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1. Specific heterozygous frameshift variants in hnRNPA2B1 cause early-onset oculopharyngeal muscular dystrophy

Author: Ambegaonkar G, Evangelista T, Maura Coughlin, O’Donovan Dg, Mark A. Tarnopolsky, Tobias B. Haack, Sarah Ennis, Foley Ar, Shatillo A, Zaharieva It, Lornage X, Sato A, Sandra Donkervoort, Nelson I, Grimmel M, Salviati L, Francesco Muntoni, Bello L, Lauren Brady, James Shorter, Iida A, Böhm J, Maja Steinlin, Ana Töpf, Ichizo Nishino, Péréon Y, Quijano-Roy S, Carsten G. Bönnemann, Ogasawara M, Hu Y, Alice Flynn Ford, Klein A, Kevin J. O'Donovan, Raymond Fl, Kuster A, Marcorelles P, Adnan Y. Manzur, Buchert R, Charlotte M. Fare, Hammans, Romero Nb, Munot P, Bertolin C, Upstill-Goddard R, Mercier S, Stojkovic T, Thomas E. Lloyd, Fleurence E, Lin Guo, Courtney E. French, Phadke R, Laporte J, Taylor Jp, Payam Mohassel, Straub, Elena Pegoraro, Hong Joo Kim, and Foulds N
Subjects: Genetics, medicine, Missense mutation, Muscular dystrophy, Amyotrophic lateral sclerosis, medicine.symptom, Biology, medicine.disease, Myopathy, Phenotype, Frameshift mutation, Frontotemporal dementia, Oculopharyngeal muscular dystrophy
Abstract: SummaryRNA-binding proteins (RBPs) are essential for post-transcriptional regulation and processing of RNAs. Pathogenic missense variants in RBPs underlie a spectrum of disease phenotypes, including amyotrophic lateral sclerosis, frontotemporal dementia, inclusion body myopathy, distal myopathy, and Paget’s disease of the bone. Here, we present ten independent families with a severe, progressive, early-onset muscular dystrophy, reminiscent of oculopharyngeal muscular dystrophy (OPMD), caused by heterozygous frameshift variants in the prion-like domain of hnRNPA2B1. We found that in contrast with the previously reported missense variants, the frameshift hnRNPA2B1 variants do not promote, but rather decelerate the fibrillization of the protein. Importantly, the frameshift variants harbor altered nuclear-localization sequences and exhibit reduced affinity for the nuclear-import receptor, Karyopherin-β2, which promotes their cytoplasmic accumulation in cells and in animal models that recapitulate the human pathology. Thus, we expand the phenotypes associated with hnRNPA2B1 to include a severe, early-onset disease reminiscent of OPMD, caused by a distinct class of frameshift variants that alter its nucleocytoplasmic transport dynamics.
Published: 2021

2. Whole genome sequencing for diagnosis of neurological repeat expansion disorders

Author: Greenhalgh L, Fowler T, Karen Temple, Kane Smith, Deshpande, Subramanian S. Ajay, Bourn D, Menzies L, James M. Polke, Pasko D, Polychronopoulos D, Augusto Rendon, Pietro Fratta, Madeleine Reilly, Daugherty L, Chitty Ls, Eggleton K, Raymond Fl, Thomas T. Warner, Paul Brennan, Sian Ellard, Denise L. Perry, Jill Davison, A. C. Need, Arianna Tucci, Prasad Korlipara Lv, Mark J. Caulfield, Meriel McEntagart, Huw R. Morris, Kikkeri N. Naresh, Jenny C. Taylor, Patrick F. Chinnery, Anette Schrag, Aditi Chawla, Deans Zc, Henry Houlden, Twiss P, Douglas A, Sheikh I, Jonathan M. Schott, Hill S, Moutsianas L, Nicholas W. Wood, Tanner Hagelstrom, Robinson R, D. Kasperaviciute, Faravelli F, Rajan, Kristina Ibáñez, Antonio Rueda Martin, Emma L. Baple, Robin Howard, Ellen M. McDonagh, Elisabeth Rosser, Oprych K, Richard Festenstein, John A. Sayer, Kailash P. Bhatia, Michael A. Eberle, Andrew D Mumford, Angus-Leppan H, Thomas E, Matilde Laura, McMullan D, Brittain H, Paola Giunti, Richard H. Scott, Wilson G, Taylor Tavares Al, Ryan J. Taft, Patch C, Hyder Z, Robyn Labrum, Almheiri G, Frances Flinter, Egor Dolzhenko, Santos L, Abbs S, William G. Newman, and Jana Vandrovcova
Subjects: Whole genome sequencing, Pediatrics, medicine.medical_specialty, medicine.diagnostic_test, business.industry, Genome, Medicine, Social care, False positive rate, Allele, Family history, business, Trinucleotide repeat expansion, Genetic testing
Abstract: BackgroundRepeat expansion (RE) disorders affect ~1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in under diagnosis of atypical clinical presentations, especially in paediatric patients without a prior positive family history. Whole genome sequencing (WGS) is emerging as a first-line test for rare genetic disorders, but until recently REs were thought to be undetectable by this approach.MethodsWGS pipelines for RE disorder detection were deployed by the 100,000 Genomes Project and Illumina Clinical Services Laboratory. Performance was retrospectively assessed across the 13 most common neurological RE loci using 793 samples with prior orthogonal testing (182 with expanded alleles and 611 with alleles within normal size) and prospectively interrogated in 13,331 patients with suspected genetic neurological disorders.FindingsWGS RE detection showed minimum 97·3% sensitivity and 99·6% specificity across all 13 disease-associated loci. Applying the pipeline to patients from the 100,000 Genomes Project identified pathogenic repeat expansions which were confirmed in 69 patients, including seven paediatric patients with no reported family history of RE disorders, with a 0.09% false positive rate.InterpretationWe show here for the first time that WGS enables the detection of causative repeat expansions with high sensitivity and specificity, and that it can be used to resolve previously undiagnosed neurological disorders. This includes children with no prior suspicion of a RE disorder. These findings are leading to diagnostic implementation of this analytical pipeline in the NHS Genomic Medicine Centres in England.FundingMedical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, Illumina Inc
Published: 2020

3. Germline selection shapes human mitochondrial DNA diversity

Author: Wei, W, Tuna, S, Keogh, MJ, Smith, KR, Aitman, TJ, Beales, PL, Bennett, DL, Gale, DP, Bitner-Glindzicz, MAK, Black, GC, Brennan, P, Elliott, P, Flinter, FA, Floto, RA, Houlden, H, Irving, M, Koziell, A, Maher, ER, Markus, HS, Morrell, NW, Newman, WG, Roberts, I, Sayer, JA, Smith, KGC, Taylor, JC, Watkins, H, Webster, AR, Wilkie, AOM, Williamson, C, Attwood, A, Brown, M, Brod, NC, Crisp-Hihn, A, Davis, J, Deevi, SVV, Dewhurst, EF, Edwards, K, Erwood, M, Fox, J, Frary, AJ, Hu, F, Jolley, J, Kingston, N, Linger, R, Mapeta, R, Martin, J, Meacham, S, Papadia, S, Rayner-Matthews, PJ, Samarghitean, C, Shamardina, O, Simeoni, I, Staines, S, Staples, E, Stark, H, Stephens, J, Titterton, C, Von Ziegenweidt, J, Watt, C, Whitehorn, D, Wood, Y, Yates, K, Yu, P, James, R, Ashford, S, Penkett, CJ, Stirrups, KE, Bariana, T, Lentaigne, C, Sivapalaratnam, S, Westbury, SK, Allsup, DJ, Bakchoul, T, Biss, T, Boyce, S, Collins, J, Collins, PW, Curry, NS, Downes, K, Dutt, T, Erber, WN, Evans, G, Everington, T, Favier, R, Gomez, K, Greene, D, Gresele, P, Hart, D, Kazmi, R, Kelly, AM, Lambert, M, Madan, B, Mangles, S, Mathias, M, Millar, C, Obaji, S, Peerlinck, K, Roughley, C, Schulman, S, Scully, M, Shapiro, SE, Sibson, K, Sims, MC, Tait, RC, Talks, K, Thys, C, Toh, C-H, Van Geet, C, Westwood, J-P, Mumford, AD, Ouwehand, WH, Freson, K, Laffan, MA, Tan, RYY, Harkness, K, Mehta, S, Muir, KW, Hassan, A, Traylor, M, Drazyk, AM, Parry, D, Ahmed, M, Kazkaz, H, Vandersteen, AM, Ormondroyd, E, Thomson, K, Dent, T, Buchan, RJ, Bueser, T, Carr-White, G, Cook, S, Daniels, MJ, Harper, AR, Ware, JS, Dixon, PH, Chambers, J, Cheng, F, Estiu, MC, Hague, WM, Marschall, H-U, Vazquez-Lopez, M, Arno, G, French, CE, Michaelides, M, Moore, AT, Sanchis-Juan, A, Carss, K, Raymond, FL, Chinnery, PF, Griffiths, P, Horvath, R, Hudson, G, Jurkute, N, Pyle, A, Yu-Wai-Man, P, Whitworth, J, Adlard, J, Armstrong, R, Brewer, C, Casey, R, Cole, TRP, Evans, DG, Greenhalgh, L, Hanson, HL, Hoffman, J, Izatt, L, Kumar, A, Lalloo, F, Ong, KR, Park, S-M, Searle, C, Side, L, Snape, K, Woodward, E, Tischkowitz, M, Grozeva, D, Kurian, MA, Themistocleous, AC, Gosal, D, Marshall, A, Matthews, E, McCarthy, MI, Renton, T, Rice, ASC, Vale, T, Walker, SM, Woods, CG, Thaventhiran, JE, Allen, HL, Savic, S, Alachkar, H, Antrobus, R, Baxendale, HE, Browning, MJ, Buckland, MS, Cooper, N, Edgar, JDM, Egner, W, Gilmour, KC, Goddard, S, Gordins, P, Grigoriadou, S, Hackett, S, Hague, R, Hayman, G, Herwadkar, A, Huissoon, AP, Jolles, S, Kelleher, P, Kumararatne, D, Longhurst, H, Lorenzo, LE, Lyons, PA, Maimaris, J, Noorani, S, Richter, A, Sargur, RB, Sewell, WAC, Thomas, D, Thomas, MJ, Worth, A, Yong, PFK, Kuijpers, TW, Thrasher, AJ, Levine, AP, Sadeghi-Alavijeh, O, Wong, EKS, Cook, HT, Chan, MMY, Hall, M, Harris, C, McAlinden, P, Marchbank, KJ, Marks, S, Maxwell, H, Mozere, M, Wessels, J, Johnson, SA, Bleda, M, Hadinnapola, C, Haimel, M, Swietlik, E, Bogaard, H, Church, C, Coghlan, G, Condliffe, R, Corris, P, Danesino, C, Eyries, M, Gall, H, Ghofrani, H-A, Gibbs, JSR, Girerd, B, Holden, S, Houweling, A, Howard, LS, Humbert, M, Kiely, DG, Kovacs, G, Lawrie, A, Ross, RVM, Moledina, S, Montani, D, Newnham, M, Olschewski, A, Olschewski, H, Peacock, A, Pepke-Zaba, J, Scelsi, L, Seeger, W, Soubrier, F, Suntharalingam, J, Toshner, M, Treacy, C, Trembath, R, Noordegraaf, AV, Waisfisz, Q, Wharton, J, Wilkins, MR, Wort, SJ, Graf, S, Louka, E, Roy, NB, Rao, A, Ancliff, P, Babbs, C, Layton, DM, Mead, AJ, O'Sullivan, J, Okoli, S, Saleem, M, Bierzynska, A, Diz, CB, Colby, E, Ekani, MN, Satchell, S, Fowler, T, Rendon, A, Scott, R, Smedley, D, Thomas, E, Caulfield, M, Abbs, S, Burrows, N, Chitre, M, Gattens, M, Gurnell, M, Kelsall, W, Poole, KES, Ross-Russell, R, Spasic-Boskovic, O, Twiss, P, Wagner, A, Banka, S, Clayton-Smith, J, Douzgou, S, Abulhoul, L, Aurora, P, Bockenhauer, D, Cleary, M, Dattani, M, Ganesan, V, Pilkington, C, Rahman, S, Shah, N, Wedderburn, L, Compton, CJ, Deshpande, C, Fassihi, H, Haque, E, Josifova, D, Mohammed, SN, Robert, L, Rose, SJ, Ruddy, DM, Sarkany, RN, Sayer, G, Shaw, AC, Campbell, C, Gibson, K, Koelling, N, Lester, T, Nemeth, AH, Palles, C, Patel, S, Sen, A, Taylor, J, Tomlinson, IP, Malka, S, Browning, AC, Burn, J, De Soyza, A, Graham, J, Pearce, S, Quinton, R, Schaefer, AM, Wilson, BT, Wright, M, Simpson, M, Syrris, P, Bradley, JR, Turro, E, ARD - Amsterdam Reproduction and Development, AII - Inflammatory diseases, Paediatric Infectious Diseases / Rheumatology / Immunology, Medical Research Council (MRC), Wellcome Trust, Wei, Wei [0000-0002-2945-3543], Tuna, Salih [0000-0003-3606-4367], Smith, Katherine R [0000-0002-0329-5938], Beales, Phil L [0000-0002-9164-9782], Bennett, David L [0000-0002-7996-2696], Gale, Daniel P [0000-0002-9170-1579], Brennan, Paul [0000-0003-1128-6254], Elliott, Perry [0000-0003-3383-3984], Floto, R Andres [0000-0002-2188-5659], Houlden, Henry [0000-0002-2866-7777], Koziell, Ania [0000-0003-4882-0246], Maher, Eamonn R [0000-0002-6226-6918], Markus, Hugh S [0000-0002-9794-5996], Morrell, Nicholas W [0000-0001-5700-9792], Newman, William G [0000-0002-6382-4678], Sayer, John A [0000-0003-1881-3782], Smith, Kenneth GC [0000-0003-3829-4326], Taylor, Jenny C [0000-0003-3602-5704], Watkins, Hugh [0000-0002-5287-9016], Webster, Andrew R [0000-0001-6915-9560], Wilkie, Andrew OM [0000-0002-2972-5481], Penkett, Christopher J [0000-0003-4006-7261], Stirrups, Kathleen E [0000-0002-6823-3252], Rendon, Augusto [0000-0001-8994-0039], Bradley, John R [0000-0002-7774-8805], Turro, Ernest [0000-0002-1820-6563], Chinnery, Patrick F [0000-0002-7065-6617], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Non-Mendelian inheritance, Genome, Mitochondrial/genetics, DNA, Mitochondrial/genetics, 0302 clinical medicine, Ovum/growth & development, MTDNA, TRANSCRIPTION, Genetics, education.field_of_study, Multidisciplinary, NIHR BioResource–Rare Diseases, ASSOCIATION, Heteroplasmy, Mitochondrial, Multidisciplinary Sciences, GENOME, REPLACEMENT, Science & Technology - Other Topics, Female, Maternal Inheritance, Mitochondrial DNA, General Science & Technology, Genetic genealogy, Population, Biology, Human mitochondrial genetics, SEQUENCE, DNA, Mitochondrial, 03 medical and health sciences, Genetic, 100,000 Genomes Project–Rare Diseases Pilot, Genetic variation, MD Multidisciplinary, Humans, Selection, Genetic, education, Selection, Ovum, Science & Technology, MUTATIONS, Genetic Variation, DNA, LEIGH-DISEASE, 030104 developmental biology, REPLICATION, Genome, Mitochondrial, HETEROPLASMY, 030217 neurology & neurosurgery
Abstract: INTRODUCTION Only 2.4% of the 16.5-kb mitochondrial DNA (mtDNA) genome shows homoplasmic variation at >1% frequency in humans. Migration patterns have contributed to geographic differences in the frequency of common genetic variants, but population genetic evidence indicates that selection shapes the evolving mtDNA phylogeny. The mechanism and timing of this process are not clear. Unlike the nuclear genome, mtDNA is maternally transmitted and there are many copies in each cell. Initially, a new genetic variant affects only a proportion of the mtDNA (heteroplasmy). During female germ cell development, a reduction in the amount of mtDNA per cell causes a “genetic bottleneck,” which leads to rapid segregation of mtDNA molecules and different levels of heteroplasmy between siblings. Although heteroplasmy is primarily governed by random genetic drift, there is evidence of selection occurring during this process in animals. Yet it has been difficult to demonstrate this convincingly in humans. RATIONALE To determine whether there is selection for or against heteroplasmic mtDNA variants during transmission, we studied 12,975 whole-genome sequences, including 1526 mother–offspring pairs of which 45.1% had heteroplasmy affecting >1% of mtDNA molecules. Harnessing both the mtDNA and nuclear genome sequences, we then determined whether the nuclear genetic background influenced mtDNA heteroplasmy, validating our findings in another 40,325 individuals. RESULTS Previously unknown mtDNA variants were less likely to be inherited than known variants, in which the level of heteroplasmy tended to increase on transmission. Variants in the ribosomal RNA genes were less likely to be transmitted, whereas variants in the noncoding displacement (D)–loop were more likely to be transmitted. MtDNA variants predicted to affect the protein sequence tended to have lower heteroplasmy levels than synonymous variants. In 12,975 individuals, we identified a correlation between the location of heteroplasmic sites and known D-loop polymorphisms, including the absence of variants in critical sites required for mtDNA transcription and replication. We defined 206 unrelated individuals for which the nuclear and mitochondrial genomes were from different human populations. In these individuals, new population-specific heteroplasmies were more likely to match the nuclear genetic ancestry than the mitochondrial genome on which the mutations occurred. These findings were independently replicated in 654 additional unrelated individuals. CONCLUSION The characteristics of mtDNA in the human population are shaped by selective forces acting on heteroplasmy within the female germ line and are influenced by the nuclear genetic background. The signature of selection can be seen over one generation, ensuring consistency between these two independent genetic systems.
Published: 2019
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4. Whole genome sequencing reveals that genetic conditions are frequent in intensively ill children

