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2. Additional file 2 of Recommendations for clinical interpretation of variants found in non-coding regions of the genome
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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
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Additional file 2: Fig S1. Identifying regulatory variants in trans with pLoF variants in GEL.
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- 2022
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3. Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language
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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.
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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.
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- 2019
4. Evaluating variants classified as pathogenic in ClinVar in the DDD Study
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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
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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.
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- 2021
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5. The contribution of X-linked coding variation to severe developmental disorders
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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
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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.
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- 2021
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6. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder
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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
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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.
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- 2020
7. The genetic architecture of aniridia and Gillespie syndrome
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Hall, Hildegard Nikki, Williamson, Kathleen A., and FitzPatrick, David R.
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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.
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- 2018
8. Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data
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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
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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.
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- 2019
9. Rare Variant Analysis of Human and Rodent Obesity Genes in Individuals with Severe Childhood Obesity
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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
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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.
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- 2017
10. Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders
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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.
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- 2019
- Full Text
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11. NAA10 polyadenylation signal variants cause syndromic microphthalmia
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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.
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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.
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- 2019
12. ITPase Deficiency Causes a Martsolf-Like Syndrome With a Lethal Infantile Dilated Cardiomyopathy
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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.
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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.
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- 2019
13. Steroid receptor coactivator-1 modulates the function of Pomc neurons and energy homeostasis
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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
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- 2019
14. CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language
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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)
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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.
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- 2018
15. Clinical and molecular consequences of disease-associated de novo mutations in SATB2
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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
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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.
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- 2017
16. The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development
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Rodor, Julie, FitzPatrick, David R., Eyras, Eduardo, and Cáceres, Javier F.
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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.
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- 2016
17. Novel de novo EEF1A2 missense mutations causing epilepsy and intellectual disability
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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.
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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.
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- 2016
18. Dysfunction of NaV1.4, a skeletal muscle voltage-gated sodium channel, in sudden infant death syndrome:a case-control study
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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
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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
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- 2018
19. BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange–like syndrome
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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.
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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.
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- 2018
20. Genetic Analysis of 'PAX6-Negative' Individuals with Aniridia or Gillespie Syndrome
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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.
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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.
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- 2016
21. A recurrent de novo mutation in ACTG1 causes isolated ocular coloboma
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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
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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.
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- 2017
22. Clinical and molecular consequences of disease-associated de novo mutations in SATB2
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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, Grozeva, Detelina, Asam, Tara, Moore, David, Sifrim, Alejandro, McRae, Jeremy, Hurles, Matthew E., Firth, Helen V., Raymond, F. Lucy, Kini, Usha, Nellaker, Christoffer, and FitzPatrick, David R.
- 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.
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- 2017
23. PUF60 variants cause a syndrome of ID, short stature, microcephaly, coloboma, craniofacial, cardiac, renal and spinal features
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Low, Karen J, Ansari, Morad, Abou Jamra, Rami, Clarke, Angus, El Chehadeh, Salima, FitzPatrick, David R, Greenslade, Mark, Henderson, Alex, Hurst, Jane, Keller, Kory, Kuentz, Paul, Prescott, Trine, Roessler, Franziska, Selmer, Kaja K, Schneider, Michael C, Stewart, Fiona, Tatton-Brown, Katrina, Thevenon, Julien, Vigeland, Magnus D, Vogt, Julie, Willems, Marjolaine, Zonana, Jonathan, Study, D D D, and Smithson, Sarah F
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Male ,Heterozygote ,Mutation, Missense ,Syndrome ,Article ,Repressor Proteins ,Phenotype ,Intellectual Disability ,Journal Article ,Codon, Terminator ,Microcephaly ,Humans ,Abnormalities, Multiple ,Exome ,Female ,RNA Splicing Factors ,Child ,Cells, Cultured - Abstract
