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3. Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features

Author

Ansari, Morad, Faour, Kamli N.W., Shimamura, Akiko, Grimes, Graeme, Kao, Emeline M., Denhoff, Erica R., Blatnik, Ana, Ben-Isvy, Daniel, Wang, Lily, Helm, Benjamin M., Firth, Helen, Breman, Amy M., Bijlsma, Emilia K., Iwata-Otsubo, Aiko, de Ravel, Thomy J.L., Fusaro, Vincent, Fryer, Alan, Nykamp, Keith, Stühn, Lara G., Haack, Tobias B., Korenke, G. Christoph, Constantinou, Panayiotis, Bujakowska, Kinga M., Low, Karen J., Place, Emily, Humberson, Jennifer, Napier, Melanie P., Hoffman, Jessica, Juusola, Jane, Deardorff, Matthew A., Shao, Wanqing, Rockowitz, Shira, Krantz, Ian, Kaur, Maninder, Raible, Sarah, Dortenzio, Victoria, Kliesch, Sabine, Singer-Berk, Moriel, Groopman, Emily, DiTroia, Stephanie, Ballal, Sonia, Srivastava, Siddharth, Rothfelder, Kathrin, Biskup, Saskia, Rzasa, Jessica, Kerkhof, Jennifer, McConkey, Haley, Sadikovic, Bekim, Hilton, Sarah, Banka, Siddharth, Tüttelmann, Frank, Conrad, Donald F., O’Donnell-Luria, Anne, Talkowski, Michael E., FitzPatrick, David R., and Boone, Philip M.

Published
2024
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4. GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder

Author

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

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

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

Published
2020

6. NAA10 polyadenylation signal variants cause syndromic microphthalmia

Author

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

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

BackgroundA 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.MethodsThree 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.ResultsGenetic 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.ConclusionThese data show that PAS variants are the most common variant type in NAA10-associated syndromic microphthalmia, suggesting reduced RNA is the molecular mechanism by which these alterations cause microphthalmia/anophthalmia. We reviewed recognised variants in PAS associated with Mendelian disorders and identified only 23 others, indicating that NAA10 harbours more than 10% of all known PAS variants. We hypothesise that PAS in other genes harbour unrecognised pathogenic variants associated with Mendelian disorders. The systematic interrogation of PAS could improve genetic testing yields.

Published
2019

7. Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Author

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

Published
2022
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8. De novo mutations in regulatory elements in neurodevelopmental disorders.

Author

Short, Patrick J, McRae, Jeremy F, Gallone, Giuseppe, Sifrim, Alejandro, Won, Hyejung, Geschwind, Daniel H, Wright, Caroline F, Firth, Helen V, FitzPatrick, David R, Barrett, Jeffrey C, and Hurles, Matthew E

Subjects
Brain, Fetus, Humans, Developmental Disabilities, Evolution, Molecular, Regulatory Sequences, Nucleic Acid, Conserved Sequence, Mutation, Female, Male, Exome, Neurodevelopmental Disorders, Evolution, Molecular, Regulatory Sequences, Nucleic Acid, MD Multidisciplinary, General Science & Technology
Abstract

We previously estimated that 42% of patients with severe developmental disorders carry pathogenic de novo mutations in coding sequences. The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant twofold enrichment of recurrently mutated elements. We estimate that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasize the importance of combining functional and evolutionary evidence to identify regulatory causes of genetic disorders.

Published
2018

9. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, primary, He, Peng, additional, Lawrence, John E. G., additional, Wang, Shuaiyu, additional, Tuck, Elizabeth, additional, Williams, Brian A., additional, Roberts, Kenny, additional, Kleshchevnikov, Vitalii, additional, Mamanova, Lira, additional, Bolt, Liam, additional, Polanski, Krzysztof, additional, Li, Tong, additional, Elmentaite, Rasa, additional, Fasouli, Eirini S., additional, Prete, Martin, additional, He, Xiaoling, additional, Yayon, Nadav, additional, Fu, Yixi, additional, Yang, Hao, additional, Liang, Chen, additional, Zhang, Hui, additional, Blain, Raphael, additional, Chedotal, Alain, additional, FitzPatrick, David R., additional, Firth, Helen, additional, Dean, Andrew, additional, Bayraktar, Omer Ali, additional, Marioni, John C., additional, Barker, Roger A., additional, Storer, Mekayla A., additional, Wold, Barbara J., additional, Zhang, Hongbo, additional, and Teichmann, Sarah A., additional