Author: French, CE, Delon, I, Dolling, H, Sanchis-Juan, A, Shamardina, O, Mégy, K, Abbs, S, Austin, T, Bowdin, S, Branco, RG, Firth, H, Tuna, S, Aitman, TJ, Ashford, S, Astle, WJ, Bennet, DL, Bleda, M, Carss, KJ, Chinnery, PF, Deevi, SVV, Fletcher, D, Gale, DP, Gräf, SF, Hu, F, James, R, Kasanicki, MA, Kingston, N, Koziell, AB, Allen, HL, Maher, ER, Markus, HS, Meacham, S, Morrell, NW, Penkett, CJ, Roberts, I, Smith, KGC, Stark, H, Stirrups, KE, Turro, E, Watkins, H, Williamson, C, Young, T, Bradley, JR, Ouwehand, WH, Raymond, FL, Agrawal, S, Armstrong, R, Beardsall, K, Belteki, G, Bohatschek, M, Broster, S, Campbell, R, Chaudhary, R, Costa, C, D’Amore, A, Fitzsimmons, A, Hague, J, Harley, J, Hoodbhoy, S, Kayani, R, Kelsall, W, Mehta, SG, O’Donnell, R, O’Hare, S, Ogilvy-Stuart, A, Papakostas, S, Park, SM, Parker, A, Pathan, N, Prapa, M, Sammut, A, Sandford, R, Schon, K, Singh, Y, Spike, K, Tavares, ALT, Wari-Pepple, D, Wong, HS, Woods, CG, Rowitch, DH, Raymond, F Lucy [0000-0003-2652-3355], and Apollo - University of Cambridge Repository
Subjects: Male, NICU, medicine.medical_specialty, Palliative care, Adolescent, PICU, Original, Critical Illness, Critically ill children, Genomics, Critical Care and Intensive Care Medicine, Intensive Care Units, Pediatric, State Medicine, Cohort Studies, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Anesthesiology, Intensive care, Intensive Care Units, Neonatal, Genetics, Medicine, Humans, Prospective Studies, Medical diagnosis, Intensive care medicine, Prospective cohort study, Child, Whole genome sequencing, Whole Genome Sequencing, business.industry, Genetic Diseases, Inborn, Infant, Newborn, Infant, 030208 emergency & critical care medicine, 030228 respiratory system, England, FOS: Biological sciences, Child, Preschool, Female, business, Genetic Background, Cohort study
Abstract: Purpose With growing evidence that rare single gene disorders present in the neonatal period, there is a need for rapid, systematic, and comprehensive genomic diagnoses in ICUs to assist acute and long-term clinical decisions. This study aimed to identify genetic conditions in neonatal (NICU) and paediatric (PICU) intensive care populations. Methods We performed trio whole genome sequence (WGS) analysis on a prospective cohort of families recruited in NICU and PICU at a single site in the UK. We developed a research pipeline in collaboration with the National Health Service to deliver validated pertinent pathogenic findings within 2–3 weeks of recruitment. Results A total of 195 families had whole genome analysis performed (567 samples) and 21% received a molecular diagnosis for the underlying genetic condition in the child. The phenotypic description of the child was a poor predictor of the gene identified in 90% of cases, arguing for gene agnostic testing in NICU/PICU. The diagnosis affected clinical management in more than 65% of cases (83% in neonates) including modification of treatments and care pathways and/or informing palliative care decisions. A 2–3 week turnaround was sufficient to impact most clinical decision-making. Conclusions The use of WGS in intensively ill children is acceptable and trio analysis facilitates diagnoses. A gene agnostic approach was effective in identifying an underlying genetic condition, with phenotypes and symptomatology being primarily used for data interpretation rather than gene selection. WGS analysis has the potential to be a first-line diagnostic tool for a subset of intensively ill children. Electronic supplementary material The online version of this article (10.1007/s00134-019-05552-x) contains supplementary material, which is available to authorized users.
Published: 2019

5. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author: Haworth, S, Shapland, CY, Hayward, C, Prins, BP, Felix, JF, Medina-Gomez, C, Rivadeneira, F, Wang, C, Ahluwalia, TS, Vrijheid, M, Guxens, M, Sunyer, J, Tachmazidou, I, Walter, K, Iotchkova, V, Jackson, A, Cleal, L, Huffmann, J, Min, JL, Sass, L, Timmers, PRHJ, Al Turki, S, Anderson, CA, Anney, R, Antony, D, Artigas, MS, Ayub, M, Bala, S, Barrett, JC, Barroso, I, Beales, P, Bentham, J, Bhattacharya, S, Birney, E, Blackwood, D, Bobrow, M, Bochukova, E, Bolton, PF, Bounds, R, Boustred, C, Breen, G, Calissano, M, Carss, K, Charlton, R, Chatterjee, K, Chen, L, Ciampi, A, Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, DA, Cosgrove, C, Cox, T, Craddock, N, Crooks, L, Curran, S, Curtis, D, Daly, A, Danecek, P, Day, INM, Day-Williams, A, Dominiczak, A, Down, T, Du, Y, Dunham, I, Durbin, R, Edkins, S, Ekong, R, Ellis, P, Evans, DM, Farooqi, IS, Fitzpatrick, DR, Flicek, P, Floyd, J, Foley, AR, Franklin, CS, Futema, M, Gallagher, L, Gaunt, TR, Geihs, M, Geschwind, D, Greenwood, CMT, Griffin, H, Grozeva, D, Guo, X, Gurling, H, Hart, D, Hendricks, AE, Holmans, P, Howie, B, Huang, J, Huang, L, Hubbard, T, Humphries, SE, Hurles, ME, Hysi, P, Jackson, DK, Jamshidi, Y, Joyce, C, Karczewski, KJ, Kaye, J, Keane, T, Kemp, JP, Kennedy, K, Kent, A, Keogh, J, Khawaja, F, van Kogelenberg, M, Kolb-Kokocinski, A, Lachance, G, Langford, C, Lawson, D, Lee, I, Lek, M, Li, R, Li, Y, Liang, J, Lin, H, Liu, R, Lonnqvist, J, Lopes, LR, Lopes, M, MacArthur, DG, Mangino, M, Marchini, J, Marenne, G, Maslen, J, Mathieson, I, McCarthy, S, McGuffin, P, McIntosh, AM, McKechanie, AG, McQuillin, A, Memari, Y, Metrustry, S, Migone, N, Mitchison, HM, Moayyeri, A, Morris, A, Morris, J, Muddyman, D, Muntoni, F, Northstone, K, O'Donovan, MC, O'Rahilly, S, Onoufriadis, A, Oualkacha, K, Owen, MJ, Palotie, A, Panoutsopoulou, K, Parker, V, Parr, JR, Paternoster, L, Paunio, T, Payne, F, Payne, SJ, Perry, JRB, Pietilainen, O, Plagnol, V, Pollitt, RC, Porteous, DJ, Povey, S, Quail, MA, Quaye, L, Raymond, FL, Rehnstrom, K, Richards, JB, Ridout, CK, Ring, S, Ritchie, GRS, Roberts, N, Robinson, RL, Savage, DB, Scambler, P, Schiffels, S, Schmidts, M, Schoenmakers, N, Scott, RH, Semple, RK, Serra, E, Sharp, SI, Shaw, A, Shihab, HA, Shin, S-Y, Skuse, D, Small, KS, Smee, C, Smith, BH, Soranzo, N, Southam, L, Spasic-Boskovic, O, Spector, TD, St Clair, D, Stalker, J, Stevens, E, Sun, J, Surdulescu, G, Suvisaari, J, Syrris, P, Taylor, R, Tian, J, Tobin, MD, Valdes, AM, Vandersteen, AM, Vijayarangakannan, P, Visscher, PM, Wain, LV, Walters, JTR, Wang, G, Wang, J, Wang, Y, Ward, K, Wheeler, E, Whyte, T, Williams, HJ, Williamson, KA, Wilson, C, Wilson, SG, Wong, K, Xu, C, Yang, J, Zhang, F, Zhang, P, Zheng, H-F, Smith, GD, Fisher, SE, Wilson, JF, Cole, TJ, Fernandez-Orth, D, Bonnelykke, K, Bisgaard, H, Pennell, CE, Jaddoe, VWV, Dedoussis, G, Timpson, N, Zeggini, E, Vitart, V, St Pourcain, B, UK10K Consortium, Epidemiology, Erasmus MC other, Pediatrics, Internal Medicine, and Child and Adolescent Psychiatry / Psychology
Abstract: Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood, suggesting a previously unrecognized role of TP53 transcripts in human cranial development.
Published: 2019

6. Deep-intronic ABCA4 variants explain missing heritability in Stargardt disease and allow correction of splice defects by antisense oligonucleotides