PUF60 encodes a nucleic acid-binding protein, a component of multimeric complexes regulating RNA splicing and transcription. In 2013, patients with microdeletions of chromosome 8q24.3 including PUF60 were found to have developmental delay, microcephaly, craniofacial, renal and cardiac defects. Very similar phenotypes have been described in six patients with variants in PUF60, suggesting that it underlies the syndrome. We report 12 additional patients with PUF60 variants who were ascertained using exome sequencing: six through the Deciphering Developmental Disorders Study and six through similar projects. Detailed phenotypic analysis of all patients was undertaken. All 12 patients had de novo heterozygous PUF60 variants on exome analysis, each confirmed by Sanger sequencing: four frameshift variants resulting in premature stop codons, three missense variants that clustered within the RNA recognition motif of PUF60 and five essential splice-site (ESS) variant. Analysis of cDNA from a fibroblast cell line derived from one of the patients with an ESS variants revealed aberrant splicing. The consistent feature was developmental delay and most patients had short stature. The phenotypic variability was striking; however, we observed similarities including spinal segmentation anomalies, congenital heart disease, ocular colobomata, hand anomalies and (in two patients) unilateral renal agenesis/horseshoe kidney. Characteristic facial features included micrognathia, a thin upper lip and long philtrum, narrow almond-shaped palpebral fissures, synophrys, flared eyebrows and facial hypertrichosis. Heterozygote loss-of-function variants in PUF60 cause a phenotype comprising growth/developmental delay and craniofacial, cardiac, renal, ocular and spinal anomalies, adding to disorders of human development resulting from aberrant RNA processing/spliceosomal function.
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- 2017
24. The UK10K project identifies rare variants in health and disease
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Walter, Klaudia, Min, Josine L., Huang, Jie, Crooks, Lucy, Memari, Yasin, McCarthy, Shane, Perry, John R. B., Xu, ChangJiang, Futema, Marta, Lawson, Daniel, Iotchkova, Valentina, Schiffels, Stephan, Hendricks, Audrey E., Danecek, Petr, Li, Rui, Floyd, James, Wain, Louise V., Barroso, Inês, Humphries, Steve E., Hurles, Matthew E., Zeggini, Eleftheria, Barrett, Jeffrey C., Plagnol, Vincent, Brent Richards, J., Greenwood, Celia M. T., Timpson, Nicholas J., Durbin, Richard, Soranzo, Nicole, Bala, Senduran, Clapham, Peter, Coates, Guy, Cox, Tony, Daly, Allan, Du, Yuanping, 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, 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, Chen, Lu, Clement, Gail, Cocca, Massimiliano, Davey Smith, George, Day, Ian N. M., Day-Williams, Aaron, Down, Thomas, Dunham, Ian, Evans, David M., Gaunt, Tom R., Geihs, Matthias, Hart, Deborah, Howie, Bryan, Hubbard, Tim, Hysi, Pirro, Jamshidi, Yalda, Karczewski, Konrad J., Kemp, John P., Lachance, Genevieve, Lek, Monkol, Lopes, Margarida, MacArthur, Daniel G., Marchini, Jonathan, Mangino, Massimo, Mathieson, Iain, Metrustry, Sarah, Moayyeri, Alireza, Northstone, Kate, Panoutsopoulou, Kalliope, Paternoster, Lavinia, Quaye, Lydia, Ring, Susan, Ritchie, Graham R. S., Shihab, Hashem A., Shin, So-Youn, Small, Kerrin S., Soler Artigas, María, Southam, Lorraine, Spector, Timothy D., St Pourcain, Beate, Surdulescu, Gabriela, Tachmazidou, Ioanna, Tobin, Martin D., Valdes, Ana M., Visscher, Peter M., Ward, Kirsten, Wilson, Scott G., Yang, Jian, Zhang, Feng, Zheng, Hou-Feng, Anney, Richard, Ayub, Muhammad, Blackwood, Douglas, Bolton, Patrick F., Breen, Gerome, Collier, David A., Craddock, Nick, Curran, Sarah, Curtis, David, Gallagher, Louise, Geschwind, Daniel, Gurling, Hugh, Holmans, Peter, Lee, Irene, Lönnqvist, 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, Rehnström, Karola, Sharp, Sally I., Skuse, David, St Clair, David, Suvisaari, Jaana, Walters, James T. R., Williams, Hywel J., Bochukova, Elena, Bounds, Rebecca, Dominiczak, Anna, Farooqi, I. Sadaf, Keogh, Julia, Marenne, Gaëlle, Morris, Andrew, O'Rahilly, Stephen, 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., Reghan Foley, A., Franklin, Christopher S., Grozeva, Detelina, Mitchison, Hannah M., Muntoni, Francesco, Onoufriadis, Alexandros, Parker, Victoria, Payne, Felicity, Lucy Raymond, F., 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, Oualkacha, Karim, 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, Pablo Casas, Juan, Chambers, John C., Dedoussis, George, Gambaro, Giovanni, Gasparini, Paolo, Isaacs, Aaron, Johnson, Jon, Kleber, Marcus E., Kooner, Jaspal S., Langenberg, Claudia, Luan, Jian'an, Malerba, Giovanni, März, 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, Zhang, Weihua, Civil Law, Epidemiology, Clinicum, Department of Psychiatry, Institute for Molecular Medicine Finland, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, Broad Institute of MIT and Harvard, Palotie, Aarno, Walter, Klaudia, Min, Josine L., Huang, Jie, Crooks, Lucy, Memari, Yasin, Mccarthy, Shane, Perry, John R. B., Xu, Changjiang, Futema, Marta, Lawson, Daniel, Iotchkova, Valentina, Schiffels, Stephan, Hendricks, Audrey E., Danecek, Petr, Li, Rui, Floyd, Jame, Wain, Louise V., Barroso, Inê, Humphries, Steve E., Hurles, Matthew E., Zeggini, Eleftheria, Barrett, Jeffrey C., Plagnol, Vincent, Brent Richards, J., Greenwood, Celia M. T., Timpson, Nicholas J., Durbin, Richard, Soranzo, Nicole, Bala, Senduran, Clapham, Peter, Coates, Guy, Cox, Tony, Daly, Allan, Du, Yuanping, Edkins, Sarah, Ellis, Peter, Flicek, Paul, Guo, Xiaosen, Guo, Xueqin, Huang, Liren, Jackson, David K., Joyce, Chri, Keane, Thoma, Kolb Kokocinski, Anja, Langford, Cordelia, Li, Yingrui, Liang, Jieqin, Lin, Hong, Liu, Ryan, Maslen, John, Muddyman, Dawn, Quail, Michael A., Stalker, Jim, Sun, Jianping, Tian, Jing, Wang, Guangbiao, Wang, Jun, Wang, Yu, Wong, Kim, Zhang, Pingbo, Birney, Ewan, Boustred, Chri, Chen, Lu, Clement, Gail, Cocca, Massimiliano, Davey Smith, George, Day, Ian N. M., Day Williams, Aaron, Down, Thoma, Dunham, Ian, Evans, David M., Gaunt, Tom R., Geihs, Matthia, Hart, Deborah, Howie, Bryan, Hubbard, Tim, Hysi, Pirro, Jamshidi, Yalda, Karczewski, Konrad J., Kemp, John P., Lachance, Genevieve, Lek, Monkol, Lopes, Margarida, Macarthur, Daniel G., Marchini, Jonathan, Mangino, Massimo, Mathieson, Iain, Metrustry, Sarah, Moayyeri, Alireza, Northstone, Kate, Panoutsopoulou, Kalliope, Paternoster, Lavinia, Quaye, Lydia, Ring, Susan, Ritchie, Graham R. S., Shihab, Hashem A., Shin, So Youn, Small, Kerrin S., Soler Artigas, María, Southam, Lorraine, Spector, Timothy D., St Pourcain, Beate, Surdulescu, Gabriela, Tachmazidou, Ioanna, Tobin, Martin D., Valdes, Ana M., Visscher, Peter M., Ward, Kirsten, Wilson, Scott G., Yang, Jian, Zhang, Feng, Zheng, Hou Feng, Anney, Richard, Ayub, Muhammad, Blackwood, Dougla, Bolton, Patrick F., Breen, Gerome, Collier, David A., Craddock, Nick, Curran, Sarah, Curtis, David, Gallagher, Louise, Geschwind, Daniel, Gurling, Hugh, Holmans, Peter, Lee, Irene, Lönnqvist, Jouko, Mcguffin, Peter, Mcintosh, Andrew M., Mckechanie, Andrew G., Mcquillin, Andrew, Morris, Jame, O'Donovan, Michael C., Owen, Michael J., Parr, Jeremy R., Paunio, Tiina, Pietilainen, Olli, Rehnström, Karola, Sharp, Sally I., Skuse, David, St Clair, David, Suvisaari, Jaana, Walters, James T. R., Williams, Hywel J., Bochukova, Elena, Bounds, Rebecca, Dominiczak, Anna, Farooqi, I. Sadaf, Keogh, Julia, Marenne, Gaëlle, Morris, Andrew, O'Rahilly, Stephen, 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., Reghan Foley, A., Franklin, Christopher S., Grozeva, Detelina, Mitchison, Hannah M., Muntoni, Francesco, Onoufriadis, Alexandro, Parker, Victoria, Payne, Felicity, Lucy Raymond, F., 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, Oualkacha, Karim, 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, Petro, Taylor, Rohan, Vandersteen, Anthony M., Amuzu, Antoinette, Pablo Casas, Juan, Chambers, John C., Dedoussis, George, Gambaro, Giovanni, Gasparini, Paolo, Isaacs, Aaron, Johnson, Jon, Kleber, Marcus E., Kooner, Jaspal S., Langenberg, Claudia, Luan, Jian'An, Malerba, Giovanni, März, 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
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APOC3 ,Male ,Genome-wide association study ,genetics,UK10K,Whole-genome sequencing ,Genome-wide association studies ,Next-generation sequencing, Genome-wide association studies, rare and low-frequency variants ,Cohort Studies ,OF-FUNCTION MUTATIONS ,genetics ,Disease ,Exome ,Exome sequencing ,POPULATION ,Genetics ,education.field_of_study ,Multidisciplinary ,HERITABILITY ,Great Britain ,Genomics ,Reference Standards ,Multidisciplinary Sciences ,Health ,Science & Technology - Other Topics ,INCIDENTAL FINDINGS ,LOW-FREQUENCY ,Female ,Adiponectin ,General Science & Technology ,Genetics, Medical ,Population ,Computational biology ,Biology ,Article ,MD Multidisciplinary ,SEQUENCE VARIATION ,UK10K Consortium ,Humans ,Genetic Predisposition to Disease ,GENOME-WIDE ASSOCIATION ,education ,COMMON ,Alleles ,Triglycerides ,Genetic association ,Whole genome sequencing ,Whole-genome sequencing ,Science & Technology ,Genome, Human ,COMPLEX TRAITS ,Genetic Variation ,Molecular Sequence Annotation ,Sequence Analysis, DNA ,Lipid Metabolism ,United Kingdom ,3141 Health care science ,Genetics, Population ,UK10K ,Receptors, LDL ,Next-generation sequencing ,rare and low-frequency variants ,Imputation (genetics) ,Genome-Wide Association Study - Abstract
M. Kivimäki työryhmäjäsen. The contribution of rare and low-frequency variants to human traits is largely unexplored. Here we describe insights from sequencing whole genomes (low read depth, 7x) or exomes (high read depth, 80x) of nearly 10,000 individuals from population-based and disease collections. In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (APOB), adiponectin (ADIPOQ) and low-density lipoprotein cholesterol (LDLR and RGAG1) from single-marker and rare variant aggregation tests. We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections. Finally, we make available an extensive resource, including individual-level genetic and phenotypic data and web-based tools to facilitate the exploration of association results.