Published
2023
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11. Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA–protein interaction

Author

Williamson, Kathleen A., Hall, H. Nikki, Owen, Liusaidh J., Livesey, Benjamin J., Hanson, Isabel M., Adams, G. G. W., Bodek, Simon, Calvas, Patrick, Castle, Bruce, Clarke, Michael, Deng, Alexander T., Edery, Patrick, Fisher, Richard, Gillessen-Kaesbach, Gabriele, Heon, Elise, Hurst, Jane, Josifova, Dragana, Lorenz, Birgit, McKee, Shane, Meire, Francoise, Moore, Anthony T., Parker, Michael, Reiff, Charlotte M., Self, Jay, Tobias, Edward S., Verheij, Joke B. G. M., Willems, Marjolaine, Williams, Denise, van Heyningen, Veronica, Marsh, Joseph A., and FitzPatrick, David R.

Published
2020
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12. Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance.

Author

Kaiser, Frank J, Ansari, Morad, Braunholz, Diana, Concepción Gil-Rodríguez, María, Decroos, Christophe, Wilde, Jonathan J, Fincher, Christopher T, Kaur, Maninder, Bando, Masashige, Amor, David J, Atwal, Paldeep S, Bahlo, Melanie, Bowman, Christine M, Bradley, Jacquelyn J, Brunner, Han G, Clark, Dinah, Del Campo, Miguel, Di Donato, Nataliya, Diakumis, Peter, Dubbs, Holly, Dyment, David A, Eckhold, Juliane, Ernst, Sarah, Ferreira, Jose C, Francey, Lauren J, Gehlken, Ulrike, Guillén-Navarro, Encarna, Gyftodimou, Yolanda, Hall, Bryan D, Hennekam, Raoul, Hudgins, Louanne, Hullings, Melanie, Hunter, Jennifer M, Yntema, Helger, Innes, A Micheil, Kline, Antonie D, Krumina, Zita, Lee, Hane, Leppig, Kathleen, Lynch, Sally Ann, Mallozzi, Mark B, Mannini, Linda, McKee, Shane, Mehta, Sarju G, Micule, Ieva, Care4Rare Canada Consortium, Mohammed, Shehla, Moran, Ellen, Mortier, Geert R, Moser, Joe-Ann S, Noon, Sarah E, Nozaki, Naohito, Nunes, Luis, Pappas, John G, Penney, Lynette S, Pérez-Aytés, Antonio, Petersen, Michael B, Puisac, Beatriz, Revencu, Nicole, Roeder, Elizabeth, Saitta, Sulagna, Scheuerle, Angela E, Schindeler, Karen L, Siu, Victoria M, Stark, Zornitza, Strom, Samuel P, Thiese, Heidi, Vater, Inga, Willems, Patrick, Williamson, Kathleen, Wilson, Louise C, University of Washington Center for Mendelian Genomics, Hakonarson, Hakon, Quintero-Rivera, Fabiola, Wierzba, Jolanta, Musio, Antonio, Gillessen-Kaesbach, Gabriele, Ramos, Feliciano J, Jackson, Laird G, Shirahige, Katsuhiko, Pié, Juan, Christianson, David W, Krantz, Ian D, Fitzpatrick, David R, and Deardorff, Matthew A