Author: Sangermano, R, Garanto, A., Khan, M. (Mubeen), Runhart, E.H., Bauwens, M., Bax, N.M.A. (Klaas), Born, L.I. (Ingeborgh) van den, Khan, M.I. (Muhammad), Cornelis, S.S., Verheij, J, Pott, J.W.R., Thiadens, A., Klaver, C.C.W. (Caroline), Puech, B., Meunier, I., Naessens, S., Arno, G., Fakin, A., Carss, K.J., Raymond, FL, Webster, A.R. (Andrew), Dhaenens, C.M., Stohr, H., Grassmann, F. (Felix), Weber, B.H.F. (Bernhard), Hoyng, C.B. (Carel), De Baere, E. (Elfride), Albert, S., Collin, R.W.J. (Rob), Cremers, F.P.M. (Frans), Sangermano, R, Garanto, A., Khan, M. (Mubeen), Runhart, E.H., Bauwens, M., Bax, N.M.A. (Klaas), Born, L.I. (Ingeborgh) van den, Khan, M.I. (Muhammad), Cornelis, S.S., Verheij, J, Pott, J.W.R., Thiadens, A., Klaver, C.C.W. (Caroline), Puech, B., Meunier, I., Naessens, S., Arno, G., Fakin, A., Carss, K.J., Raymond, FL, Webster, A.R. (Andrew), Dhaenens, C.M., Stohr, H., Grassmann, F. (Felix), Weber, B.H.F. (Bernhard), Hoyng, C.B. (Carel), De Baere, E. (Elfride), Albert, S., Collin, R.W.J. (Rob), and Cremers, F.P.M. (Frans)
Abstract: Purpose: Using exome sequencing, the underlying variants in many persons with autosomal recessive diseases remain undetected. We explored autosomal recessive Stargardt disease (STGD1) as a model to identify the missing heritability. Methods: Sequencing of ABCA4 was performed in 8 STGD1 cases with one variant and p.Asn1868Ile in trans, 25 cases with one variant, and 3 cases with no ABCA4 variant. The effect of intronic variants was analyzed using in vitro splice assays in HEK293T cells and patient-derived fibroblasts. Antisense oligonucleotides were used to correct splice defects. Results: In 24 of the probands (67%), one known and five novel deep-intronic variants were found. The five novel variants resulted in messenger RNA pseudoexon inclusions, due to strengthening of cryptic splice sites or by disrupting a splicing silencer motif. Variant c.769-784C>T showed partial insertion of a pseudoexon and was found in cis with c.5603A>T (p.Asn1868Ile), so its causal role could not be fully established. Variant c.4253+43G>A resulted in partial skipping of exon 28. Remarkably, antisense oligonucleotides targeting the aberrant splice processes resulted in (partial) correction of all splicing defects. Conclusion: Our data demonstrate the importance of assessing noncoding variants in genetic diseases, and show the great potential of splice modulation therapy for deep-intronic variants.
Published: 2019
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7. Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Author: Haworth, S., Shapland, C.Y., Hayward, C. (Caroline), Prins, B.P. (Bram), Felix, J.F. (Janine), Medina-Gomez, M.C. (Carolina), Rivadeneira Ramirez, F. (Fernando), Wang, C., Ahluwalia, TS, Vrijheid, M. (Martine), Guxens Junyent, M. (Mònica), Sunyer, J. (Jordi), Tachmazidou, I, Walter, K., Iotchkova, V, Jackson, A.U. (Anne), Cleal, L., Huffmann, J., Min, J. (Josine), Sass, L., Timmers, P, Al Turki, S., Anderson, CA, Anney, R. (Richard), Antony, D, Soler Artigas, M. (Maria), Ayub, M, Bala, S, Barrett, JC, Barroso, I.E. (Inês), Beales, P., Bentham, J, Bhattacharya, S. (Shoumo), Birney, E. (Ewan), Blackwood, D, Bobrow, M, Bochukova, E, Bolton, PF, Bounds, R, Boustred, C, Breen, G. (Gerome), Calissano, M, Carss, K, Charlton, R, Chatterjee, K. (Krishna), Chen, L. (Leslie), Ciampi, A. (Antonio), Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, D.A. (David), Cosgrove, C, Cox, T. (Tessa), Craddock, N.J. (Nick), Crooks, L, Curran, S, Curtis, D. (David), Daly, A, Danecek, P, Day, I.N.M. (Ian), Day-Williams, A, Dominiczak, A. (Anna), Down, T, Li, Y. (Yingrui), Dunham, D.M. (David), Durbin, R, Edkins, T. (Ted), Ekong, R. (Rosemary), Ellis, P. (Paul), Evans, D.M. (David), Farooqi, I.S. (Sadaf), Fitzpatrick, D.R. (David), Flicek, P, Floyd, J. (Jamie), Foley, AR, Franklin, C.S. (Christopher), Futema, M, Gallagher, L. (Louise), Gaunt, T.R. (Tom), Geihs, M, Geschwind, D., Greenwood, J.P. (John), Griffin, H, Grozeva, D. (Detelina), Guo, X.S., Guo, X. (Xiuqing), Gurling, H. (Hugh), Hart, D.J. (Deborah), Hendricks, AE, Holmans, P.A. (Peter), Howie, B, Huang, J. (Jian), Huang, L.R., Hubbard, T., Humphries, S.E. (Steve), Hurles, M.E. (Matthew), Hysi, P.G. (Pirro), Jackson, DK, Jamshidi, Y. (Yalda), Joyce, C, Karczewski, KJ, Kaye, J. (Jane), Keane, T, Kemp, J.P., Kennedy, K. (Karen), Kent, A. (Alistair), Keogh, J, Khawaja, F, van Kogelenberg, M., Kolb-Kokocinski, A, Lachance, G, Langford, C. (Cordelia), Lawson, D, Lee, I. van der, Lek, M, Li, R. (Rui), Li, Y.R. (Yun), Liang, J.Q., Lin, H., Liu, R, Lonnqvist, J, Lopes, LR, Lopes, M., MacArthur, DG, Mangino, M. (Massimo), Marchini, J. (Jonathan), Marenne, G., Maslen, J., Mathieson, I. (Iain), McCarthy, S. (Sean), Mcguffin, P. (Peter), Mcintosh, A.M. (Andrew), McKechanie, AG, McQuillin, A. (Andrew), Memari, Y, Metrustry, S. (Sarah), Migone, N, Mitchison, H.M. (Hannah), Moayyeri, A. (Alireza), Morris, A.D. (Andrew), Morris, J, Muddyman, D, Muntoni, F., Northstone, K. (Kate), O'Donovan, M. (Michael), O'Rahilly, S. (Stephen), Onoufriadis, A, Oualkacha, K., Owen, M.J., Palotie, A. (Aarno), Panoutsopoulou, K, Parker, V., Parr, D., Paternoster, L. (Lavinia), Paunio, T, Payne, F. (Felicity), Payne, SJ, Perry, J.B. (John), Pietiläinen, O.P.H. (Olli), Plagnol, V, Pollitt, RC, Porteous, D.J. (David J.), Povey, S. (Sue), Quail, MA, Quaye, L. (Lydia), Raymond, FL, Rehnström, K. (Karola), Richards, J.B. (Brent), Ridout, CK, Ring, S.M. (Susan), Ritchie, GRS, Roberts, N. (Nicola), Robinson, RL, Savage, D.B. (David), Scambler, P., Schiffels, S, Schmidts, M, Schoenmakers, N. (Nadia), Scott, RH, Semple, R.K. (Robert), Serra, E, Sharp, S.I., Shaw, A. (Alison), Shihab, HA, Shin, S.-Y., Skuse, D, Small, K.S. (Kerrin), Smee, C, Smith, B.H. (Blair), Soranzo, N. (Nicole), Southam, L. (Lorraine), Spasic-Boskovic, O, Spector, T.D. (Timothy), St. Clair, D. (David), Stalker, J, Stevens, E, Sun, J.P., Surdulescu, G, Suvisaari, J. (Jaana), Syrris, P, R. Taylor (Rohan), Tian, J., Tobin, M.D. (Martin), Valdes, A.M. (Ana Maria), Vandersteen, AM, Vijayarangakannan, P, Visscher, P.M. (Peter), Wain, L.V. (Louise), Walters, JTR, Wang, G. B., Wang, J. (Jinxia), Wang, Y. (Ying), Ward, K, Wheeler, E. (Eleanor), Whyte, T, Williams, HJ, Williamson, K.A., Wilson, C, Wilson, S.G. (Scott), Wong, K. (Kenny), Xu, CJ, Yang, J. (Jian), Zhang, F. (Feng), Zhang, P.B., Zheng, H.-F. (Hou-Feng), Smith, A.V. (Davey), Fisher, SE, Wilson, J.F. (James F), Cole, T.J. (T.), Fernandez-Orth, D., Bønnelykke, K. (Klaus), Bisgaard, H. (Hans), Pennell, C.E. (Craig), Jaddoe, V.W.V. (Vincent), Dedoussis, G, Timpson, N.J. (Nicholas), Zeggini, E. (Eleftheria), Vitart, V. (Veronique), Pourcain, B.S. (Beate), Haworth, S., Shapland, C.Y., Hayward, C. (Caroline), Prins, B.P. (Bram), Felix, J.F. (Janine), Medina-Gomez, M.C. (Carolina), Rivadeneira Ramirez, F. (Fernando), Wang, C., Ahluwalia, TS, Vrijheid, M. (Martine), Guxens Junyent, M. (Mònica), Sunyer, J. (Jordi), Tachmazidou, I, Walter, K., Iotchkova, V, Jackson, A.U. (Anne), Cleal, L., Huffmann, J., Min, J. (Josine), Sass, L., Timmers, P, Al Turki, S., Anderson, CA, Anney, R. (Richard), Antony, D, Soler Artigas, M. (Maria), Ayub, M, Bala, S, Barrett, JC, Barroso, I.E. (Inês), Beales, P., Bentham, J, Bhattacharya, S. (Shoumo), Birney, E. (Ewan), Blackwood, D, Bobrow, M, Bochukova, E, Bolton, PF, Bounds, R, Boustred, C, Breen, G. (Gerome), Calissano, M, Carss, K, Charlton, R, Chatterjee, K. (Krishna), Chen, L. (Leslie), Ciampi, A. (Antonio), Cirak, S, Clapham, P, Clement, G, Coates, G, Cocca, M, Collier, D.A. (David), Cosgrove, C, Cox, T. (Tessa), Craddock, N.J. (Nick), Crooks, L, Curran, S, Curtis, D. (David), Daly, A, Danecek, P, Day, I.N.M. (Ian), Day-Williams, A, Dominiczak, A. (Anna), Down, T, Li, Y. (Yingrui), Dunham, D.M. (David), Durbin, R, Edkins, T. (Ted), Ekong, R. (Rosemary), Ellis, P. (Paul), Evans, D.M. (David), Farooqi, I.S. (Sadaf), Fitzpatrick, D.R. (David), Flicek, P, Floyd, J. (Jamie), Foley, AR, Franklin, C.S. (Christopher), Futema, M, Gallagher, L. (Louise), Gaunt, T.R. (Tom), Geihs, M, Geschwind, D., Greenwood, J.P. (John), Griffin, H, Grozeva, D. (Detelina), Guo, X.S., Guo, X. (Xiuqing), Gurling, H. (Hugh), Hart, D.J. (Deborah), Hendricks, AE, Holmans, P.A. (Peter), Howie, B, Huang, J. (Jian), Huang, L.R., Hubbard, T., Humphries, S.E. (Steve), Hurles, M.E. (Matthew), Hysi, P.G. (Pirro), Jackson, DK, Jamshidi, Y. (Yalda), Joyce, C, Karczewski, KJ, Kaye, J. (Jane), Keane, T, Kemp, J.P., Kennedy, K. (Karen), Kent, A. (Alistair), Keogh, J, Khawaja, F, van Kogelenberg, M., Kolb-Kokocinski, A, Lachance, G, Langford, C. (Cordelia), Lawson, D, Lee, I. van der, Lek, M, Li, R. (Rui), Li, Y.R. (Yun), Liang, J.Q., Lin, H., Liu, R, Lonnqvist, J, Lopes, LR, Lopes, M., MacArthur, DG, Mangino, M. (Massimo), Marchini, J. (Jonathan), Marenne, G., Maslen, J., Mathieson, I. (Iain), McCarthy, S. (Sean), Mcguffin, P. (Peter), Mcintosh, A.M. (Andrew), McKechanie, AG, McQuillin, A. (Andrew), Memari, Y, Metrustry, S. (Sarah), Migone, N, Mitchison, H.M. (Hannah), Moayyeri, A. (Alireza), Morris, A.D. (Andrew), Morris, J, Muddyman, D, Muntoni, F., Northstone, K. (Kate), O'Donovan, M. (Michael), O'Rahilly, S. (Stephen), Onoufriadis, A, Oualkacha, K., Owen, M.J., Palotie, A. (Aarno), Panoutsopoulou, K, Parker, V., Parr, D., Paternoster, L. (Lavinia), Paunio, T, Payne, F. (Felicity), Payne, SJ, Perry, J.B. (John), Pietiläinen, O.P.H. (Olli), Plagnol, V, Pollitt, RC, Porteous, D.J. (David J.), Povey, S. (Sue), Quail, MA, Quaye, L. (Lydia), Raymond, FL, Rehnström, K. (Karola), Richards, J.B. (Brent), Ridout, CK, Ring, S.M. (Susan), Ritchie, GRS, Roberts, N. (Nicola), Robinson, RL, Savage, D.B. (David), Scambler, P., Schiffels, S, Schmidts, M, Schoenmakers, N. (Nadia), Scott, RH, Semple, R.K. (Robert), Serra, E, Sharp, S.I., Shaw, A. (Alison), Shihab, HA, Shin, S.-Y., Skuse, D, Small, K.S. (Kerrin), Smee, C, Smith, B.H. (Blair), Soranzo, N. (Nicole), Southam, L. (Lorraine), Spasic-Boskovic, O, Spector, T.D. (Timothy), St. Clair, D. (David), Stalker, J, Stevens, E, Sun, J.P., Surdulescu, G, Suvisaari, J. (Jaana), Syrris, P, R. Taylor (Rohan), Tian, J., Tobin, M.D. (Martin), Valdes, A.M. (Ana Maria), Vandersteen, AM, Vijayarangakannan, P, Visscher, P.M. (Peter), Wain, L.V. (Louise), Walters, JTR, Wang, G. B., Wang, J. (Jinxia), Wang, Y. (Ying), Ward, K, Wheeler, E. (Eleanor), Whyte, T, Williams, HJ, Williamson, K.A., Wilson, C, Wilson, S.G. (Scott), Wong, K. (Kenny), Xu, CJ, Yang, J. (Jian), Zhang, F. (Feng), Zhang, P.B., Zheng, H.-F. (Hou-Feng), Smith, A.V. (Davey), Fisher, SE, Wilson, J.F. (James F), Cole, T.J. (T.), Fernandez-Orth, D., Bønnelykke, K. (Klaus), Bisgaard, H. (Hans), Pennell, C.E. (Craig), Jaddoe, V.W.V. (Vincent), Dedoussis, G, Timpson, N.J. (Nicholas), Zeggini, E. (Eleftheria), Vitart, V. (Veronique), and Pourcain, B.S. (Beate)
Abstract: Cranial growth and development is a complex process which affects the closely related traits of head circumference (HC) and intracranial volume (ICV). The underlying genetic influences shaping these traits during the transition from childhood to adulthood are little understood, but might include both age-specific genetic factors and low-frequency genetic variation. Here, we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV + HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for lowfrequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carrie
Published: 2019
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8. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

Author: Steward, CA, Roovers, J, Suner, M-M, Gonzalez, JM, Uszczynska-Ratajczak, B, Pervouchine, D, Fitzgerald, S, Viola, M, Stamberger, H, Hamdan, FF, Ceulemans, B, Leroy, P, Nava, C, Lepine, A, Tapanari, E, Keiller, D, Abbs, S, Sanchis-Juan, A, Grozeva, D, Rogers, AS, Diekhans, M, Guigo, R, Petryszak, R, Minassian, BA, Cavalleri, G, Vitsios, D, Petrovski, S, Harrow, J, Flicek, P, Raymond, FL, Lench, NJ, De Jonghe, P, Mudge, JM, Weckhuysen, S, Sisodiya, SM, Frankish, A, Steward, CA, Roovers, J, Suner, M-M, Gonzalez, JM, Uszczynska-Ratajczak, B, Pervouchine, D, Fitzgerald, S, Viola, M, Stamberger, H, Hamdan, FF, Ceulemans, B, Leroy, P, Nava, C, Lepine, A, Tapanari, E, Keiller, D, Abbs, S, Sanchis-Juan, A, Grozeva, D, Rogers, AS, Diekhans, M, Guigo, R, Petryszak, R, Minassian, BA, Cavalleri, G, Vitsios, D, Petrovski, S, Harrow, J, Flicek, P, Raymond, FL, Lench, NJ, De Jonghe, P, Mudge, JM, Weckhuysen, S, Sisodiya, SM, and Frankish, A
Abstract: The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for exome and genome analysis as one potential explanation for a lack of current diagnoses. Therefore, we have updated the GENCODE gene annotation for 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries and other data to build 3,550 putative transcript models. Our annotations increase the transcriptional 'footprint' of these genes by over 674 kb. Using SCN1A as a case study, due to its close phenotype/genotype correlation with Dravet syndrome, we screened 122 people with Dravet syndrome or a similar phenotype with a panel of exon sequences representing eight established genes and identified two de novo SCN1A variants that now - through improved gene annotation - are ascribed to residing among our exons. These two (from 122 screened people, 1.6%) molecular diagnoses carry significant clinical implications. Furthermore, we identified a previously classified SCN1A intronic Dravet syndrome-associated variant that now lies within a deeply conserved exon. Our findings illustrate the potential gains of thorough gene annotation in improving diagnostic yields for genetic disorders.
Published: 2019

9. De Novo Mutations in PDE10A Cause Childhood-Onset Chorea with Bilateral Striatal Lesions

Author: Mencacci, NE, Kamsteeg, E-J, Nakashima, K, R'Bibo, L, Lynch, DS, Balint, B, Willemsen, MAAP, Adams, ME, Wiethoff, S, Suzuki, K, Davies, CH, Ng, J, Meyer, E, Veneziano, L, Giunti, P, Hughes, D, Raymond, FL, Carecchio, M, Zorzi, G, Nardocci, N, Barzaghi, C, Garavaglia, B, Salpietro, V, Hardy, J, Pittman, AM, Houlden, H, Kurian, MA, Kimura, H, Vissers, LELM, Wood, NW, and Bhatia, KP
Subjects: Male, Protein Conformation, Molecular Sequence Data, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Mice, Young Adult, PDE10A chorea, Chorea, Report, Cyclic AMP, Genetics, Animals, Humans, Genetics(clinical), Amino Acid Sequence, Child, Cyclic GMP, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Phosphoric Diester Hydrolases, Middle Aged, Disorders of movement Donders Center for Medical Neuroscience [Radboudumc 3], Magnetic Resonance Imaging, Corpus Striatum, Pedigree, Mutation, Female, Sequence Alignment, Signal Transduction
Abstract: Contains fulltext : 167700.pdf (Publisher’s version ) (Open Access) Chorea is a hyperkinetic movement disorder resulting from dysfunction of striatal medium spiny neurons (MSNs), which form the main output projections from the basal ganglia. Here, we used whole-exome sequencing to unravel the underlying genetic cause in three unrelated individuals with a very similar and unique clinical presentation of childhood-onset chorea and characteristic brain MRI showing symmetrical bilateral striatal lesions. All individuals were identified to carry a de novo heterozygous mutation in PDE10A (c.898T>C [p.Phe300Leu] in two individuals and c.1000T>C [p.Phe334Leu] in one individual), encoding a phosphodiesterase highly and selectively present in MSNs. PDE10A contributes to the regulation of the intracellular levels of cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Both substitutions affect highly conserved amino acids located in the regulatory GAF-B domain, which, by binding to cAMP, stimulates the activity of the PDE10A catalytic domain. In silico modeling showed that the altered residues are located deep in the binding pocket, where they are likely to alter cAMP binding properties. In vitro functional studies showed that neither substitution affects the basal PDE10A activity, but they severely disrupt the stimulatory effect mediated by cAMP binding to the GAF-B domain. The identification of PDE10A mutations as a cause of chorea further motivates the study of cAMP signaling in MSNs and highlights the crucial role of striatal cAMP signaling in the regulation of basal ganglia circuitry. Pharmacological modulation of this pathway could offer promising etiologically targeted treatments for chorea and other hyperkinetic movement disorders.
Published: 2016

10. Comprehensive cancer-predisposition gene testing in an adult multiple primary tumor series shows a broad range of deleterious variants and atypical tumor phenotypes

