart, Meriel, McGowan, Ruth, McKay, Kirsten, McKee, Shane, McMullan, Dominic J., McNerlan, Susan, McWilliam, Catherine, Mehta, Sarju, Metcalfe, Kay, Middleton, Anna, Miedzybrodzka, Zosia, Miles, Emma, Mohammed, Shehla, Montgomery, Tara, Moore, David, Morgan, Sian, Morton, Jenny, Mugalaasi, Hood, Murday, Victoria, Murphy, Helen, Naik, Swati, Nemeth, Andrea, Nevitt, Louise, Norman, Andrew, O’Shea, Rosie, Ogilvie, Caroline, Ong, Kai-Ren, Park, Soo-Mi, Parker, Michael J., Patel, Chirag, Paterson, Joan, Payne, Stewart, Perrett, Daniel, Phipps, Julie, Pilz, Daniela T., Pollard, Martin, Pottinger, Caroline, Poulton, Joanna, Pratt, Norman, Prescott, Katrina, Pridham, Abigail, Procter, Annie, Purnell, Hellen, Quarrell, Oliver, Ragge, Nicola, Rahbari, Raheleh, Randall, Josh, Raymond, Lucy, Rice, Debbie, Robert, Leema, Roberts, Eileen, Roberts, Jonathan, Roberts, Paul, Roberts, Gillian, Ross, Alison, Rosser, Elisabeth, Saggar, Anand, Samant, Shalaka, Sampson, Julian, Sandford, Richard, Sarkar, Ajoy, Schweiger, Susann, Scott, Richard, Scurr, Ingrid, Selby, Ann, Seller, Anneke, Sequeira, Cheryl, Shannon, Nora, Sharif, Saba, Shaw-Smith, Charles, Shearing, Emma, Shears, Debbie, Sheridan, Eamonn, Simonic, Ingrid, Singzon, Roldan, Skitt, Zara, Smith, Audrey, Smith, Kath, Smithson, Sarah, Sneddon, Linda, Splitt, Miranda, Squires, Miranda, Stewart, Fiona, Stewart, Helen, Straub, Volker, Suri, Mohnish, Sutton, Vivienne, Swaminathan, Ganesh Jawahar, Sweeney, Elizabeth, Tatton-Brown, Kate, Taylor, Cat, Taylor, Rohan, Tein, Mark, Temple, I. Karen, Thomson, Jenny, Tischkowitz, Marc, Tomkins, Susan, Torokwa, Audrey, Treacy, Becky, Turner, Claire, Turnpenny, Peter, Tysoe, Carolyn, Vandersteen, Anthony, Varghese, Vinod, Vasudevan, Pradeep, Vijayarangakannan, Parthiban, Vogt, Julie, Wakeling, Emma, Wallwark, Sarah, Waters, Jonathon, Weber, Astrid, Wellesley, Diana, Whiteford, Margo, Widaa, Sara, Wilcox, Sarah, Wilkinson, Emily, Williams, Denise, Williams, Nicola, Wilson, Louise, Woods, Geoff, Wragg, Christopher, Wright, Michael, Yates, Laura, Yau, Michael, Nellåker, Chris, Parker, Michael, Firth, Helen V., Wright, Caroline F., FitzPatrick, David R., Barrett, Jeffrey C., Hurles, Matthew E., Roberts, John D., Petrovich, Robert M., Machida, Shinichi, Kurumizaka, Hitoshi, Lelieveld, Stefan, Pfundt, Rolph, Jansen, Sandra, Deriziotis, Pelagia, Faivre, Laurence, Thevenon, Julien, Assoum, Mirna, Shriberg, Lawrence, Kleefstra, Tjitske, Brunner, Han G., Wade, Paul A., Fisher, Simon E., Campeau, Philippe M., Radboud University Medical Center [Nijmegen], Max Planck Institute for Psycholinguistics, Max-Planck-Gesellschaft, Donders Institute for Brain, Cognition and Behaviour, Radboud university [Nijmegen], CHU Sainte Justine [Montréal], Boston Children's Hospital, Massachusetts General Hospital [Boston], School for Oncology and Developmental Biology [Maastricht] (GROW), Maastricht University [Maastricht]-Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], Maastricht University Medical Centre (MUMC), University of British Columbia (UBC), University of Calgary, CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Service de Neuropédiatrie [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Filière Neuromusculaire (FILNEMUS), Virginia Commonwealth University (VCU), University Medical Center Groningen [Groningen] (UMCG), Seoul National University [Seoul] (SNU), Oxford University Hospitals NHS Trust, University of Oxford [Oxford], Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), University Medical Center [Utrecht], University Hospitals Bristol, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Helmholtz-Zentrum München (HZM), Mayo Clinic [Rochester], Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Waseda University, Université de Bourgogne (UB), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Department of Human Genetics [Nijmegen], The DDD study, RS: GROW - R4 - Reproductive and Perinatal Medicine, MUMC+: DA KG Polikliniek (9), Klinische Genetica, MUMC+: DA KG Lab Centraal Lab (9), and MUMC+: DA Klinische Genetica (5)