Subjects
Care4Rare Canada Consortium, University of Washington Center for Mendelian Genomics, Humans, Hypertelorism, De Lange Syndrome, Eye Abnormalities, Histone Deacetylases, Repressor Proteins, Cohort Studies, Sequence Alignment, Amino Acid Sequence, Phenotype, Mutation, Missense, Molecular Sequence Data, Child, Child, Preschool, Infant, Female, Male, Genes, X-Linked, Cranial Fontanelles, Genetics, Rare Diseases, Dental/Oral and Craniofacial Disease, Intellectual and Developmental Disabilities (IDD), Pediatric, Brain Disorders, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Aetiology, Congenital, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder with distinct facies, growth failure, intellectual disability, distal limb anomalies, gastrointestinal and neurological disease. Mutations in NIPBL, encoding a cohesin regulatory protein, account for >80% of cases with typical facies. Mutations in the core cohesin complex proteins, encoded by the SMC1A, SMC3 and RAD21 genes, together account for ∼5% of subjects, often with atypical CdLS features. Recently, we identified mutations in the X-linked gene HDAC8 as the cause of a small number of CdLS cases. Here, we report a cohort of 38 individuals with an emerging spectrum of features caused by HDAC8 mutations. For several individuals, the diagnosis of CdLS was not considered prior to genomic testing. Most mutations identified are missense and de novo. Many cases are heterozygous females, each with marked skewing of X-inactivation in peripheral blood DNA. We also identified eight hemizygous males who are more severely affected. The craniofacial appearance caused by HDAC8 mutations overlaps that of typical CdLS but often displays delayed anterior fontanelle closure, ocular hypertelorism, hooding of the eyelids, a broader nose and dental anomalies, which may be useful discriminating features. HDAC8 encodes the lysine deacetylase for the cohesin subunit SMC3 and analysis of the functional consequences of the missense mutations indicates that all cause a loss of enzymatic function. These data demonstrate that loss-of-function mutations in HDAC8 cause a range of overlapping human developmental phenotypes, including a phenotypically distinct subgroup of CdLS.

Published
2014

13. Heterozygous Loss-of-Function Mutations in YAP1 Cause Both Isolated and Syndromic Optic Fissure Closure Defects

Author

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, Consortium, UK10K, and FitzPatrick, David R

Subjects
Genetics, Brain Disorders, Clinical Research, Biotechnology, Dental/Oral and Craniofacial Disease, 2.1 Biological and endogenous factors, Aetiology, Adaptor Proteins, Signal Transducing, Adolescent, Adult, Aged, Alleles, Animals, Cell Cycle Proteins, Child, Child, Preschool, Codon, Nonsense, Exome, Eye Abnormalities, Female, Heterozygote, Humans, Introns, Male, Mice, Middle Aged, Nonsense Mediated mRNA Decay, Pedigree, Phenotype, Phosphoproteins, Transcription Factors, Transcription Initiation Site, YAP-Signaling Proteins, Young Adult, UK10K Consortium, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
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.

Published
2014

14. Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia.

Author

Hall, Hildegard Nikki, Parry, David, Halachev, Mihail, Williamson, Kathleen A., Donnelly, Kevin, Parada, Jose Campos, Bhatia, Shipra, Joseph, Jeffrey, Holden, Simon, Prescott, Trine E., Bitoun, Pierre, Kirk, Edwin P., Newbury-Ecob, Ruth, Lachlan, Katherine, Bernar, Juan, van Heyningen, Veronica, FitzPatrick, David R., and Meynert, Alison

Abstract

Background Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. Methods Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. Results Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5' non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6, 3 have deletions encompassing critical PAX6 cis-regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6. The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis-regulatory elements. Conclusion Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

Author

Attanasio, Catia, Nord, Alex S, Zhu, Yiwen, Blow, Matthew J, Li, Zirong, Liberton, Denise K, Morrison, Harris, Plajzer-Frick, Ingrid, Holt, Amy, Hosseini, Roya, Phouanenavong, Sengthavy, Akiyama, Jennifer A, Shoukry, Malak, Afzal, Veena, Rubin, Edward M, FitzPatrick, David R, Ren, Bing, Hallgrímsson, Benedikt, Pennacchio, Len A, and Visel, Axel

Subjects
Pediatric Research Initiative, Biotechnology, Dental/Oral and Craniofacial Disease, Genetics, Congenital Structural Anomalies, Human Genome, Pediatric, Animals, Craniofacial Abnormalities, Enhancer Elements, Genetic, Epigenesis, Genetic, Face, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Targeting, Maxillofacial Development, Mice, Mice, Transgenic, Sequence Deletion, Skull, General Science & Technology
Abstract

The shape of the human face and skull is largely genetically determined. However, the genomic basis of craniofacial morphology is incompletely understood and hypothesized to involve protein-coding genes, as well as gene regulatory sequences. We used a combination of epigenomic profiling, in vivo characterization of candidate enhancer sequences in transgenic mice, and targeted deletion experiments to examine the role of distant-acting enhancers in craniofacial development. We identified complex regulatory landscapes consisting of enhancers that drive spatially complex developmental expression patterns. Analysis of mouse lines in which individual craniofacial enhancers had been deleted revealed significant alterations of craniofacial shape, demonstrating the functional importance of enhancers in defining face and skull morphology. These results demonstrate that enhancers are involved in craniofacial development and suggest that enhancer sequence variation contributes to the diversity of human facial morphology.