Author: Whitworth, J, Smith, PS, Martin, J-E, West, H, Luchetti, A, Rodger, F, Clark, G, Carss, K, Stephens, J, Stirrups, K, Penkett, C, Mapeta, R, Ashford, S, Megy, K, Shakeel, H, Ahmed, M, Adlard, J, Barwell, J, Brewer, C, Casey, RT, Armstrong, R, Cole, T, Evans, DG, Fostira, F, Greenhalgh, L, Hanson, H, Henderson, A, Hoffman, J, Izatt, L, Kumar, A, Kwong, A, Lalloo, F, Ong, KR, Paterson, J, Park, S-M, Chen-Shtoyerman, R, Searle, C, Side, L, Skytte, A-B, Snape, K, Woodward, ER, Tischkowitz, MD, Maher, ER, Aitman, T, Alachkar, H, Ali, S, Allen, L, Allsup, D, Ambegaonkar, G, Anderson, J, Antrobus, R, Arno, G, Arumugakani, G, Astle, W, Attwood, A, Austin, S, Bacchelli, C, Bakchoul, T, Bariana, TK, Baxendale, H, Bennett, D, Bethune, C, Bibi, S, Bitner-Glindzicz, M, Bleda, M, Boggard, H, Bolton-Maggs, P, Booth, C, Bradley, JR, Brady, A, Brown, M, Browning, M, Bryson, C, Burns, S, Calleja, P, Canham, N, Carmichael, J, Caulfield, M, Chalmers, E, Chandra, A, Chinnery, P, Chitre, M, Church, C, Clement, E, Clements-Brod, N, Clowes, V, Coghlan, G, Collins, P, Cookson, V, Cooper, N, Corris, P, Creaser-Myers, A, Dacosta, R, Daugherty, L, Davies, S, Davis, J, De Vries, M, Deegan, P, Deevi, SVV, Deshpande, C, Devlin, L, Dewhurst, E, Dixon, P, Doffinger, R, Dormand, N, Drewe, E, Edgar, D, Egner, W, Erber, WN, Erwood, M, Everington, T, Favier, R, Firth, H, Fletcher, D, Flinter, F, Frary, A, Freson, K, Furie, B, Furnell, A, Gale, D, Gardham, A, Gattens, M, Ghali, N, Ghataorhe, PK, Ghurye, R, Gibbs, S, Gilmour, K, Gissen, P, Goddard, S, Gomez, K, Gordins, P, Graf, S, Gräf, S, Greene, D, Greenhalgh, A, Greinacher, A, Grigoriadou, S, Grozeva, D, Hackett, S, Hadinnapola, C, Hague, R, Haimel, M, Halmagyi, C, Hammerton, T, Hart, D, Hayman, G, Heemskerk, JWM, Henderson, R, Hensiek, A, Henskens, Y, Herwadkar, A, Holden, S, Holder, M, Holder, S, Hu, F, Veld, A, Huissoon, A, Humbert, M, Hurst, J, James, R, Jolles, S, Josifova, D, Kazmi, R, Keeling, D, Kelleher, P, Kelly, AM, Kennedy, F, Kiely, D, Kingston, N, Koziell, A, Krishnakumar, D, Kuijpers, TW, Kuijpers, T, Kumararatne, D, Kurian, M, Laffan, MA, Lambert, MP, Allen, HL, Lango-Allen, H, Lawrie, A, Lear, S, Lees, M, Lentaigne, C, Liesner, R, Linger, R, Longhurst, H, Lorenzo, L, Louka, E, Machado, R, Ross, RM, Maclaren, R, Maher, E, Maimaris, J, Mangles, S, Manson, A, Markus, HS, Martin, J, Masati, L, Mathias, M, Matser, V, Maw, A, McDermott, E, McJannet, C, Meacham, S, Meehan, S, Mehta, S, Michaelides, M, Millar, CM, Moledina, S, Moore, A, Morrell, N, Mumford, A, Murng, S, Murphy, E, Nejentsev, S, Noorani, S, Nurden, P, Oksenhendler, E, Othman, S, Ouwehand, WH, Papadia, S, Parker, A, Pasi, J, Patch, C, Payne, J, Peacock, A, Peerlinck, K, Penkett, CJ, Pepke-Zaba, J, Perry, D, Perry, DJ, Pollock, V, Polwarth, G, Ponsford, M, Qasim, W, Quinti, I, Rankin, S, Rankin, J, Raymond, FL, Rayner-Matthews, P, Rehnstrom, K, Reid, E, Rhodes, CJ, Richards, M, Richardson, S, Richter, A, Roberts, I, Rondina, M, Rosser, E, Roughley, C, Roy, N, Rue-Albrecht, K, Samarghitean, C, Sanchis-Juan, A, Sandford, R, Santra, S, Sargur, R, Savic, S, Schotte, G, Schulman, S, Schulze, H, Scott, R, Scully, M, Seneviratne, S, Sewell, C, Shamardina, O, Shipley, D, Simeoni, I, Sivapalaratnam, S, Smith, KGC, Sohal, A, Southgate, L, Staines, S, Staples, E, Stark, H, Stauss, H, Stein, P, Stock, S, Suntharalingam, J, Talks, K, Tan, Y, Thachil, J, Thaventhiran, J, Thomas, E, Thomas, M, Thompson, D, Thrasher, A, Tischkowitz, M, Titterton, C, Toh, C-H, Toshner, M, Treacy, C, Trembath, R, Tuna, S, Turek, W, Turro, E, Van Geet, C, Veltman, M, Vogt, J, Von Ziegenweldt, J, Noordegraaf, AV, Wakeling, E, Wanjiku, I, Warner, TQ, Wassmer, E, Watkins, H, Watt, C, Webster, N, Welch, S, Westbury, S, Wharton, J, Whitehorn, D, Wilkins, M, Willcocks, L, Williamson, C, Woods, G, Wort, J, Yeatman, N, Yong, P, Young, T, and Yu, P
Abstract: Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families. Despite previous negative genetic assessment and molecular investigations, pathogenic variants in moderate- and high-risk CPGs were detected in 67/440 (15.2%) probands. WGS detected variants that would not be (or were not) detected by targeted resequencing strategies, including low-frequency structural variants (6/440 [1.4%] probands). In most individuals with a germline variant assessed as pathogenic or likely pathogenic (P/LP), at least one of their tumor types was characteristic of variants in the relevant CPG. However, in 29 probands (42.2% of those with a P/LP variant), the tumor phenotype appeared discordant. The frequency of individuals with truncating or splice-site CPG variants and at least one discordant tumor type was significantly higher than in a control population (χ2 = 43.642; p ≤ 0.0001). 2/67 (3%) probands with P/LP variants had evidence of multiple inherited neoplasia allele syndrome (MINAS) with deleterious variants in two CPGs. Together with variant detection rates from a previous series of similarly ascertained MPT-affected individuals, the present results suggest that first-line comprehensive CPG analysis in an MPT cohort referred to clinical genetics services would detect a deleterious variant in about a third of individuals.
Published: 2018

11. Novel homozygous splicing mutations in ARL2BP cause autosomal recessive retinitis pigmentosa

Author: Fiorentino, A, Yu, J, Arno, G, Pontikos, N, Halford, S, Broadgate, S, Michaelides, M, Carss, KJ, Raymond, FL, Cheetham, ME, Webster, AR, Downes, SM, Hardcastle, AJ, NIHR-BioResource Rare Diseases Consortium, and UK Inherited Retinal Dystrophy Consortium
Abstract: Purpose: Mutations in ARL2BP, encoding ADP-ribosylation factor-like 2 binding protein, have recently been implicated as a cause of autosomal recessive retinitis pigmentosa (arRP), with three homozygous variants identified to date. In this study, we performed next-generation sequencing to reveal additional arRP cases associated with ARL2BP variants. Methods: Whole-genome sequencing (WGS) or whole-exome sequencing (WES) was performed in 1,051 unrelated individuals recruited for the UK Inherited Retinal Disease Consortium and NIHR-BioResource Rare Diseases research studies. Sanger sequencing was used to validate the next-generation sequencing data, and reverse transcriptase (RT)–PCR analysis was performed on RNA extracted from blood from affected individuals to test for altered splicing of ARL2BP. Detailed phenotyping was performed, including clinical evaluation, electroretinography, fundus photography, fundus autofluorescence imaging, and spectral-domain optical coherence tomography. Results: Homozygous variants in ARL2BP (NM_012106.3) were identified in two unrelated individuals with RP. The variants, c.207+1G>A and c.390+5G>A, at conserved splice donor sites for intron 3 and intron 5, respectively, were predicted to alter the pre-mRNA splicing of ARL2BP. RT–PCR spanning the affected introns revealed that both variants caused abnormal splicing of ARL2BP in samples from affected individuals. Conclusions: This study identified two homozygous variants in ARL2BP as a rare cause of arRP. Further studies are required to define the underlying disease mechanism causing retinal degeneration as a result of mutations in ARL2BP and any phenotype-genotype correlation associated with residual levels of the wild-type transcript.
Published: 2018

12. Bi-allelic Mutations in NDUFA6 Establish Its Role in Early-Onset Isolated Mitochondrial Complex I Deficiency

Author: Alston, CL, Heidler, J, Dibley, MG, Kremer, LS, Taylor, LS, Fratter, C, French, CE, Glasgow, RIC, Feichtinger, RG, Delon, I, Pagnamenta, AT, Dolling, H, Lemonde, H, Aiton, N, Bjørnstad, A, Henneke, L, Gärtner, J, Thiele, H, Tauchmannova, K, Quaghebeur, G, Houstek, J, Sperl, W, Raymond, FL, Prokisch, H, Mayr, JA, McFarland, R, Poulton, J, Ryan, MT, Wittig, I, Henneke, M, Taylor, RW, French, Courtney [0000-0001-7620-1544], Dolling, Helen [0000-0001-6279-3622], Raymond, Lucy [0000-0003-2652-3355], and Apollo - University of Cambridge Repository
Subjects: Male, Electron Transport Complex I, Mitochondrial Diseases, complex I, complexome profiling, Infant, Fibroblasts, Mitochondria, Mitochondrial Proteins, Complex I, Complexome Profiling, Mitochondrial Disease, Ndufa6, mitochondrial disease, Genetic Heterogeneity, NDUFA6, Phenotype, Report, Mutation, Humans, Female, ddc:610, Amino Acid Sequence, Sequence Alignment, Alleles
Abstract: Isolated complex I deficiency is a common biochemical phenotype observed in pediatric mitochondrial disease and often arises as a consequence of pathogenic variants affecting one of the similar to 65 genes encoding the complex I structural subunits or assembly factors. Such genetic heterogeneity means that application of next-generation sequencing technologies to undiagnosed cohorts has been a catalyst for genetic diagnosis and gene-disease associations. We describe the clinical and molecular genetic investigations of four unrelated children who presented with neuroradiological findings and/or elevated lactate levels, highly suggestive of an underlying mitochondrial diagnosis. Next-generation sequencing identified bi-allelic variants in NDUFA6, encoding a 15 kDa LYR-motif-containing complex I subunit that forms part of the Q-module. Functional investigations using subjects' fibroblast cell lines demonstrated complex I assembly defects, which were characterized in detail by mass-spectrometry-based complexome profiling. This confirmed a marked reduction in incorporated NDUFA6 and a concomitant reduction in other Q-module subunits, including NDUFAB1, NDUFA7, and NDUFA12. Lentiviral transduction of subjects' fibroblasts showed normalization of complex I. These data also support supercomplex formation, whereby the similar to 830 kDa complex I intermediate (consisting of the P- and Q-modules) is in complex with assembled complex III and IV holoenzymes despite lacking the N-module. Interestingly, RNA-sequencing data provided evidence that the consensus RefSeq accession number does not correspond to the predominant transcript in clinically relevant tissues, prompting revision of the NDUFA6 RefSeq transcript and highlighting not only the importance of thorough variant interpretation but also the assessment of appropriate transcripts for analysis.
Published: 2018

13. Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data

Author: Farmery, JHR, Smith, ML, Lynch, AG, Huissoon, A, Furnell, A, Mead, A, Levine, AP, Manzur, A, Thrasher, A, Greenhalgh, A, Parker, A, Sanchis-Juan, A, Richter, A, Gardham, A, Lawrie, A, Sohal, A, Creaser-Myers, A, Frary, A, Greinacher, A, Themistocleous, A, Peacock, AJ, Marshall, A, Mumford, A, Rice, A, Webster, A, Brady, A, Koziell, A, Manson, A, Chandra, A, Hensiek, A, In't Veld, AH, Maw, A, Kelly, AM, Moore, A, Noordegraaf, AV, Attwood, A, Herwadkar, A, Ghofrani, A, Houweling, AC, Girerd, B, Furie, B, Treacy, CM, Millar, CM, Sewell, C, Roughley, C, Titterton, C, Williamson, C, Hadinnapola, C, Deshpande, C, Toh, C-H, Bacchelli, C, Patch, C, Van Geet, C, Babbs, C, Bryson, C, Penkett, CJ, Rhodes, CJ, Watt, C, Bethune, C, Booth, C, Lentaigne, C, McJannet, C, Church, C, French, C, Samarghitean, C, Halmagyi, C, Gale, D, Greene, D, Hart, D, Allsup, D, Bennett, D, Edgar, D, Kiely, DG, Gosal, D, Perry, DJ, Keeling, D, Montani, D, Shipley, D, Whitehorn, D, Fletcher, D, Krishnakumar, D, Grozeva, D, Kumararatne, D, Thompson, D, Josifova, D, Maher, E, Wong, EKS, Murphy, E, Dewhurst, E, Louka, E, Rosser, E, Chalmers, E, Colby, E, Drewe, E, McDermott, E, Thomas, E, Staples, E, Clement, E, Matthews, E, Wakeling, E, Oksenhendler, E, Turro, E, Reid, E, Wassmer, E, Raymond, FL, Hu, F, Kennedy, F, Soubrier, F, Flinter, F, Kovacs, G, Polwarth, G, Ambegaonkar, G, Arno, G, Hudson, G, Woods, G, Coghlan, G, Hayman, G, Arumugakani, G, Schotte, G, Cook, HT, Alachkar, H, Allen, HL, Lango-Allen, H, Stark, H, Stauss, H, Schulze, H, Boggard, HJ, Baxendale, H, Dolling, H, Firth, H, Gall, H, Watson, H, Longhurst, H, Markus, HS, Watkins, H, Simeoni, I, Emmerson, I, Roberts, I, Quinti, I, Wanjiku, I, Gibbs, JSR, Thaventhiran, J, Whitworth, J, Hurst, J, Collins, J, Suntharalingam, J, Payne, J, Thachil, J, Martin, JM, Martin, J, Carmichael, J, Maimaris, J, Paterson, J, Pepke-Zaba, J, Heemskerk, JWM, Gebhart, J, Davis, J, Pasi, J, Bradley, JR, Wharton, J, Stephens, J, Rankin, J, Anderson, J, Vogt, J, Von Ziegenweldt, J, Rehnstrom, K, Megy, K, Talks, K, Peerlinck, K, Yates, K, Freson, K, Stirrups, K, Gomez, K, Smith, KGC, Carss, K, Rue-Albrecht, K, Gilmour, K, Masati, L, Scelsi, L, Southgate, L, Ranganathan, L, Ginsberg, L, Devlin, L, Willcocks, L, Ormondroyd, L, Lorenzo, L, Harper, L, Allen, L, Daugherty, L, Chitre, M, Kurian, M, Humbert, M, Tischkowitz, M, Bitner-Glindzicz, M, Erwood, M, Scully, M, Veltman, M, Caulfield, M, Layton, M, McCarthy, M, Ponsford, M, Toshner, M, Bleda, M, Wilkins, M, Mathias, M, Reilly, M, Afzal, M, Brown, M, Rondina, M, Stubbs, M, Haimel, M, Lees, M, Laffan, MA, Browning, M, Gattens, M, Richards, M, Michaelides, M, Lambert, MP, Makris, M, De Vries, M, Mahdi-Rogers, M, Saleem, M, Thomas, M, Holder, M, Eyries, M, Clements-Brod, N, Canham, N, Dormand, N, Van Zuydam, N, Kingston, N, Ghali, N, Cooper, N, Morrell, NW, Yeatman, N, Roy, N, Shamardina, O, Alavijeh, OS, Gresele, P, Nurden, P, Chinnery, P, Deegan, P, Yong, P, Yu-Wai-Man, P, Corris, PA, Calleja, P, Gissen, P, Bolton-Maggs, P, Rayner-Matthews, P, Ghataorhe, PK, Gordins, P, Stein, P, Collins, P, Dixon, P, Kelleher, P, Ancliff, P, Yu, P, Tait, RC, Linger, R, Doffinger, R, Machado, R, Kazmi, R, Sargur, R, Favier, R, Tan, R, Liesner, R, Antrobus, R, Sandford, R, Scott, R, Trembath, R, Horvath, R, Hadden, R, MackenzieRoss, RV, Henderson, R, MacLaren, R, James, R, Ghurye, R, DaCosta, R, Hague, R, Mapeta, R, Armstrong, R, Noorani, S, Murng, S, Santra, S, Tuna, S, Johnson, S, Chong, S, Lear, S, Walker, S, Goddard, S, Mangles, S, Westbury, S, Mehta, S, Hackett, S, Nejentsev, S, Moledina, S, Bibi, S, Meehan, S, Othman, S, Revel-Vilk, S, Holden, S, McGowan, S, Staines, S, Savic, S, Burns, S, Grigoriadou, S, Papadia, S, Ashford, S, Schulman, S, Ali, S, Park, S-M, Davies, S, Stock, S, Deevi, SVV, Graf, S, Ghio, S, Wort, SJ, Jolles, S, Austin, S, Welch, S, Meacham, S, Rankin, S, Seneviratne, S, Holder, S, Sivapalaratnam, S, Richardson, S, Kuijpers, T, Kuijpers, TW, Bariana, TK, Bakchoul, T, Everington, T, Renton, T, Young, T, Aitman, T, Warner, TQ, Vale, T, Hammerton, T, Pollock, V, Matser, V, Cookson, V, Clowes, V, Qasim, W, Wei, W, Erber, WN, Ouwehand, WH, Astle, W, Egner, W, Turek, W, Henskens, Y, Tan, Y, Lynch, Andy G [0000-0002-7876-7338], Apollo - University of Cambridge Repository, Medical Research Council (MRC), and British Heart Foundation
Subjects: Whole genome sequencing, 0303 health sciences, Multidisciplinary, Science & Technology, lcsh:R, lcsh:Medicine, Computational biology, Biology, Telomere, Multidisciplinary Sciences, 03 medical and health sciences, 0302 clinical medicine, NIHR BioResource - Rare Diseases, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Science & Technology - Other Topics, lcsh:Q, Ploidy, lcsh:Science, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Correction to: Scientific Reports https://doi.org/10.1038/s41598-017-14403-y, published online 22 January 2018 The original version of this Article contained a typographical error in the spelling of the consortium member Patrick Yu-Wai-Man which was incorrectly given as Patrick Yu Wai Man. In addition, a supplementary file containing additional algorithms and analysis was omitted from the original version of this Article. These errors have now been corrected in the HTML and PDF versions of the Article.
Published: 2018