Subjects
0301 basic medicine, DISORDER, INTELLECTUAL DISABILITY, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, General Physics and Astronomy, EXOME, Language in Interaction, fluids and secretions, 0302 clinical medicine, Intellectual disability, Missense mutation, lcsh:Science, Exome, reproductive and urinary physiology, Genetics, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Phenotype, FAMILY, DEACETYLASE COMPLEX, NURD, medicine.symptom, Neuroinformatics, Science, Biology, DIAGNOSIS, Article, General Biochemistry, Genetics and Molecular Biology, Chromatin remodeling, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, mental disorders, medicine, CHROMATIN REMODELING COMPLEX, Gene, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Macrocephaly, Helicase, General Chemistry, medicine.disease, GENE, 030104 developmental biology, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, DE-NOVO MUTATIONS, biology.protein, lcsh:Q, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], 030217 neurology & neurosurgery
Abstract

Chromatin remodeling is of crucial importance during brain development. Pathogenic alterations of several chromatin remodeling ATPases have been implicated in neurodevelopmental disorders. We describe an index case with a de novo missense mutation in CHD3, identified during whole genome sequencing of a cohort of children with rare speech disorders. To gain a comprehensive view of features associated with disruption of this gene, we use a genotype-driven approach, collecting and characterizing 35 individuals with de novo CHD3 mutations and overlapping phenotypes. Most mutations cluster within the ATPase/helicase domain of the encoded protein. Modeling their impact on the three-dimensional structure demonstrates disturbance of critical binding and interaction motifs. Experimental assays with six of the identified mutations show that a subset directly affects ATPase activity, and all but one yield alterations in chromatin remodeling. We implicate de novo CHD3 mutations in a syndrome characterized by intellectual disability, macrocephaly, and impaired speech and language., Chromodomain Helicase DNA-binding (CHD) proteins have been implicated in neurodevelopmental processes. Here, the authors identify missense variants in CHD3 that disturb its chromatin remodeling activities and cause a neurodevelopmental disorder with macrocephaly and speech and language impairment.

Published
2018

33. Dysfunction of NaV1.4, a skeletal muscle voltage-gated sodium channel, in sudden infant death syndrome:a case-control study

Author

Männikkö, Roope, Wong, Leonie, Tester, David J, Thor, Michael G, Sud, Richa, Kullmann, Dimitri M, Sweeney, Mary G, Leu, Costin, Sisodiya, Sanjay M, FitzPatrick, David R, Evans, Margaret J, Jeffrey, Iona J M, Tfelt-Hansen, Jacob, Cohen, Marta C, Fleming, Peter J, Jaye, Amie, Simpson, Michael A, Ackerman, Michael J, Hanna, Michael G, Behr, Elijah R, and Matthews, Emma