Published
2013

19. A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

Author

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

Subjects
Fundus Oculi, Humans, Pituitary Diseases, Retinal Diseases, Codon, Nonsense, Electroretinography, DNA Mutational Analysis, Age of Onset, Base Sequence, Phenotype, Molecular Sequence Data, Child, Infant, Infant, Newborn, Scotland, Male, Otx Transcription Factors, Codon, Nonsense, Newborn, Ophthalmology & Optometry, Opthalmology and Optometry
Abstract

PurposeTo 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.MethodsUsing 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.ResultsOnly 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.ConclusionsMutations 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.

Published
2009

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

Author

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

Published
2023

25. Contribution of retrotransposition to developmental disorders

Author

Gardner, Eugene J., Prigmore, Elena, Gallone, Giuseppe, Danecek, Petr, Samocha, Kaitlin E., Handsaker, Juliet, Gerety, Sebastian S., Ironfield, Holly, Short, Patrick J., Sifrim, Alejandro, Singh, Tarjinder, Chandler, Kate E., Clement, Emma, Lachlan, Katherine L., Prescott, Katrina, Rosser, Elisabeth, FitzPatrick, David R., Firth, Helen V., and Hurles, Matthew E.

Published
2019
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27. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders.

Author

Lenassi, Eva, Carvalho, Ana, Thormann, Anja, Abrahams, Liam, Arno, Gavin, Fletcher, Tracy, Hardcastle, Claire, Lopez, Javier, Hunt, Sarah E., Short, Patrick, Sergouniotis, Panagiotis I., Michaelides, Michel, Webster, Andrew, Cunningham, Fiona, Ramsden, Simon C., Kasperaviciute, Dalia, Fitzpatrick, David R., Black, Graeme C., and Ellingford, Jamie M.

Abstract

Background Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. Methods We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. Results EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. Conclusion Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders. [ABSTRACT FROM AUTHOR]

Published
2023
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28. Characterization of an eye field-like state during optic vesicle organoid development.

Author

Owen, Liusaidh J., Rainger, Jacqueline, Bengani, Hemant, Kilanowski, Fiona, FitzPatrick, David R., and Papanastasiou, Andrew S.

Subjects
TRANSCRIPTION factors, GENE expression, NUCLEOTIDE sequence, GENE regulatory networks, GROUP formation
Abstract

Specification of the eye field (EF) within the neural plate marks the earliest detectable stage of eye development. Experimental evidence, primarily from non-mammalian model systems, indicates that the stable formation of this group of cells requires the activation of a set of key transcription factors. This crucial event is challenging to probe in mammals and, quantitatively, little is known regarding the regulation of the transition of cells to this ocular fate. Using optic vesicle organoids to model the onset of the EF, we generate timecourse transcriptomic data allowing us to identify dynamic gene expression programmes that characterize this cellular-state transition. Integrating this with chromatin accessibility data suggests a direct role of canonical EF transcription factors in regulating these gene expression changes, and highlights candidate cis-regulatory elements through which these transcription factors act. Finally, we begin to test a subset of these candidate enhancer elements, within the organoid system, by perturbing the underlying DNA sequence and measuring transcriptomic changes during EF activation. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Monoallelic variants resulting in substitutions of MAB21L1 Arg51 Cause Aniridia and microphthalmia

Author

Hall, Hildegard Nikki, primary, Bengani, Hemant, additional, Hufnagel, Robert B., additional, Damante, Giuseppe, additional, Ansari, Morad, additional, Marsh, Joseph A., additional, Grimes, Graeme R., additional, Kriegsheim, Alex von, additional, Moore, David, additional, McKie, Lisa, additional, Rahmat, Jamalia, additional, Mio, Catia, additional, Blyth, Moira, additional, Keng, Wee Teik, additional, Islam, Lily, additional, McEntargart, Meriel, additional, Mannens, Marcel M., additional, Heyningen, Veronica Van, additional, Rainger, Joe, additional, Brooks, Brian P., additional, and FitzPatrick, David R., additional