14. De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures

Author: Raymond, FL, Raymond, Lucy [0000-0003-2652-3355], and Apollo - University of Cambridge Repository
Subjects: developmental delay, recurrent de novo truncating mutations, actin cytoskeleton, lamellipodia, autism, WAVE1 complex, macromolecular substances, WASF1, neurodevelopmental disorder, seizures
Abstract: Next-generation sequencing has been invaluable in the elucidation of the genetic etiology of many subtypes of intellectual disability in recent years. Here, using exome sequencing and whole genome sequencing, three de novo truncating mutations were identified in Wiskott- Aldrich syndrome protein family member 1 (WASF1) in five unrelated individuals with moderate to profound intellectual disability with autistic features and seizures. WASF1, also known as WAVE1, is part of the WAVE complex and acts as a mediator between Rac-GTPase and actin to induce actin polymerization. The three mutations connected using Matchmaker Exchange were c.1516C>T [p.Arg506Ter], which occurs in three unrelated individuals, c.1558C>T [p.Gln520Ter], and c.1482delinsGCCAGG [p.Ile494MetfsTer23]. All three variants are predicted to partially or fully disrupt the C-terminal actin-binding WCA domain. Functional studies using fibroblast cells from two affected individuals with the c.1516C>T mutation showed a truncated WASF1/WAVE1 protein and a defect in actin remodeling. This study provides evidence that de novo heterozygous mutations in WASF1 cause a rare form of intellectual disability.
Published: 2018

15. SYT1-associated neurodevelopmental disorder: a case series

Author: Baker, K, Gordon, SL, Melland, H, Bumbak, F, Scott, DJ, Jiang, TJ, Owen, D, Turner, BJ, Boyd, SG, Rossi, M, Al-Raqad, M, Elpeleg, O, Peck, D, Mancini, GMS, Wilke, M, Zollino, M, Marangi, G, Weigand, H, Borggraefe, I, Haack, T, Stark, Z, Sadedin, S, Tan, TY, Jiang, Y, Gibbs, RA, Ellingwood, S, Amaral, M, Kelley, W, Kurian, MA, Cousin, MA, Raymond, FL, Baker, K, Gordon, SL, Melland, H, Bumbak, F, Scott, DJ, Jiang, TJ, Owen, D, Turner, BJ, Boyd, SG, Rossi, M, Al-Raqad, M, Elpeleg, O, Peck, D, Mancini, GMS, Wilke, M, Zollino, M, Marangi, G, Weigand, H, Borggraefe, I, Haack, T, Stark, Z, Sadedin, S, Tan, TY, Jiang, Y, Gibbs, RA, Ellingwood, S, Amaral, M, Kelley, W, Kurian, MA, Cousin, MA, and Raymond, FL
Abstract: Synaptotagmin 1 (SYT1) is a critical mediator of fast, synchronous, calcium-dependent neurotransmitter release and also modulates synaptic vesicle endocytosis. This paper describes 11 patients with de novo heterozygous missense mutations in SYT1. All mutations alter highly conserved residues, and cluster in two regions of the SYT1 C2B domain at positions Met303 (M303K), Asp304 (D304G), Asp366 (D366E), Ile368 (I368T) and Asn371 (N371K). Phenotypic features include infantile hypotonia, congenital ophthalmic abnormalities, childhood-onset hyperkinetic movement disorders, motor stereotypies, and developmental delay varying in severity from moderate to profound. Behavioural characteristics include sleep disturbance and episodic agitation. Absence of epileptic seizures and normal orbitofrontal head circumference are important negative features. Structural MRI is unremarkable but EEG disturbance is universal, characterized by intermittent low frequency high amplitude oscillations. The functional impact of these five de novo SYT1 mutations has been assessed by expressing rat SYT1 protein containing the equivalent human variants in wild-type mouse primary hippocampal cultures. All mutant forms of SYT1 were expressed at levels approximately equal to endogenous wild-type protein, and correctly localized to nerve terminals at rest, except for SYT1M303K, which was expressed at a lower level and failed to localize at nerve terminals. Following stimulation, SYT1I368T and SYT1N371K relocalized to nerve terminals at least as efficiently as wild-type SYT1. However, SYT1D304G and SYT1D366E failed to relocalize to nerve terminals following stimulation, indicative of impairments in endocytic retrieval and trafficking of SYT1. In addition, the presence of SYT1 variants at nerve terminals induced a slowing of exocytic rate following sustained action potential stimulation. The extent of disturbance to synaptic vesicle kinetics is mirrored by the severity of the affected individuals' phenot
Published: 2018

16. Specific Alleles of CLN7/MFSD8, a Protein That Localizes to Photoreceptor Synaptic Terminals, Cause a Spectrum of Nonsyndromic Retinal Dystrophy

Author: Khan, KN, El-Asrag, ME, Ku, CA, Holder, GE, McKibbin, M, Arno, G, Poulter, JA, Carss, K, Bommireddy, T, Bagheri, S, Bakall, B, Scholl, HP, Raymond, FL, Toomes, C, Inglehearn, CF, Pennesi, ME, Moore, AT, Michaelides, M, Webster, AR, Ali, M, and for NIHR BioResource-Rare Diseases and UK Inherited Retinal Dise
Subjects: genetic structures, sense organs
Abstract: Purpose: Recessive mutations in CLN7/MFSD8 usually cause variant late-infantile onset neuronal ceroid lipofuscinosis (vLINCL), a poorly understood neurodegenerative condition, though mutations may also cause nonsyndromic maculopathy. A series of 12 patients with nonsyndromic retinopathy due to novel CLN7/MFSD8 mutation combinations were investigated in this study. Methods: Affected patients and their family members were recruited in ophthalmic clinics at each center where they were examined by retinal imaging and detailed electrophysiology. Whole exome or genome next generation sequencing was performed on genomic DNA from at least one affected family member. Immunofluorescence confocal microscopy of murine retina cross-sections were used to localize the protein. Results: Compound heterozygous alleles were identified in six cases, one of which was always p.Glu336Gln. Such combinations resulted in isolated macular disease. Six further cases were homozygous for the variant p.Met454Thr, identified as a founder mutation of South Asian origin. Those patients had widespread generalized retinal disease, characterized by electroretinography as a rod-cone dystrophy with severe macular involvement. In addition, the photopic single flash electroretinograms demonstrated a reduced b- to a-wave amplitude ratio, suggesting dysfunction occurring after phototransduction. Immunohistology identified MFSD8 in the outer plexiform layer of the retina, a site rich in photoreceptor synapses. Conclusions: This study highlights a hierarchy of MFSD8 variant severity, predicting three consequences of mutation: (1) nonsyndromic localized maculopathy, (2) nonsyndromic widespread retinopathy, or (3) syndromic neurological disease. The data also shed light on the underlying pathogenesis by implicating the photoreceptor synaptic terminals as the major site of retinal disease.
Published: 2017

17. Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia

Author: Meyer E, Carss KJ, Rankin J, Nichols JM, Grozeva D, Joseph AP, Mencacci NE, Papandreou A, Ng J, Barral S, Ngoh A, Ben-Pazi H, Willemsen MA, Arkadir D, Barnicoat A, Bergman H, Bhate S, Boys A, Darin N, Foulds N, Gutowski N, Hills A, Houlden H, Hurst JA, Israel Z, Kaminska M, Limousin P, Lumsden D, McKee S, Misra S, Mohammed SS, Nakou V, Nicolai J, Nilsson M, Pall H, Peall KJ, Peters GB, Prabhakar P, Reuter MS, Rump P, Segel R, Sinnema M, Smith M, Turnpenny P, White SM, Wieczorek D, Wiethoff S, Wilson BT, Winter G, Wragg C, Pope S, Heales SJ, Morrogh D, UK10K Consortium, Deciphering Developmental Disorders Study, NIHR BioResource Rare Diseases Consortium, Pittman A, Carr LJ, Pérez-Dueñas B, Lin JP, Reis A, Gahl WA, Toro C, Bhatia KP, Wood NW, Kamsteeg EJ, Chong WK, Gissen P, Topf M, Dale RC, Chubb JR, Raymond FL, Kurian MA, and Apollo - University of Cambridge Repository
Subjects: DNA-Binding Proteins, Histones, Male, Dystonia, Adolescent, Lysine, Mutation, Histone Methyltransferases, Humans, Nuclear Proteins, Female, Histone-Lysine N-Methyltransferase, Methylation
Abstract: Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings. Over time, the majority of affected individuals developed prominent cervical, cranial and laryngeal dystonia. Marked clinical benefit, including the restoration of independent ambulation in some cases, was observed following deep brain stimulation (DBS). These findings highlight a clinically recognizable and potentially treatable form of genetic dystonia, demonstrating the crucial role of KMT2B in the physiological control of voluntary movement.
Published: 2017

18. Neurofibromatosis 2 in a patient with a de novo balanced reciprocal translocation 46,X,t(X;22)(p 11.2;q11.2)

Author: Bovie, C, Holden, ST, Schroer, A, Smith, E, Trump, D, and Raymond, FL
Subjects: Neurofibromatosis -- Genetic aspects -- Research -- Diagnosis -- Care and treatment, Medical genetics -- Research, Health
Abstract: Neurofibromatosis 2 (NF2) is an autosomal dominant disease associated with mutations in the gene NF2. (1) In clinical practice, the diagnosis is made if a patient satisfies the 1987 National [...]
Published: 2003

19. Fetal echocardiography as a predictor of chromosomal abnormality

Author: Raymond, FL, Simpson, JM, Sharland, GK, and Ogilvie, CM Mackie
Published: 1997

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

Author: Walter, K, Min, JL, Huang, J, Crooks, L, Memari, Y, McCarthy, S, Perry, JRB, Xu, C, Futema, M, Lawson, D, Iotchkova, V, Schiffels, S, Hendricks, AE, Danecek, P, Li, R, Floyd, J, Wain, LV, Barroso, I, Humphries, SE, Hurles, ME, Zeggini, E, Barrett, JC, Plagnol, V, Richards, JB, Greenwood, CMT, Timpson, NJ, Durbin, R, Soranzo, N, Bala, S, Clapham, P, Coates, G, Cox, T, Daly, A, Du, Y, Edkins, S, Ellis, P, Flicek, P, Guo, X, Huang, L, Jackson, DK, Joyce, C, Keane, T, Kolb-Kokocinski, A, Langford, C, Li, Y, Liang, J, Lin, H, Liu, R, Maslen, J, Muddyman, D, Quail, MA, Stalker, J, Sun, J, Tian, J, Wang, G, Wang, J, Wang, Y, Wong, K, Zhang, P, Birney, E, Boustred, C, Chen, L, Clement, G, Cocca, M, Smith, GD, Day, INM, Day-Williams, A, Down, T, Dunham, I, Evans, DM, Gaunt, TR, Geihs, M, Hart, D, Howie, B, Hubbard, T, Hysi, P, Jamshidi, Y, Karczewski, KJ, Kemp, JP, Lachance, G, Lek, M, Lopes, M, MacArthur, DG, Marchini, J, Mangino, M, Mathieson, I, Metrustry, S, Moayyeri, A, Northstone, K, Panoutsopoulou, K, Paternoster, L, Quaye, L, Ring, S, Ritchie, GRS, Shihab, HA, Shin, S-Y, Small, KS, Artigas, MS, Southam, L, Spector, TD, St Pourcain, B, Surdulescu, G, Tachmazidou, I, Tobin, MD, Valdes, AM, Visscher, PM, Ward, K, Wilson, SG, Yang, J, Zhang, F, Zheng, H-F, Anney, R, Ayub, M, Blackwood, D, Bolton, PF, Breen, G, Collier, DA, Craddock, N, Curran, S, Curtis, D, Gallagher, L, Geschwind, D, Gurling, H, Holmans, P, Lee, I, Lonnqvist, J, McGuffin, P, McIntosh, AM, McKechanie, AG, McQuillin, A, Morris, J, O'Donovan, MC, Owen, MJ, Palotie, A, Parr, JR, Paunio, T, Pietilainen, O, Rehnstrom, K, Sharp, SI, Skuse, D, St Clair, D, Suvisaari, J, Walters, JTR, Williams, HJ, Bochukova, E, Bounds, R, Dominiczak, A, Farooqi, IS, Keogh, J, Marenne, GL, Morris, A, O'Rahilly, S, Porteous, DJ, Smith, BH, Wheeler, E, Al Turki, S, Anderson, CA, Antony, D, Beales, P, Bentham, J, Bhattacharya, S, Calissano, M, Carss, K, Chatterjee, K, Cirak, S, Cosgrove, C, Fitzpatrick, DR, Foley, AR, Franklin, CS, Grozeva, D, Mitchison, HM, Muntoni, F, Onoufriadis, A, Parker, V, Payne, F, Raymond, FL, Roberts, N, Savage, DB, Scambler, P, Schmidts, M, Schoenmakers, N, Semple, RK, Serra, E, Spasic-Boskovic, O, Stevens, E, van Kogelenberg, M, Vijayarangakannan, P, Williamson, KA, Wilson, C, Whyte, T, Ciampi, A, Oualkacha, K, Bobrow, M, Griffin, H, Kaye, J, Kennedy, K, Kent, A, Smee, C, Charlton, R, Ekong, R, Khawaja, F, Lopes, LR, Migone, N, Payne, SJ, Pollitt, RC, Povey, S, Ridout, CK, Robinson, RL, Scott, RH, Shaw, A, Syrris, P, Taylor, R, Vandersteen, AM, Amuzu, A, Casas, JP, Chambers, JC, Dedoussis, G, Gambaro, G, Gasparini, P, Isaacs, A, Johnson, J, Kleber, ME, Kooner, JS, Langenberg, C, Luan, J, Malerba, G, Maerz, W, Matchan, A, Morris, R, Nordestgaard, BG, Benn, M, Scott, RA, Toniolo, D, Traglia, M, Tybjaerg-Hansen, A, van Duijn, CM, van Leeuwen, EM, Varbo, A, Whincup, P, Zaza, G, Zhang, W, Walter, K, Min, JL, Huang, J, Crooks, L, Memari, Y, McCarthy, S, Perry, JRB, Xu, C, Futema, M, Lawson, D, Iotchkova, V, Schiffels, S, Hendricks, AE, Danecek, P, Li, R, Floyd, J, Wain, LV, Barroso, I, Humphries, SE, Hurles, ME, Zeggini, E, Barrett, JC, Plagnol, V, Richards, JB, Greenwood, CMT, Timpson, NJ, Durbin, R, Soranzo, N, Bala, S, Clapham, P, Coates, G, Cox, T, Daly, A, Du, Y, Edkins, S, Ellis, P, Flicek, P, Guo, X, Huang, L, Jackson, DK, Joyce, C, Keane, T, Kolb-Kokocinski, A, Langford, C, Li, Y, Liang, J, Lin, H, Liu, R, Maslen, J, Muddyman, D, Quail, MA, Stalker, J, Sun, J, Tian, J, Wang, G, Wang, J, Wang, Y, Wong, K, Zhang, P, Birney, E, Boustred, C, Chen, L, Clement, G, Cocca, M, Smith, GD, Day, INM, Day-Williams, A, Down, T, Dunham, I, Evans, DM, Gaunt, TR, Geihs, M, Hart, D, Howie, B, Hubbard, T, Hysi, P, Jamshidi, Y, Karczewski, KJ, Kemp, JP, Lachance, G, Lek, M, Lopes, M, MacArthur, DG, Marchini, J, Mangino, M, Mathieson, I, Metrustry, S, Moayyeri, A, Northstone, K, Panoutsopoulou, K, Paternoster, L, Quaye, L, Ring, S, Ritchie, GRS, Shihab, HA, Shin, S-Y, Small, KS, Artigas, MS, Southam, L, Spector, TD, St Pourcain, B, Surdulescu, G, Tachmazidou, I, Tobin, MD, Valdes, AM, Visscher, PM, Ward, K, Wilson, SG, Yang, J, Zhang, F, Zheng, H-F, Anney, R, Ayub, M, Blackwood, D, Bolton, PF, Breen, G, Collier, DA, Craddock, N, Curran, S, Curtis, D, Gallagher, L, Geschwind, D, Gurling, H, Holmans, P, Lee, I, Lonnqvist, J, McGuffin, P, McIntosh, AM, McKechanie, AG, McQuillin, A, Morris, J, O'Donovan, MC, Owen, MJ, Palotie, A, Parr, JR, Paunio, T, Pietilainen, O, Rehnstrom, K, Sharp, SI, Skuse, D, St Clair, D, Suvisaari, J, Walters, JTR, Williams, HJ, Bochukova, E, Bounds, R, Dominiczak, A, Farooqi, IS, Keogh, J, Marenne, GL, Morris, A, O'Rahilly, S, Porteous, DJ, Smith, BH, Wheeler, E, Al Turki, S, Anderson, CA, Antony, D, Beales, P, Bentham, J, Bhattacharya, S, Calissano, M, Carss, K, Chatterjee, K, Cirak, S, Cosgrove, C, Fitzpatrick, DR, Foley, AR, Franklin, CS, Grozeva, D, Mitchison, HM, Muntoni, F, Onoufriadis, A, Parker, V, Payne, F, Raymond, FL, Roberts, N, Savage, DB, Scambler, P, Schmidts, M, Schoenmakers, N, Semple, RK, Serra, E, Spasic-Boskovic, O, Stevens, E, van Kogelenberg, M, Vijayarangakannan, P, Williamson, KA, Wilson, C, Whyte, T, Ciampi, A, Oualkacha, K, Bobrow, M, Griffin, H, Kaye, J, Kennedy, K, Kent, A, Smee, C, Charlton, R, Ekong, R, Khawaja, F, Lopes, LR, Migone, N, Payne, SJ, Pollitt, RC, Povey, S, Ridout, CK, Robinson, RL, Scott, RH, Shaw, A, Syrris, P, Taylor, R, Vandersteen, AM, Amuzu, A, Casas, JP, Chambers, JC, Dedoussis, G, Gambaro, G, Gasparini, P, Isaacs, A, Johnson, J, Kleber, ME, Kooner, JS, Langenberg, C, Luan, J, Malerba, G, Maerz, W, Matchan, A, Morris, R, Nordestgaard, BG, Benn, M, Scott, RA, Toniolo, D, Traglia, M, Tybjaerg-Hansen, A, van Duijn, CM, van Leeuwen, EM, Varbo, A, Whincup, P, Zaza, G, and Zhang, W
Abstract: 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, 7×) or exomes (high read depth, 80×) 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.
Published: 2015