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- 2015
25. Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing
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Sifrim, Alejandro, Hitz, Marc-Phillip, Wilsdon, Anna, Breckpot, Jeroen, Turki, Saeed H Al, Thienpont, Bernard, McRae, Jeremy, Fitzgerald, Tomas W, Singh, Tarjinder, Swaminathan, Ganesh Jawahar, Prigmore, Elena, Rajan, Diana, Abdul-Khaliq, Hashim, Banka, Siddharth, Bauer, Ulrike MM, Bentham, Jamie, Berger, Felix, Bhattacharya, Shoumo, Bu'Lock, Frances, Canham, Natalie, Colgiu, Irina-Gabriela, Cosgrove, Catherine, Cox, Helen, Daehnert, Ingo, Daly, Allan, Danesh, John, Fryer, Alan, Gewillig, Marc, Hobson, Emma, Hoff, Kirstin, Homfray, Tessa, INTERVAL Study, Kahlert, Anne-Karin, Ketley, Ami, Kramer, Hans-Heiner, Lachlan, Katherine, Lampe, Anne Katrin, Louw, Jacoba J, Manickara, Ashok Kumar, Manase, Dorin, McCarthy, Karen P, Metcalfe, Kay, Moore, Carmel, Newbury-Ecob, Ruth, Omer, Seham Osman, Ouwehand, Willem H, Park, Soo-Mi, Parker, Michael J, Pickardt, Thomas, Pollard, Martin O, Robert, Leema, Roberts, David J, Sambrook, Jennifer, Setchfield, Kerry, Stiller, Brigitte, Thornborough, Chris, Toka, Okan, Watkins, Hugh, Williams, Denise, Wright, Michael, Mital, Seema, Daubeney, Piers EF, Keavney, Bernard, Goodship, Judith, UK10K Consortium, Abu-Sulaiman, Riyadh Mahdi, Klaassen, Sabine, Wright, Caroline F, Firth, Helen V, Barrett, Jeffrey C, Devriendt, Koenraad, FitzPatrick, David R, Brook, J David, Deciphering Developmental Disorders Study, Hurles, Matthew E, Sifrim, Alejandro [0000-0001-8247-4020], Thienpont, Bernard [0000-0002-8772-6845], Banka, Siddharth [0000-0002-8527-2210], Pollard, Martin O [0000-0001-8738-0920], Mital, Seema [0000-0002-7643-4484], Keavney, Bernard [0000-0001-9573-0812], Barrett, Jeffrey C [0000-0002-1152-370X], and Apollo - University of Cambridge Repository
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Heart Defects, Congenital ,Male ,Protein Conformation ,Syndrome ,Autoantigens ,CDC2 Protein Kinase ,Mutation ,Humans ,Exome ,Female ,cardiovascular diseases ,Protein Kinase C ,Mi-2 Nucleosome Remodeling and Deacetylase Complex ,Sequence Deletion - Abstract
Congenital heart defects (CHDs) have a neonatal incidence of 0.8-1% (refs. 1,2). Despite abundant examples of monogenic CHD in humans and mice, CHD has a low absolute sibling recurrence risk (∼2.7%), suggesting a considerable role for de novo mutations (DNMs) and/or incomplete penetrance. De novo protein-truncating variants (PTVs) have been shown to be enriched among the 10% of 'syndromic' patients with extra-cardiac manifestations. We exome sequenced 1,891 probands, including both syndromic CHD (S-CHD, n = 610) and nonsyndromic CHD (NS-CHD, n = 1,281). In S-CHD, we confirmed a significant enrichment of de novo PTVs but not inherited PTVs in known CHD-associated genes, consistent with recent findings. Conversely, in NS-CHD we observed significant enrichment of PTVs inherited from unaffected parents in CHD-associated genes. We identified three genome-wide significant S-CHD disorders caused by DNMs in CHD4, CDK13 and PRKD1. Our study finds evidence for distinct genetic architectures underlying the low sibling recurrence risk in S-CHD and NS-CHD.
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- 2016
26. A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect
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McEntagart, Meriel, Williamson, Kathleen A, Rainger, Jacqueline K, Wheeler, Ann, Seawright, Anne, De Baere, Elfride, Verdin, Hannah, Bergendahl, L Therese, Quigley, Alan, Rainger, Joe, Dixit, Abhijit, Sarkar, Ajoy, López Laso, Eduardo, Sanchez-Carpintero, Rocio, Barrio, Jesus, Bitoun, Pierre, Prescott, Trine, Riise, Ruth, McKee, Shane, Cook, Jackie, McKie, Lisa, Ceulemans, Berten, Meire, Françoise, Temple, I Karen, Prieur, Fabienne, Williams, Jonathan, Clouston, Penny, Németh, Andrea H, Banka, Siddharth, Bengani, Hemant, Handley, Mark, Freyer, Elisabeth, Ross, Allyson, DDD Study, van Heyningen, Veronica, Marsh, Joseph A, Elmslie, Frances, and FitzPatrick, David R
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Adult ,Male ,cerebellar hypoplasia ,inositol triphosphate ,Adolescent ,Cerebellar Ataxia ,Protein Conformation ,aniridia ,Mice ,Intellectual Disability ,cerebellar vermis ,Animals ,Humans ,Inositol 1,4,5-Trisphosphate Receptors ,Lymphocytes ,Child ,Cells, Cultured ,iris ,Genes, Dominant ,ITPR1 ,calcium ,Microscopy, Confocal ,Middle Aged ,Pedigree ,Mutation ,Female ,ACTA2 - Abstract
Gillespie syndrome (GS) is characterized by bilateral iris hypoplasia, congenital hypotonia, non-progressive ataxia, and progressive cerebellar atrophy. Trio-based exome sequencing identified de novo mutations in ITPR1 in three unrelated individuals with GS recruited to the Deciphering Developmental Disorders study. Whole-exome or targeted sequence analysis identified plausible disease-causing ITPR1 mutations in 10/10 additional GS-affected individuals. These ultra-rare protein-altering variants affected only three residues in ITPR1: Glu2094 missense (one de novo, one co-segregating), Gly2539 missense (five de novo, one inheritance uncertain), and Lys2596 in-frame deletion (four de novo). No clinical or radiological differences were evident between individuals with different mutations. ITPR1 encodes an inositol 1,4,5-triphosphate-responsive calcium channel. The homo-tetrameric structure has been solved by cryoelectron microscopy. Using estimations of the degree of structural change induced by known recessive- and dominant-negative mutations in other disease-associated multimeric channels, we developed a generalizable computational approach to indicate the likely mutational mechanism. This analysis supports a dominant-negative mechanism for GS variants in ITPR1. In GS-derived lymphoblastoid cell lines (LCLs), the proportion of ITPR1-positive cells using immunofluorescence was significantly higher in mutant than control LCLs, consistent with an abnormality of nuclear calcium signaling feedback control. Super-resolution imaging supports the existence of an ITPR1-lined nucleoplasmic reticulum. Mice with Itpr1 heterozygous null mutations showed no major iris defects. Purkinje cells of the cerebellum appear to be the most sensitive to impaired ITPR1 function in humans. Iris hypoplasia is likely to result from either complete loss of ITPR1 activity or structure-specific disruption of multimeric interactions.
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- 2016
27. A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect
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McEntagart, Meriel, Williamson, Kathleen A., Rainger, Jacqueline K, Wheeler, Ann, Seawright, Anne, De Baere, Elfride, Verdin, Hannah, Bergendahl, L. Therese, Quigley, Alan, Rainger, Joe, Dixit, Abhijit, Lopaz Laso, Eduardo, Sanchez-Carpintero, Rocio, Jesus, Barrio, Bitoun, Pierre, Prescott, Trine, Riise, Ruth, McKee, Shane, Cook, Jackie, McKie, Lisa, Ceulemans, Berten, Meire, Francoise, Temple, I Karen, Prieur, Fabienne, Williams, Jonathan, Clouston, Penny, Németh, Andrea H, Banka, Siddharth, Bengani, Hemant, Handley, Mark, Freyer, Elisabeth, Ross, Allyson, van Heyningen, Veronica, Marsh, Joseph A., Elmslie, Frances, and FitzPatrick, David R.