Published
2022
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33. Robust Genetic Analysis of the X-Linked Anophthalmic (Ie) Mouse

Author

Hernandez-Moran, Brianda A., primary, Papanastasiou, Andrew S., additional, Parry, David, additional, Meynert, Alison, additional, Gautier, Philippe, additional, Grimes, Graeme, additional, Adams, Ian R., additional, Trejo-Reveles, Violeta, additional, Bengani, Hemant, additional, Keighren, Margaret, additional, Jackson, Ian J., additional, Adams, David J., additional, FitzPatrick, David R., additional, and Rainger, Joe, additional

Published
2022
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34. The Gene Curation Coalition: A global effort to harmonize gene–disease evidence resources

Author

DiStefano, Marina T., primary, Goehringer, Scott, additional, Babb, Lawrence, additional, Alkuraya, Fowzan S., additional, Amberger, Joanna, additional, Amin, Mutaz, additional, Austin-Tse, Christina, additional, Balzotti, Marie, additional, Berg, Jonathan S., additional, Birney, Ewan, additional, Bocchini, Carol, additional, Bruford, Elspeth A., additional, Coffey, Alison J., additional, Collins, Heather, additional, Cunningham, Fiona, additional, Daugherty, Louise C., additional, Einhorn, Yaron, additional, Firth, Helen V., additional, Fitzpatrick, David R., additional, Foulger, Rebecca E., additional, Goldstein, Jennifer, additional, Hamosh, Ada, additional, Hurles, Matthew R., additional, Leigh, Sarah E., additional, Leong, Ivone U.S., additional, Maddirevula, Sateesh, additional, Martin, Christa L., additional, McDonagh, Ellen M., additional, Olry, Annie, additional, Puzriakova, Arina, additional, Radtke, Kelly, additional, Ramos, Erin M., additional, Rath, Ana, additional, Riggs, Erin Rooney, additional, Roberts, Angharad M., additional, Rodwell, Charlotte, additional, Snow, Catherine, additional, Stark, Zornitza, additional, Tahiliani, Jackie, additional, Tweedie, Susan, additional, Ware, James S., additional, Weller, Phillip, additional, Williams, Eleanor, additional, Wright, Caroline F., additional, Yates, Thabo Michael, additional, and Rehm, Heidi L., additional

Published
2022
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37. A human embryonic limb cell atlas resolved in space and time

Author

Zhang, Bao, He, Peng, Lawrence, John E., Wang, Shuaiyu, Tuck, Elizabeth, Williams, Brian, Roberts, Kenny, Kleshchevnikov, Vitalii, Mamanova, Lira, Bolt, Liam, Polanski, Krzysztof, Elmentaite, Rasa, Fasouli, Eirini S., Prete, Martin, He, Xiaoling, Yayon, Nadav, Fu, Yixi, Yang, Hao, Liang, Chen, Zhang, Hui, FitzPatrick, David R., Firth, Helen, Dean, Andrew, Barker, Roger A., Storer, Mekayla A., Wold, Barbara J., Zhang, Hongbo, Teichmann, Sarah A., Zhang, Bao, He, Peng, Lawrence, John E., Wang, Shuaiyu, Tuck, Elizabeth, Williams, Brian, Roberts, Kenny, Kleshchevnikov, Vitalii, Mamanova, Lira, Bolt, Liam, Polanski, Krzysztof, Elmentaite, Rasa, Fasouli, Eirini S., Prete, Martin, He, Xiaoling, Yayon, Nadav, Fu, Yixi, Yang, Hao, Liang, Chen, Zhang, Hui, FitzPatrick, David R., Firth, Helen, Dean, Andrew, Barker, Roger A., Storer, Mekayla A., Wold, Barbara J., Zhang, Hongbo, and Teichmann, Sarah A.