Subjects
Adult, Male, NONDYSTROPHIC MYOTONIA, Article, PERIODIC PARALYSIS, Gene Frequency, Risk Factors, Exome Sequencing, Humans, LARYNGEAL MUSCLE, NAV1.4 Voltage-Gated Sodium Channel, Muscle, Skeletal, TRIPLE-RISK MODEL, MUTATIONS, Genetic Variation, Infant, MYASTHENIC SYNDROME, CONGENITAL MYOPATHY, Case-Control Studies, FIBER TYPES, Mutation, FAST INACTIVATION, Channelopathies, Female, SCN4A, Sudden Infant Death
Abstract

Background: Sudden infant death syndrome (SIDS) is the leading cause of post-neonatal infant death in high-income countries. Central respiratory system dysfunction seems to contribute to these deaths. Excitation that drives contraction of skeletal respiratory muscles is controlled by the sodium channel NaV1.4, which is encoded by the gene SCN4A. Variants in NaV1.4 that directly alter skeletal muscle excitability can cause myotonia, periodic paralysis, congenital myopathy, and myasthenic syndrome. SCN4A variants have also been found in infants with life-threatening apnoea and laryngospasm. We therefore hypothesised that rare, functionally disruptive SCN4A variants might be over-represented in infants who died from SIDS. Methods: We did a case-control study, including two consecutive cohorts that included 278 SIDS cases of European ancestry and 729 ethnically matched controls without a history of cardiovascular, respiratory, or neurological disease. We compared the frequency of rare variants in SCN4A between groups (minor allele frequency

Published
2018

34. BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange–like syndrome

Author

Olley, Gabrielle, Ansari, Morad, Bengani, Hemant, Grimes, Graeme R., Rhodes, James, von Kriegsheim, Alex, Blatnik, Ana, Stewart, Fiona J., Wakeling, Emma, Carroll, Nicola, Ross, Alison, Park, Soo-Mi, Deciphering Developmental Disorders Study, Bickmore, Wendy A., Pradeepa, Madapura M., and FitzPatrick, David R.

Abstract

We found that the clinical phenotype associated with BRD4 haploinsufficiency overlapped with that of Cornelia de Lange syndrome (CdLS), which is most often caused by mutation of NIPBL. More typical CdLS was observed with a de novo BRD4 missense variant, which retained the ability to coimmunoprecipitate with NIPBL, but bound poorly to acetylated histones. BRD4 and NIPBL displayed correlated binding at super-enhancers and appeared to co-regulate developmental gene expression.

Published
2018

35. Additional file 3: of The feasibility, acceptability and preliminary testing of a novel, low-tech intervention to improve pre-hospital data recording for pre-alert and handover to the Emergency Department

Author

Fitzpatrick, David, Maxwell, Douglas, and Craigie, Alan

Subjects
genetic structures, fungi, humanities
Abstract

Emergency Department Handover Questionnaire. These are the questions used in the online questionnaire to measure ED staff perceptions of ambulance clinician handover. (PDF 20 kb)

Published
2018
Full Text
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36. Additional file 2: of The feasibility, acceptability and preliminary testing of a novel, low-tech intervention to improve pre-hospital data recording for pre-alert and handover to the Emergency Department

Author

Fitzpatrick, David, Maxwell, Douglas, and Craigie, Alan

Subjects
humanities
Abstract

Ambulance Form (AF). This is the paper based Ambulance Form used by Emergency Department staff to record the ambulance clinicians pre-alert and handover information. (PDF 71 kb)

Published
2018
Full Text
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38. Additional file 4: of The feasibility, acceptability and preliminary testing of a novel, low-tech intervention to improve pre-hospital data recording for pre-alert and handover to the Emergency Department

Author

Fitzpatrick, David, Maxwell, Douglas, and Craigie, Alan

Subjects
genetic structures, fungi
Abstract

Ambulance Questionnaire. This the paper based questionnaire used to measure ambulance clinicians perceptions of the feasibility and acceptability of the prompt card. (PDF 179 kb)