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cerebellar hypoplasia ,ITPR1 ,calcium ,inositol triphosphate ,aniridia ,cerebellar ataxia ,ACTA2 ,iris - Abstract
Gillespie syndrome (GS) is characterized by bilateral iris hypoplasia, congenital hypotonia, non-progressive ataxia, and progressive cerebellar atrophy. Trio-based exome sequencing identified de novo mutations in ITPR1 in three unrelated individuals with GS recruited to the Deciphering Developmental Disorders study. Whole-exome or targeted sequence analysis identified plausible disease-causing ITPR1 mutations in 10/10 additional GS-affected individuals. These ultra-rare protein-altering variants affected only three residues in ITPR1: Glu2094 missense (one de novo, one co-segregating), Gly2539 missense (five de novo, one inheritance uncertain), and Lys2596 in-frame deletion (four de novo). No clinical or radiological differences were evident between individuals with different mutations. ITPR1 encodes an inositol 1,4,5-triphosphate-responsive calcium channel. The homo-tetrameric structure has been solved by cryoelectron microscopy. Using estimations of the degree of structural change induced by known recessive- and dominant-negative mutations in other disease-associated multimeric channels, we developed a generalizable computational approach to indicate the likely mutational mechanism. This analysis supports a dominant-negative mechanism for GS variants in ITPR1. In GS-derived lymphoblastoid cell lines (LCLs), the proportion of ITPR1-positive cells using immunofluorescence was significantly higher in mutant than control LCLs, consistent with an abnormality of nuclear calcium signaling feedback control. Super-resolution imaging supports the existence of an ITPR1-lined nucleoplasmic reticulum. Mice with Itpr1 heterozygous null mutations showed no major iris defects. Purkinje cells of the cerebellum appear to be the most sensitive to impaired ITPR1 function in humans. Iris hypoplasia is likely to result from either complete loss of ITPR1 activity or structure-specific disruption of multimeric interactions.
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- 2016
28. Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families
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Akawi, Nadia, McRae, Jeremy, Ansari, Morad, Balasubramanian, Meena, Blyth, Moira, Brady, Angela F, Clayton, Stephen, Cole, Trevor, Deshpande, Charu, Fitzgerald, Tomas W, Foulds, Nicola, Francis, Richard, Gabriel, George, Gerety, Sebastian S, Goodship, Judith, Hobson, Emma, Jones, Wendy D, Joss, Shelagh, King, Daniel, Klena, Nikolai, Kumar, Ajith, Lees, Melissa, Lelliott, Chris, Lord, Jenny, McMullan, Dominic, O'Regan, Mary, Osio, Deborah, Piombo, Virginia, Prigmore, Elena, Rajan, Diana, Rosser, Elisabeth, Sifrim, Alejandro, Smith, Audrey, Swaminathan, Ganesh J, Turnpenny, Peter, Whitworth, James, Wright, Caroline F, Firth, Helen V, Barrett, Jeffrey C, Lo, Cecilia W, FitzPatrick, David R, Hurles, Matthew E, DDD Study, Kumar, Ajith [0000-0003-3878-2856], Lelliott, Chris [0000-0001-8087-4530], Barrett, Jeffrey C [0000-0002-1152-370X], and Apollo - University of Cambridge Repository
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Family Health ,Male ,Protein-Arginine N-Methyltransferases ,Genotype ,Developmental Disabilities ,Ubiquitin-Protein Ligases ,Genetic Variation ,Cell Cycle Proteins ,Genes, Recessive ,Sequence Analysis, DNA ,United Kingdom ,Pedigree ,Phenotype ,Matrix Metalloproteinases, Secreted ,Humans ,Exome ,Female ,Genetic Predisposition to Disease ,human activities ,Genetic Association Studies - Abstract
Discovery of most autosomal recessive disease-associated genes has involved analysis of large, often consanguineous multiplex families or small cohorts of unrelated individuals with a well-defined clinical condition. Discovery of new dominant causes of rare, genetically heterogeneous developmental disorders has been revolutionized by exome analysis of large cohorts of phenotypically diverse parent-offspring trios1,2. Here we analyzed 4,125 families with diverse, rare and genetically heterogeneous developmental disorders and identified four new autosomal recessive disorders. These four disorders were identified by integrating Mendelian filtering (selecting probands with rare, biallelic and putatively damaging variants in the same gene) with statistical assessments of (i) the likelihood of sampling the observed genotypes from the general population and (ii) the phenotypic similarity of patients with recessive variants in the same candidate gene. This new paradigm promises to catalyze the discovery of novel recessive disorders, especially those with less consistent or nonspecific clinical presentations and those caused predominantly by compound heterozygous genotypes.
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- 2015
29. De novo, heterozygous, loss-of-function mutations in SYNGAP1 cause a syndromic form of intellectual disability
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Parker, Michael J, Fryer, Alan E, Shears, Deborah J, Lachlan, Katherine L, McKee, Shane A, Magee, Alex C, Mohammed, Shehla, Vasudevan, Pradeep C, Park, Soo-Mi, Benoit, Valérie, Lederer, Damien, Maystadt, Isabelle, Study, Ddd, and FitzPatrick, David R
- Abstract
De novo mutations (DNM) in SYNGAP1, encoding Ras/Rap GTPase-activating protein SynGAP, have been reported in individuals with nonsyndromic intellectual disability (ID). We identified 10 previously unreported individuals with SYNGAP1 DNM; seven via the Deciphering Developmental Disorders (DDD) Study, one through clinical analysis for copy number variation and the remaining two (monozygotic twins) via a research multi-gene panel analysis. Seven of the nine heterozygous mutations are likely to result in loss-of-function (3 nonsense; 3 frameshift; 1 whole gene deletion). The remaining two mutations, one of which affected the monozygotic twins, were missense variants. Each individual carrying a DNM in SYNGAP1 had moderate-to-severe ID and 7/10 had epilepsy; typically myoclonic seizures, absences or drop attacks. 8/10 had hypotonia, 5/10 had significant constipation, 7/10 had wide-based/unsteady gait, 3/10 had strabismus, and 2/10 had significant hip dysplasia. A proportion of the affected individuals had a similar, myopathic facial appearance, with broad nasal bridge, relatively long nose and full lower lip vermilion. A distinctive behavioral phenotype was also observed with aggressive/challenging behavior and significant sleep problems being common. 7/10 individuals had MR imaging of the brain each of which was reported as normal. The clinical features of the individuals reported here show significant overlap with those associated with 6p21.3 microdeletions, confirming that haploinsufficiency for SYNGAP1 is responsible for both disorders. © 2015 Wiley Periodicals, Inc.
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- 2015
30. Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome
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Naville, Magali, Ishibashi, Minaka, Ferg, Marco, Bengani, Hemant, Rinkwitz, Silke, Krecsmarik, Monika, Hawkins, Thomas A., Wilson, Stephen W., Manning, Elizabeth, Chilamakuri, Chandra S. R., Wilson, David I., Louis, Alexandra, Lucy Raymond, F., Rastegar, Sepand, Strähle, Uwe, Lenhard, Boris, Bally-Cuif, Laure, van Heyningen, Veronica, FitzPatrick, David R., Becker, Thomas S., Roest Crollius, Hugues, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Brain and Mind Research Institute, University of Technology Sydney (UTS), Karlsruhe Institute of Technology (KIT), MRC Human Genetics Unit, MRC Institute of Medical Genetic and Molecular Medicine, Institut des Neurosciences de Paris-Saclay (Neuro-PSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), C.D.B. Division of Biosciences, Anatomy building UCL, Department of Tumor Biology, The Norwegian Radium Hospital, University of Southampton and University Hospital Southampton NHS Foundation Trust, Centre for Human Development, Stem Cells and Regeneration, MP808, Faculty of Medicine, Cambridge Institute for Medical Research (CIMR), University of Cambridge [UK] (CAM), Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, University of Bergen (UIB), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences Paris-Saclay (NeuroPSI), University of Bergen (UiB), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris
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Life sciences ,biology ,Genetic Linkage ,DATABASE ,Evolution ,[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology ,Gene Expression ,Article ,DISEASE ,Animals, Genetically Modified ,Evolution, Molecular ,Midical sciences: 700::Basic medical, dental and veterinary sciences: 710::Medical genetics: 714 [VDP] ,Medisinske Fag: 700 [VDP] ,ddc:570 ,ELEMENTS ,Genetics ,Animals ,Humans ,Selection, Genetic ,Zebrafish ,GENE-EXPRESSION ,Gene Rearrangement ,TOOLS ,Chromosomes, Human, X ,[SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior ,[SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences ,GENOMIC SEQUENCES ,IN-SITU HYBRIDIZATION ,ENHANCERS ,Biological sciences ,Medisinske fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk genetikk: 714 [VDP] ,Enhancer Elements, Genetic ,HUMAN CELL-TYPES ,CONSERVED SYNTENY - Abstract
Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression., Enhancers regulate the transcription of genes over long genomic distances. Here, the authors show that enhancer function is correlated with maintenance of linkage between non-coding elements and neighbouring genes in the human X chromosome and that enhancers in zebrafish drive expression in a pattern consistent with the expression of a linked gene.