21. Mutations in a novel member of the FERM family, FRMD7 cause X-linked idiopathic congenital nystagmus (NYS1)

Author: Tarpey, P, Thomas, S, Sarvananthan, N, Mallya, U, Lisgo, S, Talbot, CJ, Roberts, EO, Awan, M, Surendran, M, McLean, RJ, Reinecke, RD, Langmann, A, Lindner, S, Koch, M, Woodruff, G, Gale, R, Degg, C, Droutsas, K, Asproudis, I, Zubcov, AA, Pieh, C, Veal, CD, Machado, RD, Backhouse, OC, Baumber, L, Jain, S, Constantinescu, CS, Brodsky, MC, Hunter, DG, Hertle, RW, Read, RJ, Edkins, S, O’Meara, S, Parker, A, Stevens, C, Teague, J, Wooster, R, Futreal, PA, Trembath, RC, Stratton, MR, Raymond, FL, and Gottlob, I
Subjects: Male, Chromosomes, Human, X, genetic structures, Eye Movements, Genetic Linkage, Brain, Chromosome Mapping, Gene Expression Regulation, Developmental, Membrane Proteins, eye diseases, Article, Retina, Pedigree, Cytoskeletal Proteins, Genes, X-Linked, Mutation, Humans, Female, Nystagmus, Congenital
Abstract: Idiopathic congenital nystagmus is characterized by involuntary, periodic, predominantly horizontal oscillations of both eyes. We identified 22 mutations in FRMD7 in 26 families with X-linked idiopathic congenital nystagmus. Screening of 42 singleton cases of idiopathic congenital nystagmus (28 male, 14 females) yielded three mutations (7%). We found restricted expression of FRMD7 in human embryonic brain and developing neural retina, suggesting a specific role in the control of eye movement and gaze stability.
Published: 2006

22. CNS involvement in OFD1 syndrome: a clinical, molecular, and neuroimaging study

Author: Del Giudice, E, Macca, M, Imperati, F, D'Amico, A, Parent, P, Pasquier, L, Layet, V, Lyonnet, S, Stamboul Darmency, V, Thauvin Robinet, C, Franco, B, OFD1 Collaborative Group including Bankier A, Oral Facial Digital Type I., White, S, Collins, F, Gardner, M, Keeling, Sl, Tan, T, Mcgaughran, J, Mckenzie, F, Lhotta, K, Abdulla, F, Destree, A, Devriendt, K, Matthijs, G, Ferrier, R, Mcleod, Dr, Friedman, Jm, Heran, H, Graham, Ge, Klatt, R, Teebi, A, Jensen, P, Gilbert, B, Marlin, S, Trousseau, A, Toutain, A, David, A, Odent, S, Héron, D, Burglen, L, Rio, M, Jouk, Ps, Plessis, G, Lespinasse, J, Giuliano, F, Turc Carel, C, Betz, Rc, Heim, S, Klehr Martinelli, M, Kotzot, D, Minnerop, M, Schell Apacik, C, Gal, A, Orth, U, Gillessen Kaesbach, G, Zoll, B, Mucke, J, Tzschach, A, Godde, E, Carmi, R, Brunetti, N, Scarcella, A, Castelluccio, P, Castellan, C, Gerola, O, Bigoni, S, Zelante, L, Foggia, S, Sabato, A, Bianchini, G, Nuova, As, Virdis, R, Ferrero, Giovanni Battista, Selicorni, A, Gurrieri, F, Cuore, S, Megarbane, A, Chiong, Ma, Cutiongco, Em, Obersztyn, E, Kutkowska Kazmierczak, A, Mota, Cr, de Magalhaes, D, Stevanovic, G, Del Pozo JS, Barcina, Mg, Iwarsson, E, Graber, V, Okhowat, R, Shinzel, A, Brunner, Hg, Krapels, I, Hovers, V, Beemer, Fa, Terhal, P, Rump, P, Elcioglu, N, Toprak, O, Burn, J, Henderson, A, Jones, E, Dean, J, Castle, B, Macdonald, F, Farndon, P, Williams, D, Homfray, T, Lees, M, Loughlin, S, Raymond, Fl, Trump, D, Whittaker, J, Smithson, S, Rankin, J, Turner, C, Bird, L, Chibuk, J, Masser Frye, D, Sell, S, Amy, S, Schafer, I, Bartoshesky, Le, Jenny, K, Benke, P, Curry, C, Swenerton, A, Treisman, T, Dunlap, Jw, Shashi, V, Reich, E, Reimschisel, T, Pfau, R, Pober, B, Robertson, J, Roggenbuck, J, Thiese, H., DEL GIUDICE, Ennio, M., Macca, F., Imperati, A., D’Amico, P., Parent, L., Pasquier, V., Layet, S., Lyonnet, V., Stamboul Darmency, C., Thauvin Robinet, Franco, Brunella, and Oral Facial Digital Type, I. Collaborative G. r. o. u. p.
Subjects: Central nervous system, Neuroimaging, Neuropsychological Tests, Pharmacology, Bioinformatics, Settore MED/03 - GENETICA MEDICA, Ciliopathies, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Central Nervous System Diseases, medicine, Humans, Genetics(clinical), Pharmacology (medical), Orofaciodigital type 1, Neurodevelopmental phenotype, OFD1, Female, Magnetic Resonance Imaging, Mutation, Orofaciodigital Syndromes, Medicine (all), Genetics (clinical), Agenesis of the corpus callosum, 030304 developmental biology, Medicine(all), 0303 health sciences, business.industry, Research, Cilium, Neuropsychology, Cognition, General Medicine, medicine.disease, central nervous system, Porencephaly, 3. Good health, medicine.anatomical_structure, business, 030217 neurology & neurosurgery
Abstract: Background Oral-facial-digital type 1 syndrome (OFD1; OMIM 311200) belongs to the expanding group of disorders ascribed to ciliary dysfunction. With the aim of contributing to the understanding of the role of primary cilia in the central nervous system (CNS), we performed a thorough characterization of CNS involvement observed in this disorder. Methods A cohort of 117 molecularly diagnosed OFD type I patients was screened for the presence of neurological symptoms and/or cognitive/behavioral abnormalities on the basis of the available information supplied by the collaborating clinicians. Seventy-one cases showing CNS involvement were further investigated through neuroimaging studies and neuropsychological testing. Results Seventeen patients were molecularly diagnosed in the course of this study and five of these represent new mutations never reported before. Among patients displaying neurological symptoms and/or cognitive/behavioral abnormalities, we identified brain structural anomalies in 88.7%, cognitive impairment in 68%, and associated neurological disorders and signs in 53% of cases. The most frequently observed brain structural anomalies included agenesis of the corpus callosum and neuronal migration/organisation disorders as well as intracerebral cysts, porencephaly and cerebellar malformations. Conclusions Our results support recent published findings indicating that CNS involvement in this condition is found in more than 60% of cases. Our findings correlate well with the kind of brain developmental anomalies described in other ciliopathies. Interestingly, we also described specific neuropsychological aspects such as reduced ability in processing verbal information, slow thought process, difficulties in attention and concentration, and notably, long-term memory deficits which may indicate a specific role of OFD1 and/or primary cilia in higher brain functions.
Published: 2014
Full Text: View/download PDF

23. Spinal muscular atrophy of childhood: genetics

Author: Raymond Fl
Subjects: Exon, Text mining, Developmental Neuroscience, business.industry, Pediatrics, Perinatology and Child Health, medicine, Neurology (clinical), Spinal muscular atrophy, Gene deletion, medicine.disease, business, Bioinformatics
Published: 2008

24. Spectrum of clinical features associated with interstitial chromosome 22q11 deletions: a European collaborative study

Author: Ryan, AK, Goodship, JA, Wilson, DI, Philip, N, Levy, A, Seidel, H, Schuffenhauer, S, Oechsler, H, Belohradsky, B, Prieur, M, Aurias, A, Raymond, FL, ClaytonSmith, J, Hatchwell, E, McKeown, C, Beemer, FA, Dallapiccola, B, Novelli, G, Hurst, JA, Ignatius, J, Green, AJ, Brueton, L, BrondumNielsen, K, Stewart, F, VanEssen, T, Patton, M, Paterson, J, and Scambler, PJ
Subjects: CARDIO-FACIAL SYNDROME, VELOCARDIOFACIAL SYNDROME, HYPOPARATHYROIDISM, chromosome 22q11 deletion, CATCH-22, DIGEORGE-SYNDROME, PART, PHENOTYPE, DiGeorge syndrome
Abstract: We present clinical data on 558 patients with deletions within the DiGeorge syndrome critical region of chromosome 22q11. Twenty-eight percent of the cases where parents had been tested had inherited deletions, with a marked excess of maternally inherited deletions (maternal 61, paternal 18). Eight percent of the patients had died, over half of these within a month of birth and the majority within 6 months. All but one of the deaths were the result of congenital heart disease. Clinically significant immunological problems were very uncommon. Nine percent of patients had cleft palate and 32% had velopharyngeal insufficiency, 60% of patients were hypocalcaemic, 75% of patients had cardiac problems, and 36% of patients had cardiac problems, and 36% of patients who had abdominal ultrasound had a renal abnormality. Sixty-two percent of surviving patients were developmentally normal or had only mild learning problems. The majority of patients were constitutionally small, with 36% of patients below the 3rd centile for either height or weight parameters.
Published: 1997

25. Genetic testing and screening of individuals at risk of NF2

Author: Evans, DG, primary, Raymond, FL, additional, Barwell, JG, additional, and Halliday, D, additional
Published: 2011
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26. Mutations in the RSK2(RPS6KA3) gene cause Coffin-Lowry syndrome and nonsyndromic X-linked mental retardation

Author: Field, M, primary, Tarpey, P, additional, Boyle, J, additional, Edkins, S, additional, Goodship, J, additional, Luo, Y, additional, Moon, J, additional, Teague, J, additional, Stratton, MR, additional, Futreal, PA, additional, Wooster, R, additional, Raymond, FL, additional, and Turner, G, additional
Published: 2006
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27. Four cases of amelia of the upper limb associated with anal atresia???is this VACTERL with extreme limb involvement?

Author: Price Sm, Berry Ac, Young Id, Turnpenny P, and Raymond Fl
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, Pediatrics, medicine.medical_specialty, business.industry, Incidence (epidemiology), General Medicine, medicine.disease, VACTERL association, Pathology and Forensic Medicine, medicine.anatomical_structure, Anal atresia, Pediatrics, Perinatology and Child Health, medicine, Upper limb, Anatomy, Abnormality, business, Genetics (clinical)
Abstract: Amelia is an extremely rare abnormality with a highest reported incidence of 1 in 67,500 liveborn infants. We now report four cases in each of which amelia involving one upper limb occurred in association with anal atresia. The pattern of other abnormalities present in these cases suggests that this combination of amelia and anal atresia falls within the spectrum of the VACTERL association.
Published: 1998

28. Genetic testing and screening of individuals at risk of NF2.

Author: Evans, DG, Raymond, FL, Barwell, JG, and Halliday, D
Subjects: *GENETIC testing, *NEUROFIBROMATOSIS, *MOSAICISM, *MEDICAL protocols, *MAGNETIC resonance imaging
Abstract: Evans DG, Raymond FL, Barwell JG, Halliday D. Genetic testing and screening of individuals at risk of NF2. Genetic testing and management of the at-risk individual for neurofibromatosis type 2 (NF2) is complicated by the well-documented risk of mosaicism that causes a milder later onset more asymmetrical disease course. Risks of NF2 were derived from genetic testing of over 1000 individuals through the Manchester NF2-testing service. Individuals are at risk of NF2 or have 'potential' NF2 if they have features of the disease that fall short of diagnostic criteria or are the first-degree relative of someone with NF2 or suspected NF2. The present protocol devised for the Nationally Commissioned Group (NCG) NF2 service in England addresses the risks, genetic testing and screening protocol for individuals at risk of NF2. Screening with cranial magnetic resonance imaging is advised until the risk of NF2 falls below a pragmatic threshold of 1%. Multiple case scenarios are shown to illustrate how to use the protocol. [ABSTRACT FROM AUTHOR]
Published: 2012
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29. Surgical management of vestibular schwannomas and hearing rehabilitation in neurofibromatosis type 2.

Author: Tysome JR, Macfarlane R, Durie-Gair J, Donnelly N, Mannion R, Knight R, Harris F, Vanat ZH, Tam YC, Burton K, Hensiek A, Raymond FL, Moffat DA, and Axon PR
Published: 2012
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30. Mutational spectrum of the oral-facial-digital type I syndrome: a study on a large collection of patients

Author: Prattichizzo, C, Macca, M, Novelli, V, Giorgio, G, Barra, A, Franco, B, OFDI COLLABORATIVE GROUP ABDULLA F, ORAL FACIAL DIGITAL TYPE I., Abramowicz, M, Amy, S, Schafer, I, Bankier, A, White, S, Barcina, Mg, Bartoshesky, Le, Jenny, K, Beemer, Fa, Benke, P, Betz, Rc, Bianchini, G, Garavelli, L, Bigoni, S, Bird, L, Chibuk, J, MASSER FRYE, D, Brunetti, N, Scarcella, A, Brunner, Hg, Burn, J, Carmi, R, Castellan, C, Castelluccio, P, Castle, B, Chiong, Ma, Cutiongco, Em, Collins, F, Couchon, E, Curry, A, Pastore, M, Curry, C, Swenerton, A, Treisman, T, Dean, J, Devriendt, K, Matthijs, G, Dunlap, Jw, Shashi, V, Elcioglu, N, Farndon, P, Ferrero, Gb, Ferrier, R, Foulds, N, Friedman, Jm, Gal, A, Orth, U, Gardner, M, Gerola, O, GILLESSEN KAESBACH, G, Giuliano, F, TURC CAREL, C, Gödde, E, Graber, V, Graham, Ge, Gurrieri, F, Harbour, L, Henderson, A, Jones, E, Heran, H, Homfray, T, Taylor, R, Iwarsson, E, Jensen, P, JEZELA STANEK, A, Joss, S, Taylor, G, Keeling, Sl, Klatt, R, Teebi, A, KLEHR MARTINELLI, M, Kotzot, D, Lees, M, Loughlin, S, Lhotta, K, Macdonald, F, Mari, Francesca, Renieri, Alessandra, Marlin, S, Mcgaughran, J, Mckenzie, F, Mcleod, Dr, Megarbane, A, Mota, Cr, Mucke, J, Tzschach, A, Obersztyn, E, Okhowat, R, Shinzel, A, Pfau, R, Pober, B, Raymond, Fl, Reich, E, Reimschisel, T, Robertson, J, Roggenbuck, J, Sabato, A, SANCHEZ DEL POZO, J, SCHELL APACIK, C, Schwaab, E, Selicorni, A, Sell, S, Smithson, S, STRAY PEDERSEN, A, Tan, T, Thiese, H, Tol, J, Toprak, O, Trump, D, Whittaker, J, Williams, D, Zelante, L, and Zoll, B.
Subjects: Male, Adolescent, Genotype, Genetics and epigenetic pathways of disease [NCMLS 6], primary ciliary dysfunction, DNA Mutational Analysis, Molecular Sequence Data, Nonsense mutation, Biology, X-linked dominant male lethal, medicine.disease_cause, Bioinformatics, Frameshift mutation, Cohort Studies, Genomic disorders and inherited multi-system disorders [IGMD 3], 03 medical and health sciences, Cystic kidney disease, OFDI, Genetics, medicine, Humans, Missense mutation, Amino Acid Sequence, Child, mutation analysis, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Mutation, Cilium, 030305 genetics & heredity, Genetic disorder, Proteins, OFD1, Orofaciodigital Syndromes, medicine.disease, 3. Good health, Developmental disorder, Phenotype, Genetic defects of metabolism [UMCN 5.1], Mutation analysis OFD1 OFDI Primary ciliary dysfunction X-linked dominant male lethal, Female, Sequence Alignment, Immunity, infection and tissue repair [NCMLS 1]
Abstract: Contains fulltext : 70803.pdf (Publisher’s version ) (Closed access) Oral-facial-digital type I (OFDI) syndrome is a male-lethal X-linked dominant developmental disorder belonging to the heterogeneous group of oral-facial-digital syndromes (OFDS). OFDI is characterized by malformations of the face, oral cavity, and digits. Central nervous system (CNS) abnormalities and cystic kidney disease can also be part of this condition. This rare genetic disorder is due to mutations in the OFD1 gene that encodes a centrosome/basal body protein necessary for primary cilium assembly and for left-right axis determination, thus ascribing OFDI to the growing number of disorders associated to ciliary dysfunction. We now report a mutation analysis study in a cohort of 100 unrelated affected individuals collected worldwide. Putative disease-causing mutations were identified in 81 patients (81%). We describe 67 different mutations, 64 of which represent novel mutations, including 36 frameshift, nine missense, 11 splice-site, and 11 nonsense mutations. Most of them concentrate in exons 3, 8, 9, 12, 13, and 16, suggesting that these exons may represent mutational hotspots. Phenotypic characterization of the patients provided a better definition of the clinical features of OFDI syndrome. Our results indicate that renal cystic disease is present in 60% of cases >18 years of age. Genotype-phenotype correlation did not reveal significant associations apart for the high-arched/cleft palate most frequently associated to missense and splice-site mutations. Our results contribute to further expand our knowledge on the molecular basis of OFDI syndrome.