Published
2018
Full Text
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39. Additional file 29: of Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

Author

Rahman, Farzana, Mehedi Hassan, Abdulsamie Hanano, Fitzpatrick, David, McCarthy, Charley, and Murphy, Denis

Abstract

Figure S6. Phylogenetic network reconstructed using the representative 199 plant and fungal CLO/PXG proteins. The neighbour-joining network method was used to infer splits within the alignment. Species names are coloured relative to their taxonomy. Strongly supported monophyletic clades are evident within the network. However relationships between these clades is conflicting as illustrated by many alternative splits at the base of the network. (PDF 556 kb)

Published
2018
Full Text
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43. Additional file 28: of Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi

Author

Rahman, Farzana, Mehedi Hassan, Abdulsamie Hanano, Fitzpatrick, David, McCarthy, Charley, and Murphy, Denis

Abstract

Figure S5. Maximum Likelihood phylogeny for all 462 analysed plant and fungal CLO/PXG proteins. The optimum model of protein substitution was found to be LGâ +â G. Bootstrap resampling (100 iterations) was undertaken and are shown on internal nodes. There are several strongly supported clades but support values inferring sister group relationships between these are extremely low. Species names are coloured relative to their taxonomy. The presence of MEME predicted motifs are shown for individual proteins. (PDF 5353 kb)

Published
2018
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44. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

Author

Sipos, György, Prasanna, Arun N, Walter, Mathias C, O'Connor, Eoin, Bálint, Balázs, Krizsán, Krisztina, Kiss, Brigitta, Hess, Jaqueline, Varga, Torda, Slot, Jason, Riley, Robert, Bóka, Bettina, Rigling, Daniel, Barry, Kerrie, Lee, Juna, Mihaltcheva, Sirma, LaButti, Kurt, Lipzen, Anna, Waldron, Rose, Moloney, Nicola M, Sperisen, Christoph, Kredics, László, Vágvölgyi, Csaba, Patrignani, Andrea, Fitzpatrick, David, Nagy, István, Doyle, Sean, Anderson, James B, Grigoriev, Igor V, Güldener, Ulrich, et al, University of Zurich, and Sipos, György

Subjects
1105 Ecology, Evolution, Behavior and Systematics, 570 Life sciences, biology, 610 Medicine & health, 10071 Functional Genomics Center Zurich, 2303 Ecology
Published
2017

45. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome

Author

Ansari, Morad, Rainger, Jacqueline, Hanson, Isabel M, Williamson, Kathleen A, Sharkey, Freddie, Harewood, Louise, Sandilands, Angela, Clayton-Smith, Jill, Dollfus, Helene, Bitoun, Pierre, Meire, Francoise, Fantes, Judy, Franco, Brunella, Lorenz, Birgit, Taylor, David S, Stewart, Fiona, Willoughby, Colin E, McEntagart, Meriel, Khaw, Peng Tee, Clericuzio, Carol, Van Maldergem, Lionel, Williams, Denise, Newbury-Ecob, Ruth, Traboulsi, Elias I, Silva, Eduardo D, Madlom, Mukhlis M, Goudie, David R, Fleck, Brian W, Wieczorek, Dagmar, Kohlhase, Juergen, McTrusty, Alice D, Gardiner, Carol, Yale, Christopher, Moore, Anthony T, Russell-Eggitt, Isabelle, Islam, Lily, Lees, Melissa, Beales, Philip L, Tuft, Stephen J, Solano, Juan B, Splitt, Miranda, Hertz, Jens Michael, Prescott, Trine E, Shears, Deborah J, Nischal, Ken K, Doco-Fenzy, Martine, Prieur, Fabienne, Temple, I Karen, Lachlan, Katherine L, Damante, Giuseppe, Morrison, Danny A, van Heyningen, Veronica, FitzPatrick, David R, Ansari, Morad, Rainger, Jacqueline, Hanson, Isabel M., Williamson, Kathleen A., Sharkey, Freddie, Harewood, Louise, Sandilands, Angela, Clayton Smith, Jill, Dollfus, Helene, Bitoun, Pierre, Meire, Francoise, Fantes, Judy, Franco, Brunella, Lorenz, Birgit, Taylor, David S., Stewart, Fiona, Willoughby, Colin E., Mcentagart, Meriel, Khaw, Peng Tee, Clericuzio, Carol, Van Maldergem, Lionel, Williams, Denise, Newbury Ecob, Ruth, Traboulsi, Elias I., Silva, Eduardo D., Madlom, Mukhlis M., Goudie, David R., Fleck, Brian W., Wieczorek, Dagmar, Kohlhase, Juergen, Mctrusty, Alice D., Gardiner, Carol, Yale, Christopher, Moore, Anthony T., Russell Eggitt, Isabelle, Islam, Lily, Lees, Melissa, Beales, Philip L., Tuft, Stephen J., Solano, Juan B., Splitt, Miranda, Hertz, Jens Michael, Prescott, Trine E., Shears, Deborah J., Nischal, Ken K., Doco Fenzy, Martine, Prieur, Fabienne, Temple, I. Karen, Lachlan, Katherine L., Damante, Giuseppe, Morrison, Danny A., Van Heyningen, Veronica, and Fitzpatrick, David R.