Abstract

Human limbs emerge during the fourth post-conception week as mesenchymal buds which develop into fully-formed limbs over the subsequent months. Limb development is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common. Decades of work with model organisms has outlined the fundamental processes underlying vertebrate limb development, but an in-depth characterisation of this process in humans has yet to be performed. Here we detail the development of the human embryonic limb across space and time, using both single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells, progressing from a restricted number of multipotent progenitors to myriad mature cell states, and identify several novel cell populations, including perineural fibroblasts and multiple distinct mesenchymal states. We uncover two waves of human muscle development, each characterised by different cell states regulated by separate gene expression programmes. We identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity and validate this by performing MSC knock down in human embryonic myoblasts, which results in significant upregulation of late myogenic genes. Spatially mapping the cell types of the limb across a range of gestational ages demonstrates a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncovers two transcriptionally and spatially distinct populations of the progress zone, which we term “outer” and “transitional” layers. The latter exhibits a transcriptomic profile similar to that of the chondrocyte lineage, but lacking the key chondrogenic transcription factors SOX5,6 & 9. Finally, we perform scRNA-seq on murine embryonic limbs to facilitate cross-species developmental comparison at single-cell resolution, finding substantial homology between the two species.

Published
2022

38. Prevalence and architecture of de novo mutations in developmental disorders

Author

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, Paul A., 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, Ajith Kumar, V. K., 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, Newbury-Ecob, Ruth, 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, Price, Sue, Pridham, Abigail, Procter, Annie, Purnell, Hellen, Quarrell, Oliver, Ragge, Nicola, Rahbari, Raheleh, Randall, Josh, Rankin, Julia, 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, Karen I., 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., and Hurles, Matthew E.

Published
2017
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39. Additional file 2 of Recommendations for clinical interpretation of variants found in non-coding regions of the genome

Author

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

Abstract

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

Published
2022
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41. Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders

Author

Gardner, Eugene J., primary, Sifrim, Alejandro, additional, Lindsay, Sarah J., additional, Prigmore, Elena, additional, Rajan, Diana, additional, Danecek, Petr, additional, Gallone, Giuseppe, additional, Eberhardt, Ruth Y., additional, Martin, Hilary C., additional, Wright, Caroline F., additional, FitzPatrick, David R., additional, Firth, Helen V., additional, and Hurles, Matthew E., additional

Published
2021
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42. Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability

Author

Bengani, Hemant, primary, Grozeva, Detelina, additional, Moyon, Lambert, additional, Bhatia, Shipra, additional, Louros, Susana R., additional, Hope, Jilly, additional, Jackson, Adam, additional, Prendergast, James G., additional, Owen, Liusaidh J., additional, Naville, Magali, additional, Rainger, Jacqueline, additional, Grimes, Graeme, additional, Halachev, Mihail, additional, Murphy, Laura C., additional, Spasic-Boskovic, Olivera, additional, van Heyningen, Veronica, additional, Kind, Peter, additional, Abbott, Catherine M., additional, Osterweil, Emily, additional, Raymond, F. Lucy, additional, Roest Crollius, Hugues, additional, and FitzPatrick, David R., additional

Published
2021
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43. Author Correction: CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language