31. Nouveau sistême de musique : Théorique et pratique

Author: Mercadier de Belestá, Jean-Baptiste, Valade, Jacques-François 1727?-1784 editor, Laporte, Antoine-Louis-Guillaume-Catherine 1746-1817 editor, Heirisson, Raymond fl. 1766-1823 impresor, Mercadier de Belestá, Jean-Baptiste, Valade, Jacques-François 1727?-1784 editor, Laporte, Antoine-Louis-Guillaume-Catherine 1746-1817 editor, and Heirisson, Raymond fl. 1766-1823 impresor
Abstract: Dedicatoria en p. V-VI: "A Monsieur d'Alembert", Anglés y Subirá, Nombre de impresor tomado del colofón, Sign.: a-d⁴, e², A-T⁴, Anteportada, Incluye ocho láminas de música desplegables, numeradas: "Planche I, pl. II-VIII"

32. Mémoires sur la cour de Louis XIV et de la Régence

Author: Orléans, Charlotte Elisabeth de Bavière, duchesse d' 1652-1722, Ponthieu editor, Plassan, Joseph-Raymond fl. 1810-1835 impresor, Orléans, Charlotte Elisabeth de Bavière, duchesse d' 1652-1722, Ponthieu editor, and Plassan, Joseph-Raymond fl. 1810-1835 impresor
Abstract: GBV, Los datos de impresor constan en verso de anteportada, Sign.: [a]-b⁸, c²⁻¹, 1-23⁸, 24², Anteportada, Notas a pie de página

33. Nouveau sistême de musique : Théorique et pratique

Author: Mercadier de Belestá, Jean-Baptiste, Valade, Jacques-François 1727?-1784 editor, Laporte, Antoine-Louis-Guillaume-Catherine 1746-1817 editor, Heirisson, Raymond fl. 1766-1823 impresor, Mercadier de Belestá, Jean-Baptiste, Valade, Jacques-François 1727?-1784 editor, Laporte, Antoine-Louis-Guillaume-Catherine 1746-1817 editor, and Heirisson, Raymond fl. 1766-1823 impresor
Abstract: Dedicatoria en p. V-VI: "A Monsieur d'Alembert", Anglés y Subirá, Nombre de impresor tomado del colofón, Sign.: a-d⁴, e², A-T⁴, Anteportada, Incluye ocho láminas de música desplegables, numeradas: "Planche I, pl. II-VIII"

34. The Black Panther

Author: Anonymous Author for the Black Panther Newspaper Author, Cleaver, Eldridge, 1935-1998 Author, Collier, Hal, fl. 1970 Author, Harris, Bennie, fl. 1969 Author, Hewitt, Shirley, fl. 1970 Author, Lewis, Raymond, fl. 1969 Author, Turner, Margaret, fl. 1970 Author, X, Malcolm, 1925-1965 Author, Young, George, fl. 1970 Author, and Anonymous Author for the Black Panther Newspaper Author

35. The Black Panther

Author: Anonymous Author for the Black Panther Newspaper Author, Cleaver, Kathleen Neal, 1945- Author, Du Bois, William Edward Burghardt, 1868-1963 Author, Lewis, Raymond, fl. 1969 Author, Pearson, Evette, fl. 1969 Author, Schoner, P., fl. 1969 Author, Stewart, Ronnell, fl. 1969 Author, Wald, Karen Lee, fl. 1969 Author, Wyse, Iris, fl. 1969 Author, and Anonymous Author for the Black Panther Newspaper Author

36. The Black Panther

Author: Anonymous Author for the Black Panther Newspaper Author, Abed, George T., 1939- Author, Bennett, Fred, fl. 1968 Author, Jones, Ernest, Jr., fl. 1968 Author, Lewis, Raymond, fl. 1969 Author, Nolan, Boston Fred, fl. 1968 Author, Schoner, Penny, fl. 1968 Author, Seale, Bobby, 1936- Author, and Anonymous Author for the Black Panther Newspaper Author

37. Personal journeys to and in human genetics and dysmorphology.

Author: Schwartz CE, Aylsworth AS, Allanson J, Battaglia A, Carey JC, Curry CJ, Davies KE, Eichler EE, Graham JM Jr, Hall B, Hall JG, Holmes LB, Hoyme HE, Hunter A, Innis J, Johnson J, Keppler-Noreuil KM, Leroy JG, Moore C, Nelson DL, Neri G, Opitz JM, Picketts D, Raymond FL, Shalev SA, Stevenson RE, Stumpel CTRM, Sutherland G, Viskochil DH, Weaver DD, and Zackai EH
Subjects: Humans, History, 20th Century, History, 21st Century, Human Genetics, Genetics, Medical
Abstract: Genetics has become a critical component of medicine over the past five to six decades. Alongside genetics, a relatively new discipline, dysmorphology, has also begun to play an important role in providing critically important diagnoses to individuals and families. Both have become indispensable to unraveling rare diseases. Almost every medical specialty relies on individuals experienced in these specialties to provide diagnoses for patients who present themselves to other doctors. Additionally, both specialties have become reliant on molecular geneticists to identify genes associated with human disorders. Many of the medical geneticists, dysmorphologists, and molecular geneticists traveled a circuitous route before arriving at the position they occupied. The purpose of collecting the memoirs contained in this article was to convey to the reader that many of the individuals who contributed to the advancement of genetics and dysmorphology since the late 1960s/early 1970s traveled along a journey based on many chances taken, replying to the necessities they faced along the way before finding full enjoyment in the practice of medical and human genetics or dysmorphology. Additionally, and of equal importance, all exhibited an ability to evolve with their field of expertise as human genetics became human genomics with the development of novel technologies., (© 2024 Wiley Periodicals LLC.)
Published: 2024
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38. Population screening requires robust evidence-genomics is no exception.

Author: Turnbull C, Firth HV, Wilkie AOM, Newman W, Raymond FL, Tomlinson I, Lachmann R, Wright CF, Wordsworth S, George A, McCartney M, and Lucassen A
Subjects: Humans, Genomics, Genetic Testing
Abstract: Competing Interests: Declaration of interests HVF acknowledges former chairing of the Joint Committee on Genomics in Medicine for the Royal Colleges 2018–22, and royalties from UpToDate (as a Section Editor in Genetics). RL acknowledges membership of the Foetal Maternal and Child Health Group of the UK National Screening Committee. MM acknowledges membership of a steering group for the 2024 St Andrews Evidence Based Early Diagnosis conference. AOMW acknowledges non-remunerated roles on the Science Advisory Committee of Genomics England and the Medical Research Council Molecular and Cellular Medicine Board. SW acknowledges non-financial support from Illumina (outside of the submitted work). All other authors declare no competing interests.
Published: 2024
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39. Genome sequencing and comprehensive rare-variant analysis of 465 families with neurodevelopmental disorders.

Author: Sanchis-Juan A, Megy K, Stephens J, Armirola Ricaurte C, Dewhurst E, Low K, French CE, Grozeva D, Stirrups K, Erwood M, McTague A, Penkett CJ, Shamardina O, Tuna S, Daugherty LC, Gleadall N, Duarte ST, Hedrera-Fernández A, Vogt J, Ambegaonkar G, Chitre M, Josifova D, Kurian MA, Parker A, Rankin J, Reid E, Wakeling E, Wassmer E, Woods CG, Raymond FL, and Carss KJ
Subjects: Humans, Chromosome Mapping, Base Sequence, INDEL Mutation, Genome, Human genetics, Neurodevelopmental Disorders genetics
Abstract: Despite significant progress in unraveling the genetic causes of neurodevelopmental disorders (NDDs), a substantial proportion of individuals with NDDs remain without a genetic diagnosis after microarray and/or exome sequencing. Here, we aimed to assess the power of short-read genome sequencing (GS), complemented with long-read GS, to identify causal variants in participants with NDD from the National Institute for Health and Care Research (NIHR) BioResource project. Short-read GS was conducted on 692 individuals (489 affected and 203 unaffected relatives) from 465 families. Additionally, long-read GS was performed on five affected individuals who had structural variants (SVs) in technically challenging regions, had complex SVs, or required distal variant phasing. Causal variants were identified in 36% of affected individuals (177/489), and a further 23% (112/489) had a variant of uncertain significance after multiple rounds of re-analysis. Among all reported variants, 88% (333/380) were coding nuclear SNVs or insertions and deletions (indels), and the remainder were SVs, non-coding variants, and mitochondrial variants. Furthermore, long-read GS facilitated the resolution of challenging SVs and invalidated variants of difficult interpretation from short-read GS. This study demonstrates the value of short-read GS, complemented with long-read GS, in investigating the genetic causes of NDDs. GS provides a comprehensive and unbiased method of identifying all types of variants throughout the nuclear and mitochondrial genomes in individuals with NDD., Competing Interests: Declaration of interests K.J.C. and K.M. are currently employees of AstraZeneca., (Copyright © 2023 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)
Published: 2023
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40. Identifying the neurodevelopmental and psychiatric signatures of genomic disorders associated with intellectual disability: a machine learning approach.

Author: Donnelly N, Cunningham A, Salas SM, Bracher-Smith M, Chawner S, Stochl J, Ford T, Raymond FL, Escott-Price V, and van den Bree MBM
Subjects: Male, Humans, Adolescent, Child, Female, Cohort Studies, Cross-Sectional Studies, Genomics, Machine Learning, Intellectual Disability, Autism Spectrum Disorder
Abstract: Background: Genomic conditions can be associated with developmental delay, intellectual disability, autism spectrum disorder, and physical and mental health symptoms. They are individually rare and highly variable in presentation, which limits the use of standard clinical guidelines for diagnosis and treatment. A simple screening tool to identify young people with genomic conditions associated with neurodevelopmental disorders (ND-GCs) who could benefit from further support would be of considerable value. We used machine learning approaches to address this question., Method: A total of 493 individuals were included: 389 with a ND-GC, mean age = 9.01, 66% male) and 104 siblings without known genomic conditions (controls, mean age = 10.23, 53% male). Primary carers completed assessments of behavioural, neurodevelopmental and psychiatric symptoms and physical health and development. Machine learning techniques (penalised logistic regression, random forests, support vector machines and artificial neural networks) were used to develop classifiers of ND-GC status and identified limited sets of variables that gave the best classification performance. Exploratory graph analysis was used to understand associations within the final variable set., Results: All machine learning methods identified variable sets giving high classification accuracy (AUROC between 0.883 and 0.915). We identified a subset of 30 variables best discriminating between individuals with ND-GCs and controls which formed 5 dimensions: conduct, separation anxiety, situational anxiety, communication and motor development., Limitations: This study used cross-sectional data from a cohort study which was imbalanced with respect to ND-GC status. Our model requires validation in independent datasets and with longitudinal follow-up data for validation before clinical application., Conclusions: In this study, we developed models that identified a compact set of psychiatric and physical health measures that differentiate individuals with a ND-GC from controls and highlight higher-order structure within these measures. This work is a step towards developing a screening instrument to identify young people with ND-GCs who might benefit from further specialist assessment., (© 2023. The Author(s).)
Published: 2023
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41. Abrogation of MAP4K4 protein function causes congenital anomalies in humans and zebrafish.

Author: Patterson V, Ullah F, Bryant L, Griffin JN, Sidhu A, Saliganan S, Blaile M, Saenz MS, Smith R, Ellingwood S, Grange DK, Hu X, Mireguli M, Luo Y, Shen Y, Mulhern M, Zackai E, Ritter A, Izumi K, Hoefele J, Wagner M, Riedhammer KM, Seitz B, Robin NH, Goodloe D, Mignot C, Keren B, Cox H, Jarvis J, Hempel M, Gibson CF, Tran Mau-Them F, Vitobello A, Bruel AL, Sorlin A, Mehta S, Raymond FL, Gilmore K, Powell BC, Weck K, Li C, Vulto-van Silfhout AT, Giacomini T, Mancardi MM, Accogli A, Salpietro V, Zara F, Vora NL, Davis EE, Burdine R, and Bhoj E
Subjects: Animals, Humans, Protein Serine-Threonine Kinases, Intracellular Signaling Peptides and Proteins, Zebrafish, Signal Transduction
Abstract: We report 21 families displaying neurodevelopmental differences and multiple congenital anomalies while bearing a series of rare variants in mitogen-activated protein kinase kinase kinase kinase 4 ( MAP4K4 ). MAP4K4 has been implicated in many signaling pathways including c-Jun N-terminal and RAS kinases and is currently under investigation as a druggable target for multiple disorders. Using several zebrafish models, we demonstrate that these human variants are either loss-of-function or dominant-negative alleles and show that decreasing Map4k4 activity causes developmental defects. Furthermore, MAP4K4 can restrain hyperactive RAS signaling in early embryonic stages. Together, our data demonstrate that MAP4K4 negatively regulates RAS signaling in the early embryo and that variants identified in affected humans abrogate its function, establishing MAP4K4 as a causal locus for individuals with syndromic neurodevelopmental differences.
Published: 2023
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42. Clinical and Neurophysiologic Phenotypes in Neonates With BRAT1 Encephalopathy.

Author: Carapancea E, Cornet MC, Milh M, De Cosmo L, Huang EJ, Granata T, Striano P, Ceulemans B, Stein A, Morris-Rosendahl D, Conti G, Mitra N, Raymond FL, Rowitch DH, Solazzi R, Vercellino F, De Liso P, D'Onofrio G, Boniver C, Danhaive O, Carkeek K, Salpietro V, Weckhuysen S, Fedrigo M, Angelini A, Castellotti B, Lederer D, Benoit V, Raviglione F, Guerrini R, Dilena R, and Cilio MR
Subjects: Humans, Apnea, Bradycardia, Seizures genetics, Phenotype, Muscle Hypertonia, Nuclear Proteins genetics, Myoclonus, Hyperekplexia, Brain Diseases diagnosis, Brain Diseases genetics
Abstract: Background and Objectives: BRAT1 encephalopathy is an ultra-rare autosomal recessive neonatal encephalopathy. We delineate the neonatal electroclinical phenotype at presentation and provide insights for early diagnosis., Methods: Through a multinational collaborative, we studied a cohort of neonates with encephalopathy associated with biallelic pathogenic variants in BRAT1 for whom detailed clinical, neurophysiologic, and neuroimaging information was available from the onset of symptoms. Neuropathologic changes were also analyzed., Results: We included 19 neonates. Most neonates were born at term (16/19) from nonconsanguineous parents. 15/19 (79%) were admitted soon after birth to a neonatal intensive care unit, exhibiting multifocal myoclonus, both spontaneous and exacerbated by stimulation. 7/19 (37%) had arthrogryposis at birth, and all except 1 progressively developed hypertonia in the first week of life. Multifocal myoclonus, which was present in all but 1 infant, was the most prominent manifestation and did not show any EEG correlate in 16/19 (84%). Video-EEG at onset was unremarkable in 14/19 (74%) infants, and 6 (33%) had initially been misdiagnosed with hyperekplexia. Multifocal seizures were observed at a median age of 14 days (range: 1-29). During the first months of life, all infants developed progressive encephalopathy, acquired microcephaly, prolonged bouts of apnea, and bradycardia, leading to cardiac arrest and death at a median age of 3.5 months (range: 20 days to 30 months). Only 7 infants (37%) received a definite diagnosis before death, at a median age of 34 days (range: 25-126), and almost two-thirds (12/19, 63%) were diagnosed 8 days to 12 years postmortem (median: 6.5 years). Neuropathology examination, performed in 3 patients, revealed severely delayed myelination and diffuse astrogliosis, sparing the upper cortical layers., Discussion: BRAT1 encephalopathy is a neonatal-onset, rapidly progressive neurologic disorder. Neonates are often misdiagnosed as having hyperekplexia, and many die undiagnosed. The key phenotypic features are multifocal myoclonus, an organized EEG, progressive, persistent, and diffuse hypertonia, and an evolution into refractory multifocal seizures, prolonged bouts of apnea, bradycardia, and early death. Early recognition of BRAT1 encephalopathy allows for prompt workup, appropriate management, and genetic counseling., (© 2023 American Academy of Neurology.)
Published: 2023
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43. Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins.