Subjects
Male, Genetics and Molecular Biology (all), Eye Diseases, PAX6 Transcription Factor, Mutagenesis and Gene Deletion Techniques, Gene Identification and Analysis, Iris, lcsh:Medicine, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Biochemistry, axenfeld-rieger syndrome gtpase-activating protein linear skin defects cerebellar-ataxia mental-retardation pax6 gene missense mutations impaired accommodation pitx2 mutations phenotype Science & Technology - Other Topics, Medicine and Health Sciences, Pair 11, lcsh:Science, Aniridia, Comparative Genomic Hybridization, Medicine (all), GTPase-Activating Proteins, Forkhead Transcription Factors, Genomics, Deletion Mutation, Female, Anatomy, Research Article, Human, congenital, hereditary, and neonatal diseases and abnormalities, Cerebellar Ataxia, Ocular Anatomy, Research and Analysis Methods, Human Genomics, Chromosomes, Histone Deacetylases, Ocular System, Intellectual Disability, Genetics, Humans, Genetic Testing, Molecular Biology Techniques, Molecular Biology, Mutation Detection, Homeodomain Proteins, Chromosomes, Human, X, Biochemistry, Genetics and Molecular Biology (all), Chromosomes, Human, Pair 11, lcsh:R, Biology and Life Sciences, Glaucoma, Mutation, Transcription Factors, Agricultural and Biological Sciences (all), eye diseases, Ophthalmology, Mutational Analysis, Genetic Loci, lcsh:Q, sense organs
Abstract

We report molecular genetic analysis of 42 affected individuals referred with a diagnosis of aniridia who previously screened as negative for intragenic PAX6 mutations. Of these 42, the diagnoses were 31 individuals with aniridia and 11 individuals referred with a diagnosis of Gillespie syndrome (iris hypoplasia, ataxia and mild to moderate developmental delay). Array-based comparative genomic hybridization identified six whole gene deletions: four encompassing PAX6 and two encompassing FOXC1. Six deletions with plausible cis-regulatory effects were identified: five that were 3′ (telomeric) to PAX6 and one within a gene desert 5′ (telomeric) to PITX2. Sequence analysis of the FOXC1 and PITX2 coding regions identified two plausibly pathogenic de novo FOXC1 missense mutations (p.Pro79Thr and p. Leu101Pro). No intragenic mutations were detected in PITX2. FISH mapping in an individual with Gillespie-like syndrome with an apparently balanced X;11 reciprocal translocation revealed disruption of a gene at each breakpoint: ARHGAP6 on the X chromosome and PHF21A on chromosome 11. In the other individuals with Gillespie syndrome no mutations were identified in either of these genes, or in HCCS which lies close to the Xp breakpoint. Disruption of PHF21A has previously been implicated in the causation of intellectual disability (but not aniridia). Plausibly causative mutations were identified in 15 out of 42 individuals (12/32 aniridia; 3/11 Gillespie syndrome). Fourteen of these mutations presented in the known aniridia genes; PAX6, FOXC1 and PITX2. The large number of individuals in the cohort with no mutation identified suggests greater locus heterogeneity may exist in both isolated and syndromic aniridia than was previously appreciated.