Author

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

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

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

Published
2019

44. The UK10K project identifies rare variants in health and disease

Author

Walter, Klaudia, Min, Josine L., Huang, Jie, Crooks, Lucy, Memari, Yasin, 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., Humphries, Steve E., Barrett, Jeffrey C., 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, McCarthy, Shane, (co-chair), Muddyman, Dawn, Quail, Michael A., Stalker, Jim, (co-chair), Sun, Jianping, Tian, Jing, Wang, Guangbiao, Wang, Jun, Wang, Yu, Wong, Kim, Zhang, Pingbo, Birney, Ewan, Boustred, Chris, Chen, Lu, Clement, Gail, Cocca, Massimiliano, Smith, George Davey, 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, Richards, Brent J., (co-chair), Ring, Susan, Ritchie, Graham R. S., Shihab, Hashem A., Shin, So-Youn, Small, Kerrin S., Artigas, María Soler, Soranzo, Nicole, (co-chair), Southam, Lorraine, Spector, Timothy D., St Pourcain, Beate, Surdulescu, Gabriela, Tachmazidou, Ioanna, Timpson, Nicholas J., (co-chair), 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, OʼDonovan, Michael C., Owen, Michael J., (co-chair), Palotie, Aarno, (co-chair), 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., Barroso, Inês, (co-chair), Bochukova, Elena, Bounds, Rebecca, Dominiczak, Anna, Farooqi, Sadaf I., (co-chair), Keogh, Julia, Marenne, Gaëlle, Morris, Andrew, OʼRahilly, 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., (co-chair), Foley, Reghan A., Franklin, Christopher S., Grozeva, Detelina, Hurles, Matthew E., (co-chair), Mitchison, Hannah M., Muntoni, Francesco, Onoufriadis, Alexandros, Parker, Victoria, Payne, Felicity, Raymond, Lucy 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, Greenwood, Celia M. T., (co-chair), Oualkacha, Karim, Zeggini, Eleftheria, (co-chair), Bobrow, Martin, Griffin, Heather, Kaye, Jane, (co-chair), Kennedy, Karen, Kent, Alastair, Smee, Carol, Charlton, Ruth, Ekong, Rosemary, Khawaja, Farrah, Lopes, Luis R., Migone, Nicola, Payne, Stewart J., Plagnol, Vincent, (chair), Pollitt, Rebecca C., Povey, Sue, Ridout, Cheryl K., Robinson, Rachel L., Scott, Richard H., Shaw, Adam, Syrris, Petros, Taylor, Rohan, Vandersteen, Anthony M., Durbin, Richard, (chair), Amuzu, Antoinette, Casas, Juan Pablo, Chambers, John C., Dedoussis, George, Gambaro, Giovanni, Gasparini, Paolo, Isaacs, Aaron, Johnson, Jon, Kleber, Marcus E., Kooner, Jaspal S., Langenberg, Claudia, Luan, Jianʼan, 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

Published
2015
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45. B56δ-related protein phosphatase 2A dysfunction identified in patients with intellectual disability

Author

Houge, Gunnar, Haesen, Dorien, Vissers, Lisenka E.L.M., Mehta, Sarju, Parker, Michael J., Wright, Michael, Vogt, Julie, McKee, Shane, Tolmie, John L., Cordeiro, Nuno, Kleefstra, Tjitske, Willemsen, Marjolein H., Reijnders, Margot R.F., Berland, Siren, Hayman, Eli, Lahat, Eli, Brilstra, Eva H., van Gassen, Koen L.I., Zonneveld-Huijssoon, Evelien, de Bie, Charlotte I., Hoischen, Alexander, Eichler, Evan E., Holdhus, Rita, Steen, Vidar M., Døskeland, Stein Ove, Hurles, Matthew E., FitzPatrick, David R., and Janssens, Veerle

Published
2015
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46. TAOK1 is associated with neurodevelopmental disorder and essential for neuronal maturation and cortical development

Author

Genetica Klinische Genetica, van Woerden, Geeske M, Bos, Melanie, de Konink, Charlotte, Distel, Ben, Avagliano Trezza, Rossella, Shur, Natasha E, Barañano, Kristin, Mahida, Sonal, Chassevent, Anna, Schreiber, Allison, Erwin, Angelika L, Gripp, Karen W, Rehman, Fatima, Brulleman, Saskia, McCormack, Róisín, de Geus, Gwynna, Kalsner, Louisa, Sorlin, Arthur, Bruel, Ange-Line, Koolen, David A, Gabriel, Melissa K, Rossi, Mari, Fitzpatrick, David R, Wilkie, Andrew O M, Calpena, Eduardo, Johnson, David, Brooks, Alice, van Slegtenhorst, Marjon, Fleischer, Julie, Groepper, Daniel, Lindstrom, Kristin, Innes, A Micheil, Goodwin, Allison, Humberson, Jennifer, Noyes, Amanda, Langley, Katherine G, Telegrafi, Aida, Blevins, Amy, Hoffman, Jessica, Guillen Sacoto, Maria J, Juusola, Jane, Monaghan, Kristin G, Punj, Sumit, Simon, Marleen, Pfundt, Rolph, Elgersma, Ype, Kleefstra, Tjitske, Genetica Klinische Genetica, van Woerden, Geeske M, Bos, Melanie, de Konink, Charlotte, Distel, Ben, Avagliano Trezza, Rossella, Shur, Natasha E, Barañano, Kristin, Mahida, Sonal, Chassevent, Anna, Schreiber, Allison, Erwin, Angelika L, Gripp, Karen W, Rehman, Fatima, Brulleman, Saskia, McCormack, Róisín, de Geus, Gwynna, Kalsner, Louisa, Sorlin, Arthur, Bruel, Ange-Line, Koolen, David A, Gabriel, Melissa K, Rossi, Mari, Fitzpatrick, David R, Wilkie, Andrew O M, Calpena, Eduardo, Johnson, David, Brooks, Alice, van Slegtenhorst, Marjon, Fleischer, Julie, Groepper, Daniel, Lindstrom, Kristin, Innes, A Micheil, Goodwin, Allison, Humberson, Jennifer, Noyes, Amanda, Langley, Katherine G, Telegrafi, Aida, Blevins, Amy, Hoffman, Jessica, Guillen Sacoto, Maria J, Juusola, Jane, Monaghan, Kristin G, Punj, Sumit, Simon, Marleen, Pfundt, Rolph, Elgersma, Ype, and Kleefstra, Tjitske