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- 2015
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31. Heterozygous loss-of-function mutations in YAP1 cause both isolated and syndromic optic fissure closure defects
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Williamson, Kathleen A, Rainger, Joe, Floyd, James AB, Ansari, Morad, Meynert, Alison, Aldridge, Kishan V, Rainger, Jacqueline K, Anderson, Carl A, Moore, Anthony T, Hurles, Matthew E, Clarke, Angus, van Heyningen, Veronica, Verloes, Alain, Taylor, Martin S, Wilkie, Andrew OM, UK10K Consortium, and Fitzpatrick, David R
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Adult ,Male ,Heterozygote ,Adolescent ,Cell Cycle Proteins ,Medical and Health Sciences ,Mice ,Young Adult ,Clinical Research ,Genetics ,UK10K Consortium ,Animals ,Humans ,2.1 Biological and endogenous factors ,Exome ,Eye Abnormalities ,Dental/Oral and Craniofacial Disease ,Aetiology ,Codon ,Child ,Preschool ,Alleles ,Aged ,Genetics & Heredity ,Signal Transducing ,Adaptor Proteins ,YAP-Signaling Proteins ,Middle Aged ,Biological Sciences ,Phosphoproteins ,Introns ,Pedigree ,Nonsense Mediated mRNA Decay ,Brain Disorders ,Phenotype ,Nonsense ,Female ,Transcription Initiation Site ,Transcription Factors ,Biotechnology - Abstract
Exome sequence analysis of affected individuals from two families with autosomal-dominant inheritance of coloboma identified two different cosegregating heterozygous nonsense mutations (c.370C>T [p.Arg124*] and c. 1066G>T [p.Glu356*]) in YAP1. The phenotypes of the affected families differed in that one included no extraocular features and the other manifested with highly variable multisystem involvement, including hearing loss, intellectual disability, hematuria, and orofacial clefting. A combined LOD score of 4.2 was obtained for the association between YAP1 loss-of-function mutations and the phenotype in these families. YAP1 encodes an effector of the HIPPO-pathway-induced growth response, and whole-mount in situ hybridization in mouse embryos has shown that Yap1 is strongly expressed in the eye, brain, and fusing facial processes. RT-PCR showed that an alternative transcription start site (TSS) in intron 1 of YAP1 and Yap1 is widely used in human and mouse development, respectively. Transcripts from the alternative TSS are predicted to initiate at codon Met179 relative to the canonical transcript (RefSeq NM_001130145). In these alternative transcripts, the c.370C>T mutation in family 1305 is within the 5' UTR and cannot result in nonsense-mediated decay (NMD). The c. 1066G>T mutation in family 132 should result in NMD in transcripts from either TSS. Amelioration of the phenotype by the alternative transcripts provides a plausible explanation for the phenotypic differences between the families.
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- 2014
32. Disruption of ST5 is associated with mental retardation and multiple congenital anomalies
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Göhring, Ina, Tagariello, Andreas, Endele, Sabine, Stolt, Claus C., Ghassibe, Michaella, Vikkula, Miika, Winterpacht, Andreas, FitzPatrick, David R., and Rauch, Anita
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Medizinische Fakultät ,ddc:610 - Abstract
Background The authors observed a patient with a cryptic subtelomeric de novo balanced translocation 46,XY.ish t(11;20)(p15.4;q13.2) presenting with severe mental retardation, muscular hypotonia, seizures, bilateral sensorineural hearing loss, submucous cleft palate, persistent ductus Botalli, unilateral cystic kidney dysplasia and frequent infections. Methods and Results Fluorescence in situ hybridisation mapping and sequencing of the translocation breakpoints showed that no known genes are disrupted at 20q13.2 and that ST5 (suppression of tumorigenicity 5; MIM 140750) is disrupted on 11p15.4. By quantitative PCR from different human tissues, the authors found ST5 to be relatively evenly expressed in fetal tissues. ST5 expression was more pronounced in adult brain, kidney and muscle than in the corresponding fetal tissues, whereas expression in other tissues was generally lower than in the fetal tissue. Using RNA in situ hybridisation in mouse, the authors found that St5 is expressed in the frontal cortex during embryonic development. In adult mouse brain, expression of St5 was especially high in the hippocampal area and cerebellum. Conclusion Hence, the authors suppose that ST5 plays an important role in central nervous system development probably due to disturbance of DENN-domain-mediated vesicle formation and neurotransmitter trafficking. Thus, these findings implicate ST5 in the aetiology of mental retardation, seizures and multiple congenital anomalies.
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- 2010
33. A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction
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Henderson, Robert H, Williamson, Kathleen A, Kennedy, Joanna S, Webster, Andrew R, Holder, Graham E, Robson, Anthony G, FitzPatrick, David R, van Heyningen, Veronica, and Moore, Anthony T
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Male ,genetic structures ,Fundus Oculi ,Pituitary Diseases ,DNA Mutational Analysis ,Molecular Sequence Data ,Eye ,Ophthalmology & Optometry ,Rare Diseases ,Retinal Diseases ,Clinical Research ,Opthalmology and Optometry ,Electroretinography ,2.1 Biological and endogenous factors ,Humans ,Age of Onset ,Codon ,Child ,Eye Disease and Disorders of Vision ,Pediatric ,Otx Transcription Factors ,Base Sequence ,Neurosciences ,Infant, Newborn ,Infant ,Newborn ,eye diseases ,Brain Disorders ,Phenotype ,Nonsense ,Scotland ,Codon, Nonsense ,sense organs ,Research Article - Abstract
To describe the clinical findings of a patient with an early onset retinal dystrophy and a novel mutation in OTX2, and to compare these findings with previously reported cases.Methods: Using direct sequencing, we screened 142 patients, who had either Leber congenital amaurosis (LCA) or early onset retinal dystrophy (EORD), for mutations in OTX2. All patients received a detailed ophthalmic examination including electroretinography and retinal imaging.Results: Only one mutation in OTX2 was identified. A novel heterozygous p.S138X stop mutation was identified in a seven-year-old male who had an infantile onset retinal dystrophy. The mutation was not present in either parent or in 181 blood donor samples. There was a history of failure to thrive in infancy, poor feeding, and growth hormone deficiency. Poor vision and nyctalopia was present from the first year. Funduscopy revealed a hyperpigmented peripapillary ring with a fine granular pigmentation of the RPE throughout the fundus. The scotopic bright flash ERG a-wave was subnormal and the waveform electronegative, in keeping with dysfunction both at the level of the photoreceptor and post-phototransduction. Visual function has been stable to date.Conclusions: Mutations in OTX2 have been reported in association with major developmental malformations of the eye, with retinal dystrophies such as LCA, and with pituitary dysfunction and seizure activity in some cases. This case adds further support for a role of OTX2 both in retinal development and pituitary function, and highlights a novel retinal dystrophy phenotype seen in association with mutations in OTX2.