Published
2016

46. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

Author

Boldt, Karsten, van Reeuwijk, Jeroen, Dougherty, Gerard, Lamers, Ideke J C, Coene, Karlien L M, Arts, Heleen H, Betts, Matthew J, Beyer, Tina, Bolat, Emine, Gloeckner, Christian Johannes, Haidari, Khatera, Hetterschijt, Lisette, Lu, Qianhao, Iaconis, Daniela, Jenkins, Dagan, Klose, Franziska, Knapp, Barbara, Latour, Brooke, Letteboer, Stef J F, Marcelis, Carlo L, Mitic, Dragana, Morleo, Manuela, Oud, Machteld M, Koutroumpas, Konstantinos, Riemersma, Moniek, Rix, Susan, Terhal, Paulien A, Toedt, Grischa, van Dam, Teunis J P, de Vrieze, Erik, Wissinger, Yasmin, Wu, Ka Man, Apic, Gordana, Beales, Philip L, Nguyen, Thanh-Minh T, Blacque, Oliver E, Gibson, Toby J, Huynen, Martijn A, Katsanis, Nicholas, Kremer, Hannie, Omran, Heymut, van Wijk, Erwin, Wolfrum, Uwe, Kepes, François, Davis, Erica E, Texier, Yves, Franco, Brunella, Giles, Rachel H, Ueffing, Marius, Russell, Robert B, Roepman, Ronald, Group, UK10K Rare Diseases, Al-Turki, Saeed, Anderson, Carl, Antony, Dinu, Barroso, Inês, van Beersum, Sylvia E C, Bentham, Jamie, Bhattacharya, Shoumo, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Danecek, Petr, Durbin, Richard, Fitzpatrick, David, Floyd, Jamie, Horn, Nicola, Reghan Foley, A., Franklin, Chris, Futema, Marta, Humphries, Steve E, Hurles, Matt, Joyce, Chris, McCarthy, Shane, Mitchison, Hannah M, Muddyman, Dawn, Muntoni, Francesco, Willer, Jason R, O'Rahilly, Stephen, Onoufriadis, Alexandros, Payne, Felicity, Plagnol, Vincent, Raymond, Lucy, Savage, David B, Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert, Mans, Dorus A, Serra, Eva, Stalker, Jim, van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Walter, Klaudia, Whittall, Ros, Williamson, Kathy, Boldt, K, van Reeuwijk, J, Lu, Q, Koutroumpas, K, Nguyen, Tmt, Texier, Y, van Beersum, Sec, Horn, N, Willer, Jr, Mans, Da, Dougherty, G, Lamers, Ijc, Coene, Klm, Arts, Hh, Betts, Mj, Beyer, T, Bolat, E, Gloeckner, Cj, Haidari, K, Hetterschijt, L, Iaconis, D, Jenkins, D, Klose, F, Knapp, B, Latour, B, Letteboer, Sjf, Marcelis, Cl, Mitic, D, Morleo, M, Oud, Mm, Riemersma, M, Rix, S, Terhal, Pa, Toedt, G, van Dam, Tjp, de Vrieze, E, Wissinger, Y, Wu, Km, Apic, G, Beales, Pl, Blacque, Oe, Gibson, Tj, Huynen, Ma, Katsanis, N, Kremer, H, Omran, H, van Wijk, E, Wolfrum, U, Kepes, F, Davis, Ee, Franco, B, Giles, Rh, Ueffing, M, Russell, Rb, Roepman, R, Boldt, Karsten, Van Reeuwijk, Jeroen, Lu, Qianhao, Koutroumpas, Konstantino, Nguyen, Thanh Minh T., Texier, Yve, Van Beersum, Sylvia E. C., Horn, Nicola, Willer, Jason R., Mans, Dorus A., Dougherty, Gerard, Lamers, Ideke J. C., Coene, Karlien L. M., Arts, Heleen H., Betts, Matthew J., Beyer, Tina, Bolat, Emine, Gloeckner, Christian Johanne, Haidari, Khatera, Hetterschijt, Lisette, Iaconis, Daniela, Jenkins, Dagan, Klose, Franziska, Knapp, Barbara, Latour, Brooke, Letteboer, Stef J. F., Marcelis, Carlo L., Mitic, Dragana, Morleo, Manuela, Oud, Machteld M., Riemersma, Moniek, Rix, Susan, Terhal, Paulien A., Toedt, Grischa, Van Dam, Teunis J. P., De Vrieze, Erik, Wissinger, Yasmin, Wu, Ka Man, Al Turki, Saeed, Anderson, Carl, Antony, Dinu, Barroso, Inê, Bentham, Jamie, Bhattacharya, Shoumo, Carss, Keren, Chatterjee, Krishna, Cirak, Sebahattin, Cosgrove, Catherine, Danecek, Petr, Durbin, Richard, Fitzpatrick, David, Floyd, Jamie, Foley, A. Reghan, Franklin, Chri, Futema, Marta, Humphries, Steve E., Hurles, Matt, Joyce, Chri, Mccarthy, Shane, Mitchison, Hannah M., Muddyman, Dawn, Muntoni, Francesco, O'Rahilly, Stephen, Onoufriadis, Alexandro, Payne, Felicity, Plagnol, Vincent, Raymond, Lucy, Savage, David B., Scambler, Peter, Schmidts, Miriam, Schoenmakers, Nadia, Semple, Robert, Serra, Eva, Stalker, Jim, Van Kogelenberg, Margriet, Vijayarangakannan, Parthiban, Walter, Klaudia, Whittall, Ro, Williamson, Kathy, Apic, Gordana, Beales, Philip L., Blacque, Oliver E., Gibson, Toby J., Huynen, Martijn A., Katsanis, Nichola, Kremer, Hannie, Omran, Heymut, Van Wijk, Erwin, Wolfrum, Uwe, Kepes, Françoi, Davis, Erica E., Franco, Brunella, Giles, Rachel H., Ueffing, Mariu, Russell, Robert B., and Roepman, Ronald