Author: Hasenahuer MA, Sanchis-Juan A, Laskowski RA, Baker JA, Stephenson JD, Orengo CA, Raymond FL, and Thornton JM
Subjects: Humans, Base Sequence, Genomics, Chromosome Mapping, Genome, Human genetics, Proteins genetics, Open Reading Frames
Abstract: Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases. As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein-protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder-order transitions upon binding with other protein partners and liquid-liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects., Competing Interests: Declaration of Competing Interest, (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)
Published: 2023
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44. Mental health impact of autism on families of children with intellectual and developmental disabilities of genetic origin.

Author: Wolstencroft J, Srinivasan R, Hall J, van den Bree MBM, Owen MJ, Raymond FL, and Skuse D
Abstract: Background: Many children with an intellectual or developmental disability (IDD) have associated autism spectrum disorders (ASD), as well as an increased risk of mental health difficulties. In a cohort with IDD of genetic aetiology, we tested the hypothesis that excess risk attached to those with ASD + IDD, in terms of both children's mental health and parental psychological distress., Methods: Participants with a copy number variant or single nucleotide variant (5-19 years) were recruited via UK National Health Service. 1904 caregivers competed an online assessment of child mental health and reported on their own psychological wellbeing. We used regression to examine the association between IDD with and without co-occurring ASD, and co-occurring mental health difficulties, as well as with parental psychological distress. We adjusted for children's sex, developmental level, physical health, and socio-economic deprivation., Results: Of the 1904 participants with IDD, 701 (36.8%) had co-occurring ASD. Children with both IDD and ASD were at higher risk of associated disorders than those with IDD alone (ADHD: OR = 1.84, 95% confidence interval [CI] 1.46-2.32, p < 0.0001; emotional disorders: OR = 1.85, 95%CI 1.36-2.5, p < 0.0001; disruptive behaviour disorders: OR = 1.79, 95%CI 1.36-2.37, p < 0.0001). The severity of associated symptoms was also greater in those with ASD (hyperactivity: B = 0.25, 95%CI 0.07-0.34, p = 0.006; emotional difficulties: B = 0.91, 95%CI 0.67 to 1.14, p < 0.0001; conduct problems: B = 0.25, 95%CI 0.05 to 0.46, p = 0.013). Parents of children with IDD and ASD also reported greater psychological distress than those with IDD alone ( β = 0.1, 95% CI 0.85 to 2.21, p < 0.0001). Specifically, in those with ASD, symptoms of hyperactivity ( β = 0.13, 95% CI 0.29-0.63, p < 0.0001), emotional difficulties ( β = 0.15, 95% CI 0.26-0.51, p < 0.0001) and conduct difficulties ( β = 0.07, 95% CI 0.07-0.37, p < 0.004) all significantly contributed to parental psychological distress., Conclusions: Among children with IDD of genetic aetiology, one third have co-occurring ASD. Not only do those with co-occurring ASD present with a wider range of associated mental health disorders and more severe mental health difficulties than those with IDD alone, but their parents also experience more psychological distress. Our findings suggest that the additional mental health and behavioural symptoms in those with ASD contributed to the degree of parental psychological distress., Competing Interests: MJO, MvdB and JH have a research grant from Takeda Pharmaceuticals that is outside the scope of the present study. The remaining authors have declared that they have no competing or potential conflicts of interest., (© 2023 The Authors. JCPP Advances published by John Wiley & Sons Ltd on behalf of Association for Child and Adolescent Mental Health.)
Published: 2023
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45. Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism.

Author: Annear DJ, Vandeweyer G, Sanchis-Juan A, Raymond FL, and Kooy RF
Subjects: Humans, Microsatellite Repeats genetics, Alleles, Fragile X Mental Retardation Protein genetics, Autistic Disorder genetics, Autism Spectrum Disorder genetics
Abstract: As expansions of CGG short tandem repeats (STRs) are established as the genetic etiology of many neurodevelopmental disorders, we aimed to elucidate the inheritance patterns and role of CGG STRs in autism-spectrum disorder (ASD). By genotyping 6063 CGG STR loci in a large cohort of trios and quads with an ASD-affected proband, we determined an unprecedented rate of CGG repeat length deviation across a single generation. Although the concept of repeat length being linked to deviation rate was solidified, we show how shorter STRs display greater degrees of size variation. We observed that CGG STRs did not segregate by Mendelian principles but with a bias against longer repeats, which appeared to magnify as repeat length increased. Through logistic regression, we identified 19 genes that displayed significantly higher rates and degrees of CGG STR expansion within the ASD-affected probands ( P < 1 × 10 -5 ). This study not only highlights novel repeat expansions that may play a role in ASD but also reinforces the hypothesis that CGG STRs are specifically linked to human cognition., (© 2022 Annear et al.; Published by Cold Spring Harbor Laboratory Press.)
Published: 2022
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46. Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype.

Author: Jurkute N, Cancellieri F, Pohl L, Li CHZ, Heaton RA, Reurink J, Bellingham J, Quinodoz M, Yioti G, Stefaniotou M, Weener M, Zuleger T, Haack TB, Stingl K, Hoyng CB, Mahroo OA, Hargreaves I, Raymond FL, Michaelides M, Rivolta C, Kohl S, Roosing S, Webster AR, and Arno G
Abstract: The aim of this study was to investigate coenzyme Q10 (CoQ 10 ) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ 10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ 10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ 10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects., (© 2022. The Author(s).)
Published: 2022
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47. MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia.

Author: Reid KM, Spaull R, Salian S, Barwick K, Meyer E, Zhen J, Hirata H, Sheipouri D, Benkerroum H, Gorman KM, Papandreou A, Simpson MA, Hirano Y, Farabella I, Topf M, Grozeva D, Carss K, Smith M, Pall H, Lunt P, De Gressi S, Kamsteeg EJ, Haack TB, Carr L, Guerreiro R, Bras J, Maher ER, Scott RH, Vandenberg RJ, Raymond FL, Chong WK, Sudhakar S, Mankad K, Reith ME, Campeau PM, Harvey RJ, and Kurian MA
Subjects: Animals, Proline, RNA, Zebrafish genetics, Dystonia diagnosis, Dystonia genetics, Dystonic Disorders genetics, Movement Disorders genetics, Neurodevelopmental Disorders genetics
Abstract: Background: Despite advances in next generation sequencing technologies, the identification of variants of uncertain significance (VUS) can often hinder definitive diagnosis in patients with complex neurodevelopmental disorders., Objective: The objective of this study was to identify and characterize the underlying cause of disease in a family with two children with severe developmental delay associated with generalized dystonia and episodic status dystonicus, chorea, epilepsy, and cataracts., Methods: Candidate genes identified by autozygosity mapping and whole-exome sequencing were characterized using cellular and vertebrate model systems., Results: Homozygous variants were found in three candidate genes: MED27, SLC6A7, and MPPE1. Although the patients had features of MED27-related disorder, the SLC6A7 and MPPE1 variants were functionally investigated. SLC6A7 variant in vitro overexpression caused decreased proline transport as a result of reduced cell-surface expression, and zebrafish knockdown of slc6a7 exhibited developmental delay and fragile motor neuron morphology that could not be rescued by L-proline transporter-G396S RNA. Lastly, patient fibroblasts displayed reduced cell-surface expression of glycophosphatidylinositol-anchored proteins linked to MPPE1 dysfunction., Conclusions: We report a family harboring a homozygous MED27 variant with additional loss-of-function SLC6A7 and MPPE1 gene variants, which potentially contribute to a blended phenotype caused by multilocus pathogenic variants. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society., (© 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.)
Published: 2022
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48. Rare pathogenic variants in WNK3 cause X-linked intellectual disability.

Author: Küry S, Zhang J, Besnard T, Caro-Llopis A, Zeng X, Robert SM, Josiah SS, Kiziltug E, Denommé-Pichon AS, Cogné B, Kundishora AJ, Hao LT, Li H, Stevenson RE, Louie RJ, Deb W, Torti E, Vignard V, McWalter K, Raymond FL, Rajabi F, Ranza E, Grozeva D, Coury SA, Blanc X, Brischoux-Boucher E, Keren B, Õunap K, Reinson K, Ilves P, Wentzensen IM, Barr EE, Guihard SH, Charles P, Seaby EG, Monaghan KG, Rio M, van Bever Y, van Slegtenhorst M, Chung WK, Wilson A, Quinquis D, Bréhéret F, Retterer K, Lindenbaum P, Scalais E, Rhodes L, Stouffs K, Pereira EM, Berger SM, Milla SS, Jaykumar AB, Cobb MH, Panchagnula S, Duy PQ, Vincent M, Mercier S, Gilbert-Dussardier B, Le Guillou X, Audebert-Bellanger S, Odent S, Schmitt S, Boisseau P, Bonneau D, Toutain A, Colin E, Pasquier L, Redon R, Bouman A, Rosenfeld JA, Friez MJ, Pérez-Peña H, Akhtar Rizvi SR, Haider S, Antonarakis SE, Schwartz CE, Martínez F, Bézieau S, Kahle KT, and Isidor B
Subjects: Brain abnormalities, Catalytic Domain genetics, Hemizygote, Humans, Loss of Function Mutation, Male, Maternal Inheritance genetics, Mutation, Missense, Phosphorylation, Mental Retardation, X-Linked genetics, Protein Serine-Threonine Kinases chemistry, Protein Serine-Threonine Kinases genetics, Symporters metabolism
Abstract: Purpose: WNK3 kinase (PRKWNK3) has been implicated in the development and function of the brain via its regulation of the cation-chloride cotransporters, but the role of WNK3 in human development is unknown., Method: We ascertained exome or genome sequences of individuals with rare familial or sporadic forms of intellectual disability (ID)., Results: We identified a total of 6 different maternally-inherited, hemizygous, 3 loss-of-function or 3 pathogenic missense variants (p.Pro204Arg, p.Leu300Ser, p.Glu607Val) in WNK3 in 14 male individuals from 6 unrelated families. Affected individuals had ID with variable presence of epilepsy and structural brain defects. WNK3 variants cosegregated with the disease in 3 different families with multiple affected individuals. This included 1 large family previously diagnosed with X-linked Prieto syndrome. WNK3 pathogenic missense variants localize to the catalytic domain and impede the inhibitory phosphorylation of the neuronal-specific chloride cotransporter KCC2 at threonine 1007, a site critically regulated during the development of synaptic inhibition., Conclusion: Pathogenic WNK3 variants cause a rare form of human X-linked ID with variable epilepsy and structural brain abnormalities and implicate impaired phospho-regulation of KCC2 as a pathogenic mechanism., Competing Interests: Conflict of Interest E.T., K.M., K.R., I.M.W., K.G.M., and L.R. are employees of GeneDx, LLC. K.R. is a shareholder of OPKO Health, Inc. The Department of Molecular and Human Genetics at Baylor College of Medicine receives revenue from clinical genetic testing conducted at Baylor Genetics Laboratories. All other authors declare no conflicts of interest., (Copyright © 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.)
Published: 2022
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49. Neuropsychiatric risk in children with intellectual disability of genetic origin: IMAGINE, a UK national cohort study.

Author: Wolstencroft J, Wicks F, Srinivasan R, Wynn S, Ford T, Baker K, Chawner SJRA, Hall J, van den Bree MBM, Owen MJ, Skuse D, and Raymond FL
Subjects: Adolescent, Child, Child, Preschool, Cohort Studies, Female, Humans, Male, Prospective Studies, State Medicine, United Kingdom epidemiology, Autism Spectrum Disorder epidemiology, Intellectual Disability epidemiology, Intellectual Disability genetics
Abstract: Background: Children with intellectual disability frequently have multiple co-morbid neuropsychiatric conditions and poor physical health. Genomic testing is increasingly recommended as a first-line investigation for these children. We aim to determine the effect of genomics, inheritance, and socioeconomic deprivation on neuropsychiatric risk in children with intellectual disability of genetic origin as compared with the general population., Methods: IMAGINE is a prospective cohort study using online mental health and medical assessments in a cohort of 3407 UK participants with intellectual disability and pathogenic genomic variants as identified by the UK's National Health Service (NHS). Our study is on a subset of these participants, including all children aged 4-19 years. We collected diagnostic genomic reports from NHS records and asked primary caregivers to provide an assessment of their child using the Development and Well-Being Assessment (DAWBA), the Strengths and Difficulties Questionnaire (SDQ), the Adaptive Behaviour Assessment System 3 (ABAS-3), and a medical history questionnaire. Each child was assigned a rank based on their postcode using the index of multiple deprivation (IMD). We compared the IMAGINE cohort with the 2017 National Survey of Children's Mental Health in England. The main outcomes of interest were mental health and neurodevelopment according to the DAWBA and SDQ., Findings: We recruited 2770 children from the IMAGINE study between Oct 1, 2014 and June 30, 2019, of whom 2397 (86·5%) had a basic assessment of their mental health completed by their families and 1277 (46·1%) completed a medical history questionnaire. The mean age of participants was 9·2 years (SD 3·9); 1339 (55·9%) were boys and 1058 (44·1%) were girls. 355 (27·8%) of 1277 reported a seizure disorder and 814 (63·7%) reported movement or co-ordination problems. 1771 (73·9%) of 2397 participants had a pathogenic copy number variant (CNV) and 626 (26·1%) had a pathogenic single nucleotide variant (SNV). Participants were representative of the socioeconomic spectrum of the UK general population. The relative risk (RR) of co-occurring neuropsychiatric diagnoses, compared with the English national population, was high: autism spectrum disorder RR 29·2 (95% CI 23·9-36·5), ADHD RR 13·5 (95% CI 11·1-16·3). In children with a CNV, those with a familial variant tended to live in more socioeconomically deprived areas than those with a de novo variant. Both inheritance and socioeconomic deprivation contributed to neuropsychiatric risk in those with a CNV., Interpretation: Children with genomic variants and intellectual disability are at an increased risk of neuropsychiatric difficulties. CNV variant inheritance and socioeconomic deprivation also contribute to the risk. Early genomic investigations of children with intellectual disability could facilitate the identification of the most vulnerable children. Additionally, harnessing parental expertise using online DAWBA assessments could rapidly identify children with exceptional needs to child mental health services., Funding: UK Medical Research Council and Medical Research Foundation., Competing Interests: Declaration of interests FLR and ERM were supported by Cambridge National Institute of Health Research (NIHR) Biomedical Research Centre. SJRAC is supported by an Institutional Strategic Support Fund Wellcome Trust Fellowship (204824/Z/16/Z) and RS from a Wellcome Trust grant (211163/Z/18/Z). EM and FLR receive salary support through the University of Cambridge from the NHS in the East of England through the Clinical Academic Reserve. All other authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)
Published: 2022
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50. Novel phosphopantothenoylcysteine synthetase (PPCS) mutations with prominent neuromuscular features: Expanding the phenotypical spectrum of PPCS-related disorders.

Author: Lok A, Fernandez-Garcia MA, Taylor RW, French C, MacFarland R, Bodi I, Champion M, Josifova D, Raymond FL, Iuso A, Jungbluth H, Milan A, and Singh RR
Subjects: Female, Humans, Mutation, Cardiomyopathy, Dilated genetics
Abstract: Biallelic pathogenic variants in phosphopantothenoylcysteine synthetase, PPCS, are a rare cause of a severe early-onset dilated cardiomyopathy with high morbidity and mortality. To date, only five individuals with PPCS-mutations have been reported. Here, we report a female infant who presented in the neonatal period with hypotonia, a necrotizing myopathy with intermittent rhabdomyolysis and other extracardiac manifestations before developing a progressive and ultimately fatal dilated cardiomyopathy. Gene agnostic trio genome sequencing revealed two rare variants in the PPCS [MIM: 609853] in trans, a previously reported pathogenic c.320_334del p. (Pro107_Ala111del) variant, and a c.613-3C>G intronic variant of uncertain significance. Functional studies confirmed the likely pathogenicity of this variant. Our case provides clinical and histopathological evidence for an associated neuromuscular phenotype not previously recognized and expands the evolving phenotypic spectrum of PPCS-related disorders. We also performed a literature search of all previously published cases and summarize the common features., (© 2022 Wiley Periodicals LLC.)
Published: 2022
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