Published
2021

47. Genetic heterogeneity in Cornelia de Lange syndrome (CdLS) and CdLS-like phenotypes with observed and predicted levels of mosaicism

Author

Ansari, Morad, Poke, Gemma, Ferry, Quentin, Williamson, Kathleen, Aldridge, Roland, Meynert, Alison M, Bengani, Hemant, Chan, Cheng Yee, Kayserili, Hülya, Avci, Şahin, Hennekam, Raoul C M, Lampe, Anne K, Redeker, Egbert, Homfray, Tessa, Ross, Alison, Falkenberg Smeland, Marie, Mansour, Sahar, Parker, Michael J, Cook, Jacqueline A, Splitt, Miranda, Fisher, Richard B, Fryer, Alan, Magee, Alex C, Wilkie, Andrew, Barnicoat, Angela, Brady, Angela F, Cooper, Nicola S, Mercer, Catherine, Deshpande, Charu, Bennett, Christopher P, Pilz, Daniela T, Ruddy, Deborah, Cilliers, Deirdre, Johnson, Diana S, Josifova, Dragana, Rosser, Elisabeth, Thompson, Elizabeth M, Wakeling, Emma, Kinning, Esther, Stewart, Fiona, Flinter, Frances, Girisha, Katta M, Cox, Helen, Firth, Helen V, Kingston, Helen, Wee, Jamie S, Hurst, Jane A, Clayton-Smith, Jill, Tolmie, John, Vogt, Julie, Tatton–Brown, Katrina, Chandler, Kate, Prescott, Katrina, Wilson, Louise, Behnam, Mahdiyeh, McEntagart, Meriel, Davidson, Rosemarie, Lynch, Sally-Ann, Sisodiya, Sanjay, Mehta, Sarju G, McKee, Shane A, Mohammed, Shehla, Holden, Simon, Park, Soo-Mi, Holder, Susan E, Harrison, Victoria, McConnell, Vivienne, Lam, Wayne K, Green, Andrew J, Donnai, Dian, Bitner-Glindzicz, Maria, Donnelly, Deirdre E, Nellåker, Christoffer, Taylor, Martin S, and FitzPatrick, David R

Published
2014
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49. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Author

Köhler, Sebastian, Doelken, Sandra C., Mungall, Christopher J., Bauer, Sebastian, Firth, Helen V., Bailleul-Forestier, Isabelle, Black, Graeme C. M., Brown, Danielle L., Brudno, Michael, Campbell, Jennifer, FitzPatrick, David R., Eppig, Janan T., Jackson, Andrew P., Freson, Kathleen, Girdea, Marta, Helbig, Ingo, Hurst, Jane A., Jähn, Johanna, Jackson, Laird G., Kelly, Anne M., Ledbetter, David H., Mansour, Sahar, Martin, Christa L., Moss, Celia, Mumford, Andrew, Ouwehand, Willem H., Park, Soo-Mi, Riggs, Erin Rooney, Scott, Richard H., Sisodiya, Sanjay, Van Vooren, Steven, Wapner, Ronald J., Wilkie, Andrew O. M., Wright, Caroline F., Vulto-van Silfhout, Anneke T., de Leeuw, Nicole, de Vries, Bert B. A., Washingthon, Nicole L., Smith, Cynthia L., Westerfield, Monte, Schofield, Paul, Ruef, Barbara J., Gkoutos, Georgios V., Haendel, Melissa, Smedley, Damian, Lewis, Suzanna E., and Robinson, Peter N.

Published
2014
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