Subjects
Proteomics, 0301 basic medicine, Systems Analysis, DNA Mutational Analysis, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], General Physics and Astronomy, Datasets as Topic, methods [Chromatography, Affinity], Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Chromatography, Affinity, Mass Spectrometry, Protein Interaction Mapping, therapy [Ciliopathies], genetics [Ciliopathies], methods [Molecular Targeted Therapy], Molecular Targeted Therapy, Protein Interaction Maps, Multidisciplinary, Cilium, Chemistry (all), abnormalities [Spine], pathology [Ciliopathies], genetics [Muscle Hypotonia], therapy [Muscle Hypotonia], Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], metabolism [Proteins], isolation & purification [Proteins], physiology [Biological Transport], 3. Good health, Cell biology, Vesicular transport protein, pathology [Dwarfism], metabolism [Cilia], Muscle Hypotonia, ddc:500, pathology [Muscle Hypotonia], pathology [Spine], genetics [Dwarfism], Rare cancers Radboud Institute for Health Sciences [Radboudumc 9], Science, Dwarfism, Exocyst, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Physics and Astronomy (all), 03 medical and health sciences, Intraflagellar transport, Ciliogenesis, Organelle, Humans, Cilia, Biochemistry, Genetics and Molecular Biology (all), Proteins, Biological Transport, General Chemistry, therapy [Dwarfism], Fibroblasts, genetics [Proteins], Ciliopathies, Spine, methods [Protein Interaction Mapping], Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], 030104 developmental biology, Proteostasis, HEK293 Cells, methods [Proteomics]
Abstract

Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine., Mutations in proteins that localize to primary cilia cause devastating diseases, yet the primary cilium is a poorly understood organelle. Here the authors use interaction proteomics to identify a network of human ciliary proteins that provides new insights into several biological processes and diseases.

Published
2016

47. Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom

Author

McCarthy, Charley G.P. and Fitzpatrick, David A.

Abstract

Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.

Published
2017

49. Clinical and Molecular Consequences of Disease-Associated De Novo Mutations in SATB2

Author

FitzPatrick, David

Abstract

Purpose:To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability.Methods:Twenty previously unreported individuals with 19 different SATB2 mutations (11 loss-of-function and 8 missense variants) were studied. Fibroblasts were used to measure mutant protein production. Subcellular localization and mobility of wild-type and mutant SATB2 were assessed using fluorescently tagged protein.Results:Recurrent clinical features included neurodevelopmental impairment (19/19), absent/near absent speech (16/19), normal somatic growth (17/19), cleft palate (9/19), drooling (12/19), and dental anomalies (8/19). Six of eight missense variants clustered in the first CUT domain. Sibling recurrence due to gonadal mosaicism was seen in one family. A nonsense mutation in the last exon resulted in production of a truncated protein retaining all three DNA-binding domains. SATB2 nuclear mobility was mutation-dependent; p.Arg389Cys in CUT1 increased mobility and both p.Gly515Ser in CUT2 and p.Gln566Lys between CUT2 and HOX reduced mobility. The clinical features in individuals with missense variants were indistinguishable from those with loss of function.Conclusion:SATB2 haploinsufficiency is a common cause of syndromic intellectual disability. When mutant SATB2 protein is produced, the protein appears functionally inactive with a disrupted pattern of chromatin or matrix association.

Published
2017

50. A recurrent de novo mutation in ACTG1 causes isolated ocular coloboma

Author

Rainger, Joe, Williamson, Kathleen A, Soares, Dinesh C, Truch, Julia, Kurian, Dominic, Gillessen‐Kaesbach, Gabriele, Seawright, Anne, Prendergast, James, Halachev, Mihail, Wheeler, Ann, McTeir, Lynn, Gill, Andrew C, van Heyningen, Veronica, Davey, Megan G, and FitzPatrick, David R

Subjects
Male, Brief Report, Microfilament Proteins, Protein-Tyrosine Kinases, Ocular Coloboma, Actins, Coloboma, C431 Medical Genetics, Mice, ACTG1, Mutation, eye development, ocular coloboma, Animals, Humans, tissue fusion, Brief Reports, Female, Actin
Abstract

Ocular coloboma (OC) is a defect in optic fissure closure and is a common causeof severe congenital visual impairment. Bilateral OC is primarily genetically determined and shows marked locus heterogeneity. Whole exome sequencing was used to analyse twelve trios (child affected with OC and both unaffected parents), This identified de novo mutations in ten different genes in eight probands. Three of these genes encoded proteins associated with actin cytoskeleton dynamics: ACTG1, TWF1 and LCP1. Proband-only whole exome sequencing identified a second unrelated individual with isolated OC carrying the same ACTG1 allele, encoding p.(Pro70Leu). Both individuals have normal neurodevelopment with no extra-ocular signs of Baraitser Winter syndrome. We found this mutant protein to be incapable of incorporation into F-actin. The LCP1 and TWF1 variants each resulted in only minor disturbance of actin-interactions and no further plausibly causative variants were identified in these genes on re-sequencing 380 unrelated individuals with OC.

Published
2017

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