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- 2009
34. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip
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Fedik, Rahimov, Marazita, Mary L., Axel, Visel, Cooper, Margaret E., Hitchler, Michael J., Rubini, Michele, Domann, Frederick E., Manika, Govil, Kaare, Christensen, Camille, Bille, Mads, Melbye, Astanand, Jugessur, Lie, Rolv T., Wilcox, Allen J., Fitzpatrick, David R., Green, Eric D., NISC Comparative Sequencing Program, Mossey, Peter A., Julian, Little, Steegers Theunissen, Regine P., Pennacchio, Len A., Schutte, Brian C., and Murray, Jeffrey C.
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AP-2A ,Cleft lip ,IRF6 ,Genetics ,SNP ,Transcription factor - Published
- 2008
35. Role of SOX2 mutations in human hippocampal malformations and epilepsy
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Sisodiya, Sanjay M., Ragge, Nicola K., Cavalleri, Gianpiero L., Hever, Ann, Lorenz, Birgit, Schneider, Adele, Williamson, Kathleen A., Stevens, John M., Free, Samantha L., Thompson, Pamela J., van Heyningen, Veronica, and Fitzpatrick, David R.
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stomatognathic system ,fungi ,embryonic structures ,610 Medizin ,sense organs ,biological phenomena, cell phenomena, and immunity - Abstract
PURPOSE: Seizures are noted in a significant proportion of cases of de novo, heterozygous, loss-of-function mutations in SOX2, ascertained because of severe bilateral eye malformations. We wished to determine the underlying cerebral phenotype in SOX2 mutation and to test the candidacy of SOX2 as a gene contributing to human epilepsies. METHODS: We examined high-resolution MRI scans in four patients with SOX2 mutations, two of whom had seizures. We determined the Sox2 expression pattern in developing murine brain. We searched for SOX2 mutation in 24 patients with typical hippocampal sclerosis and for common variations in SOX2 in 655 patients without eye disease but with epilepsy, including 91 patients with febrile seizures, 93 with hippocampal sclerosis, and 258 with temporal lobe epilepsy. RESULTS: Striking hippocampal and parahippocampal malformations were seen in all cases, with a history of febrile seizures or epilepsy in two of four cases. The Sox2 expression pattern in developing mouse brain supports the pattern of malformations observed. Mutation screening in patients with epilepsy did not reveal any abnormalities in SOX2. No associations were found between any clinical epilepsy phenotype and common variation in SOX2. CONCLUSIONS: SOX2 haploinsufficiency causes mesial temporal malformation in humans, making SOX2 dysfunction a candidate mechanism for mesial temporal abnormalities associated with chronic epilepsy. However, although mutation of SOX2 in humans causes hippocampal malformation, SOX2 mutation or variation is unlikely to contribute commonly to mesial temporal lobe epilepsy or its structural (hippocampal sclerosis) or historic (febrile seizures) associations in humans.
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- 2006
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36. A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect
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McEntagart, Meriel, Williamson, Kathleen A, Rainger, Jacqueline K, Wheeler, Ann, Seawright, Anne, De Baere, Elfride, Verdin, Hannah, Bergendahl, L Therese, Quigley, Alan, Rainger, Joe, Dixit, Abhijit, Sarkar, Ajoy, López Laso, Eduardo, Sanchez-Carpintero, Rocio, Barrio, Jesus, Bitoun, Pierre, Prescott, Trine, Riise, Ruth, McKee, Shane, Cook, Jackie, McKie, Lisa, Ceulemans, Berten, Meire, Françoise, Temple, I Karen, Prieur, Fabienne, Williams, Jonathan, Clouston, Penny, Németh, Andrea H, Banka, Siddharth, Bengani, Hemant, Handley, Mark, Freyer, Elisabeth, Ross, Allyson, van Heyningen, Veronica, Marsh, Joseph A, Elmslie, Frances, FitzPatrick, David R, and DDD Study
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Adult ,Male ,MISSENSE MUTATIONS ,cerebellar hypoplasia ,Génétique clinique ,inositol triphosphate ,Adolescent ,Protein Conformation ,aniridia ,PHENOTYPE ,FAMILIES ,GENE DELETION ,PROTEIN COMPLEXES ,Mice ,Report ,Intellectual Disability ,cerebellar vermis ,Journal Article ,Genetics ,Animals ,Humans ,Inositol 1,4,5-Trisphosphate Receptors ,Genetics(clinical) ,Lymphocytes ,Child ,Cells, Cultured ,CEREBELLAR-ATAXIA ,Genes, Dominant ,iris ,SPINOCEREBELLAR ATAXIA ,ITPR1 ,Microscopy, Confocal ,calcium ,Biology and Life Sciences ,ANIRIDIA ,Middle Aged ,Pedigree ,ATAXIA TYPE 15 ,CHANNELOPATHIES ,Mutation ,Female ,Human medicine ,cerebellar ataxia ,ACTA2 ,Biologie - Abstract
Gillespie syndrome (GS) is characterized by bilateral iris hypoplasia, congenital hypotonia, non-progressive ataxia, and progressive cerebellar atrophy. Trio-based exome sequencing identified de novo mutations in ITPR1 in three unrelated individuals with GS recruited to the Deciphering Developmental Disorders study. Whole-exome or targeted sequence analysis identified plausible disease-causing ITPR1 mutations in 10/10 additional GS-affected individuals. These ultra-rare protein-altering variants affected only three residues in ITPR1: Glu2094 missense (one de novo, one co-segregating), Gly2539 missense (five de novo, one inheritance uncertain), and Lys2596 in-frame deletion (four de novo). No clinical or radiological differences were evident between individuals with different mutations. ITPR1 encodes an inositol 1,4,5-triphosphate-responsive calcium channel. The homo-tetrameric structure has been solved by cryoelectron microscopy. Using estimations of the degree of structural change induced by known recessive- and dominant-negative mutations in other disease-associated multimeric channels, we developed a generalizable computational approach to indicate the likely mutational mechanism. This analysis supports a dominant-negative mechanism for GS variants in ITPR1. In GS-derived lymphoblastoid cell lines (LCLs), the proportion of ITPR1-positive cells using immunofluorescence was significantly higher in mutant than control LCLs, consistent with an abnormality of nuclear calcium signaling feedback control. Super-resolution imaging supports the existence of an ITPR1-lined nucleoplasmic reticulum. Mice with Itpr1 heterozygous null mutations showed no major iris defects. Purkinje cells of the cerebellum appear to be the most sensitive to impaired ITPR1 function in humans. Iris hypoplasia is likely to result from either complete loss of ITPR1 activity or structure-specific disruption of multimeric interactions., SCOPUS: ar.j, info:eu-repo/semantics/published
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37. Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability
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Catherine M. Abbott, Mihail Halachev, Detelina Grozeva, Hugues Roest Crollius, F. Lucy Raymond, James Prendergast, Peter C. Kind, Hemant Bengani, Jacqueline K. Rainger, Laura C. Murphy, Liusaidh J Owen, Veronica van Heyningen, Adam Jackson, Lambert Moyon, Graeme R. Grimes, Olivera Spasic-Boskovic, Magali Naville, Emily K. Osterweil, Jilly Hope, David R. FitzPatrick, Shipra Bhatia, Susana R. Louros, MRC Institute of Genetics and Molecular Medicine [Edinburgh] (IGMM), University of Edinburgh-Medical Research Council, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Edinburgh, University of Cambridge [UK] (CAM), Cardiff University, Cambridge University Hospitals NHS Foundation Trust, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Grozeva, Detelina [0000-0003-3239-8415], Moyon, Lambert [0000-0003-2390-3942], Bhatia, Shipra [0000-0002-2091-7858], Louros, Susana R. [0000-0002-1012-0386], Jackson, Adam [0000-0002-3554-6682], Prendergast, James G. [0000-0001-8916-018X], Owen, Liusaidh J. [0000-0003-0363-1775], Naville, Magali [0000-0002-6821-2427], Grimes, Graeme [0000-0002-3106-5996], Halachev, Mihail [0000-0002-4594-4588], Murphy, Laura C. [0000-0003-0029-0434], Spasic-Boskovic, Olivera [0000-0003-1583-8132], van Heyningen, Veronica [0000-0003-0359-0141], Abbott, Catherine M. [0000-0001-8794-7173], Osterweil, Emily [0000-0003-0582-2284], FitzPatrick, David R. [0000-0003-4861-969X], Apollo - University of Cambridge Repository, Louros, Susana R [0000-0002-1012-0386], Prendergast, James G [0000-0001-8916-018X], Owen, Liusaidh J [0000-0003-0363-1775], Murphy, Laura C [0000-0003-0029-0434], Abbott, Catherine M [0000-0001-8794-7173], and FitzPatrick, David R [0000-0003-4861-969X]
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Male ,Embryology ,Embryo, Nonmammalian ,X-linked intellectual disability ,medicine.disease_cause ,Hippocampus ,Midbrain ,Animals, Genetically Modified ,Cohort Studies ,Fragile X Mental Retardation Protein ,Mice ,0302 clinical medicine ,Gene Frequency ,Genes, X-Linked ,Medicine and Health Sciences ,Exome ,Regulatory Elements, Transcriptional ,Zebrafish ,X chromosome ,Genetics ,0303 health sciences ,education.field_of_study ,Mutation ,Mammalian Genomics ,Multidisciplinary ,Eukaryota ,Brain ,Chromosome Mapping ,Tenascin ,Animal Models ,Genomics ,Pedigree ,Phenotype ,Experimental Organism Systems ,Osteichthyes ,Vertebrates ,Medicine ,[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC] ,Anatomy ,Brainstem ,Research Article ,Genotype ,Science ,Population ,Mouse Models ,Nerve Tissue Proteins ,Biology ,Research and Analysis Methods ,03 medical and health sciences ,Model Organisms ,medicine ,Animals ,Humans ,Allele ,education ,Gene ,Alleles ,030304 developmental biology ,Whole genome sequencing ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Genome, Human ,Embryos ,Organisms ,Biology and Life Sciences ,medicine.disease ,FMR1 ,Disease Models, Animal ,Fish ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Animal Genomics ,Genetic Loci ,Animal Studies ,Mental Retardation, X-Linked ,Zoology ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
Funder: BBSRC studentship, Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bases in CRE targeting known XLID genes and segregated appropriately in families. Two of these variants, FMR1CRE and TENM1CRE, showed consistent site- and stage-specific differences of enhancer function in the developing zebrafish brain using dual-color fluorescent reporter assay. Mouse models were created for both variants. In male mice Fmr1CRE induced alterations in neurodevelopmental Fmr1 expression, olfactory behavior and neurophysiological indicators of FMRP function. The absence of another likely causative variant on whole genome sequencing further supported FMR1CRE as the likely basis of the XLID in this family. Tenm1CRE mice showed no phenotypic anomalies. Following the release of gnomAD 2.1, reanalysis showed that TENM1CRE exceeded the maximum plausible population frequency of a XLID causative allele. Assigning causative status to any ultra-rare CRE variant remains problematic and requires disease-relevant in vivo functional data from multiple sources. The sequential and bespoke nature of such analyses renders them time-consuming and challenging to scale for routine clinical use.
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- 2021
38. Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP
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William M. McLaren, Victoria Svinti, Sarah E. Hunt, Malcolm G. Dunlop, David R. FitzPatrick, Archie Campbell, Shona M. Kerr, Marc Tischkowitz, Fiona Cunningham, Caroline F. Wright, David Moore, Matthew E. Hurles, Mihail Halachev, Anja Thormann, Helen V. Firth, Svinti, Victoria [0000-0001-9926-0416], Campbell, Archie [0000-0003-0198-5078], Hunt, Sarah E [0000-0002-8350-1235], Dunlop, Malcolm G [0000-0002-3033-5851], Wright, Caroline F [0000-0003-2958-5076], Cunningham, Fiona [0000-0002-7445-2419], FitzPatrick, David R [0000-0003-4861-969X], and Apollo - University of Cambridge Repository
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0301 basic medicine ,Genotype ,Computer science ,Science ,Developmental Disabilities ,General Physics and Astronomy ,Locus (genetics) ,02 engineering and technology ,Computational biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Exome Sequencing ,Genetics ,medicine ,Ensembl ,Humans ,Clinical genetics ,Genetic Testing ,Allele ,lcsh:Science ,Exome ,Exome sequencing ,Alleles ,Cancer ,Genetic testing ,Whole genome sequencing ,Multidisciplinary ,medicine.diagnostic_test ,Whole Genome Sequencing ,Genetic heterogeneity ,Genome, Human ,General Chemistry ,Sequence Analysis, DNA ,021001 nanoscience & nanotechnology ,Computational biology and bioinformatics ,030104 developmental biology ,Phenotype ,Molecular Diagnostic Techniques ,Mutation ,lcsh:Q ,0210 nano-technology - Abstract
We aimed to develop an efficient, flexible and scalable approach to diagnostic genome-wide sequence analysis of genetically heterogeneous clinical presentations. Here we present G2P (www.ebi.ac.uk/gene2phenotype) as an online system to establish, curate and distribute datasets for diagnostic variant filtering via association of allelic requirement and mutational consequence at a defined locus with phenotypic terms, confidence level and evidence links. An extension to Ensembl Variant Effect Predictor (VEP), VEP-G2P was used to filter both disease-associated and control whole exome sequence (WES) with Developmental Disorders G2P (G2PDD; 2044 entries). VEP-G2PDD shows a sensitivity/precision of 97.3%/33% for de novo and 81.6%/22.7% for inherited pathogenic genotypes respectively. Many of the missing genotypes are likely false-positive pathogenic assignments. The expected number and discriminative features of background genotypes are defined using control WES. Using only human genetic data VEP-G2P performs well compared to other freely-available diagnostic systems and future phenotypic matching capabilities should further enhance performance., Diagnostic filtering is an important step to analyze the functional and clinical significance of the large number of genetic variants identified from next-generation genome sequencing data. Here, the authors develop a flexible and scalable system for diagnostic filtering of genetic variants using G2P with Ensembl VEP.
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- 2019
39. A syndromic form of Pierre Robin sequence is caused by 5q23 deletions encompassing FBN2 and PHAX
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Laura Mazzanti, Jacqueline K. Rainger, Felicity V. Mehendale, Morad Ansari, Antonio Percesepe, Jeanne Amiel, Helen V. Firth, Isabel M. Hanson, I. Karen Temple, Paola Ferrari, Koenraad Devriendt, David R. FitzPatrick, Alan Fryer, Jennie E. Murray, Christopher T. Gordon, Ansari, Morad, Rainger, Jacqueline K., Murray, Jennie E., Hanson, Isabel, Firth, Helen V., Mehendale, Felicity, Amiel, Jeanne, Gordon, Christopher T., Percesepe, Antonio, Mazzanti, Laura, Fryer, Alan, Ferrari, Paola, Devriendt, Koenraad, Temple, I. Karen, and Fitzpatrick, David R.
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Male ,Candidate gene ,Nucleocytoplasmic Transport Proteins ,5q deletion ,Congenital contractural arachnodactyly ,Fibrillin 2 (FBN2) ,Phosphorylated adaptor for RNA export (PHAX) ,Pierre Robin sequence ,Talipes equinovarus ,Fibrillin-2 ,Haploinsufficiency ,Genome ,Nucleocytoplasmic Transport Protein ,Ear, External ,Child ,Genetics (clinical) ,Sequence Deletion ,Genetics ,0303 health sciences ,Robin Sequence ,Pierre Robin Syndrome ,Medicine (all) ,030305 genetics & heredity ,Microfilament Proteins ,General Medicine ,Syndrome ,Phenotype ,Talipes equinovaru ,Cleft Palate ,Clubfoot ,Phosphoprotein ,Pierre Robin syndrome ,Chromosomes, Human, Pair 5 ,Female ,Human ,Contracture ,Adolescent ,Mutation, Missense ,Biology ,Fibrillins ,Fingers ,03 medical and health sciences ,Young Adult ,Genetic ,Finger ,medicine ,Humans ,Gene ,030304 developmental biology ,Microfilament Protein ,medicine.disease ,Phosphoproteins ,Gene Deletion - Abstract
Pierre Robin sequence (PRS) is an aetiologically distinct subgroup of cleft palate. We aimed to define the critical genomic interval from five different 5q22-5q31 deletions associated with PRS or PRS-associated features and assess each gene within the region as a candidate for the PRS component of the phenotype. Clinical array-based comparative genome hybridisation (aCGH) data were used to define a 2.08 Mb minimum region of overlap among four de novo deletions and one mother-son inherited deletion associated with at least one component of PRS. Commonly associated anomalies were talipes equinovarus (TEV), finger contractures and crumpled ear helices. Expression analysis of the orthologous genes within the PRS critical region in embryonic mice showed that the strongest candidate genes were FBN2 and PHAX. Targeted aCGH of the critical region and sequencing of these genes in a cohort of 25 PRS patients revealed no plausible disease-causing mutations. In conclusion, deletion of ?2 Mb on 5q23 region causes a clinically recognisable subtype of PRS. Haploinsufficiency for FBN2 accounts for the digital and auricular features. A possible critical region for TEV is distinct and telomeric to the PRS region. The molecular basis of PRS in these cases remains undetermined but haploinsufficiency for PHAX is a plausible mechanism.
- Published
- 2014
40. Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice
- Author
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Kishan Sokhi, Jacqueline Ramsay, Tanya Bardakjian, Adele Schneider, Nursel Elcioglu, Raoul C.M. Hennekam, C. Nur Semerci, Ferda Ozkinay, Joe Rainger, David Sexton, Andrea Superti Furga, Anita Saponari, Lina Ramos, Ellen van Beusekom, Malcolm E. Fisher, Gabriele Gillessen-Kaesbach, Anita Wischmeijer, Ian J. Jackson, Sérgio B. Sousa, Hans van Bokhoven, Rainer Koenig, Lihadh Al-Gazali, Paul Perry, Peter Branney, Louise S. Bicknell, Harris Morrison, Livia Garavelli, Dagmar Wieczorek, André Mégarbané, Rosanna Pallotta, Han G. Brunner, Lisa McKie, Saemah Nuzhat Zafar, Philippe Gautier, Ayesha Khan, David R. FitzPatrick, ANS - Amsterdam Neuroscience, APH - Amsterdam Public Health, Paediatrics, Ege Üniversitesi, Rainger, Joe, van Beusekom, Ellen, Ramsay, Jacqueline K., McKie, Lisa, Al-Gazali, Lihadh, Pallotta, Rosanna, Saponari, Anita, Branney, Peter, Fisher, Malcolm, Morrison, Harris, Bicknell, Louise, Gautier, Philippe, Perry, Paul, Sokhi, Kishan, Sexton, David, Bardakjian, Tanya M., Schneider, Adele S., Elcioglu, Nursel, Ozkinay, Ferda, Koenig, Rainer, Megarbane, Andre, Semerci, C. Nur, Khan, Ayesha, Zafar, Saemah, Hennekam, Raoul, Sousa, Sergio B., Ramos, Lina, Garavelli, Livia, Furga, Andrea Superti, Wischmeijer, Anita, Jackson, Ian J., Gillessen-Kaesbach, Gabriele, Brunner, Han G., Wieczorek, Dagmar, van Bokhoven, Hans, FitzPatrick, David R., and Faculteit der Geneeskunde
- Subjects
ANOMALIES ,DNA Mutational Analysis ,PROTEIN ,anophthalmia ,gene targeting ,Bone Morphogenetic Protein 1 ,hindlimb ,Mice ,Xenopus laevis ,genetic linkage ,BINDING ,genetics ,Waardenburg's Syndrome ,Waardenburg Syndrome ,clinical article ,C57BL mouse ,adult ,Mus ,microsatellite marker ,DEFECTS ,gene expression regulation ,Disease gene identification ,BMP1 protein, human ,Pedigree ,Medicine ,down regulation ,mutational analysis ,drug antagonism ,medicine.medical_specialty ,SMOC1 protein, human ,embryo ,Bone morphogenetic protein ,animal tissue ,loss of function mutation ,Smoc1 gene ,Genetics ,Humans ,human ,Biology ,Molecular Biology ,Waardenburg syndrome ,mouse ,Ecology, Evolution, Behavior and Systematics ,MUTATIONS ,animal model ,Correction ,SMOC-1 protein, mouse ,school child ,medicine.disease ,Mice, Inbred C57BL ,Human Reproduction [NCEBP 12] ,gene function ,Endocrinology ,decapentaplegic protein ,Genetics and epigenetic pathways of disease Functional Neurogenomics [NCMLS 6] ,Mutation ,Cancer Research ,frameshift mutation ,Medizin ,nonsense mutation ,Gene Expression ,mouse mutant ,Eye ,Bmp1 protein, mouse ,Autosomal Recessive ,bone morphogenetic protein ,Missense mutation ,animal ,Osteonectin ,SPECIFICATION ,Genetics (clinical) ,RECESSIVE ANOPHTHALMIA ,limb ,cleft palate ,Mice, Knockout ,child ,Coloboma ,ABNORMALITIES ,messenger RNA ,article ,pedigree ,female ,Mammalia ,Models, Animal ,Drosophila ,Research Article ,gene locus ,lcsh:QH426-470 ,Nonsense mutation ,procollagen C proteinase ,male ,ddc:570 ,Internal medicine ,medicine ,Animalia ,Animals ,gene ,SMOC 1 protein, mouse ,gene identification ,growth, development and aging ,Clinical Genetics ,Phenocopy ,nonhuman ,Anophthalmia ,missense mutation ,syndactyly ,Anophthalmos ,nucleotide sequence ,Human Genetics ,Extremities ,infant ,lcsh:Genetics ,XENOPUS ,CELL-DEATH ,adolescent ,Genetics of Disease ,Syndactyly ,homozygosity ,Genetics and epigenetic pathways of disease Genomic disorders and inherited multi-system disorders [NCMLS 6] ,metabolism ,Animal Genetics - Abstract
WOS: 000293338600004, PubMed ID: 21750680, Ophthalmo-acromelic syndrome (OAS), also known as Waardenburg Anophthalmia syndrome, is defined by the combination of eye malformations, most commonly bilateral anophthalmia, with post-axial oligosyndactyly. Homozygosity mapping and subsequent targeted mutation analysis of a locus on 14q24.2 identified homozygous mutations in SMOC1 (SPARC-related modular calcium binding 1) in eight unrelated families. Four of these mutations are nonsense, two frame-shift, and two missense. The missense mutations are both in the second Thyroglobulin Type-1 (Tg1) domain of the protein. The orthologous gene in the mouse, Smoc1, shows site-and stage-specific expression during eye, limb, craniofacial, and somite development. We also report a targeted pre-conditional gene-trap mutation of Smoc1 (Smoc(1tm1a)) that reduces mRNA to similar to 10% of wild-type levels. This gene-trap results in highly penetrant hindlimb post-axial oligosyndactyly in homozygous mutant animals (Smoc(1tm1a/tm1a)). Eye malformations, most commonly coloboma, and cleft palate occur in a significant proportion of Smoc(1tm1a/tm1a) embryos and pups. Thus partial loss of Smoc-1 results in a convincing phenocopy of the human disease. SMOC-1 is one of the two mammalian paralogs of Drosophila Pentagone, an inhibitor of decapentaplegic. The orthologous gene in Xenopus laevis, Smoc-1, also functions as a Bone Morphogenic Protein (BMP) antagonist in early embryogenesis. Loss of BMP antagonism during mammalian development provides a plausible explanation for both the limb and eye phenotype in humans and mice., Medical Research Council (UK)Medical Research Council UK (MRC); Medical Research CouncilMedical Research Council UK (MRC) [MC_U127561093, MC_PC_U127561112, MC_U127561112], Funding for this project was provided as an intramural program grant from the Medical Research Council (UK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- Published
- 2011
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