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McGlacken-Byrne SM, Le Quesne Stabej P, Del Valle I, Ocaka L, Gagunashvili A, Crespo B, Moreno N, James C, Bacchelli C, Dattani MT, Williams HJ, Kelberman D, Achermann JC, Conway GS. ZSWIM7 Is Associated With Human Female Meiosis and Familial Primary Ovarian Insufficiency. J Clin Endocrinol Metab 2022; 107:e254-e263. [PMID: 34402903 PMCID: PMC8684494 DOI: 10.1210/clinem/dgab597] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Primary ovarian insufficiency (POI) affects 1% of women and is associated with significant medical consequences. A genetic cause for POI can be found in up to 30% of women, elucidating key roles for these genes in human ovary development. OBJECTIVE We aimed to identify the genetic mechanism underlying early-onset POI in 2 sisters from a consanguineous pedigree. METHODS Genome sequencing and variant filtering using an autosomal recessive model was performed in the 2 affected sisters and their unaffected family members. Quantitative reverse transcriptase PCR (qRT-PCR) and RNA sequencing were used to study the expression of key genes at critical stages of human fetal gonad development (Carnegie Stage 22/23, 9 weeks post conception (wpc), 11 wpc, 15/16 wpc, 19/20 wpc) and in adult tissue. RESULTS Only 1 homozygous variant cosegregating with the POI phenotype was found: a single nucleotide substitution in zinc finger SWIM-type containing 7 (ZSWIM7), NM_001042697.2: c.173C > G; resulting in predicted loss-of-function p.(Ser58*). qRT-PCR demonstrated higher expression of ZSWIM7 in the 15/16 wpc ovary compared with testis, corresponding to peak meiosis in the fetal ovary. RNA sequencing of fetal gonad samples showed that ZSWIM7 has a similar temporal expression profile in the developing ovary to other homologous recombination genes. MAIN CONCLUSIONS Disruption of ZSWIM7 is associated with POI in humans. ZSWIM7 is likely to be important for human homologous recombination; these findings expand the range of genes associated with POI in women.
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Affiliation(s)
- Sinéad M McGlacken-Byrne
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Institute for Women’s Health, University College London, London WC1N 1EH, UK
- Correspondence: Sinéad McGlacken-Byrne, Wellcome Trust Clinical Training Fellow, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, WC1N 1EH, UK.
| | - Polona Le Quesne Stabej
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Ignacio Del Valle
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Louise Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Andrey Gagunashvili
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Berta Crespo
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Nadjeda Moreno
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Chela James
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Chiara Bacchelli
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Mehul T Dattani
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Hywel J Williams
- Division of Cancer and Genetics, Genetic and Genomic Medicine, Cardiff University, Cardiff CF14 4AY, UK
| | - Dan Kelberman
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - John C Achermann
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Gerard S Conway
- Institute for Women’s Health, University College London, London WC1N 1EH, UK
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Gagunashvili AN, Ocaka L, Kelberman D, Munot P, Bacchelli C, Beales PL, Ganesan V. Novel missense variants in the RNF213 gene from a European family with Moyamoya disease. Hum Genome Var 2019; 6:35. [PMID: 31645973 PMCID: PMC6804521 DOI: 10.1038/s41439-019-0066-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/06/2019] [Accepted: 06/21/2019] [Indexed: 01/30/2023] Open
Abstract
In this report, we present a European family with six individuals affected with Moyamoya disease (MMD). We detected two novel missense variants in the Moyamoya susceptibility gene RNF213, c.12553A>G (p.(Lys4185Glu)) and c.12562G>A (p.(Ala4188Thr)). Cosegregation of the variants with MMD, as well as a previous report of a variant affecting the same amino acid residue in unrelated MMD patients, supports the role of RNF213 in the pathogenesis of MMD.
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Affiliation(s)
- Andrey N Gagunashvili
- 1GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Louise Ocaka
- 1GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Daniel Kelberman
- 1GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Pinki Munot
- 2Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Chiara Bacchelli
- 1GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Philip L Beales
- 1GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Vijeya Ganesan
- 2Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,3Clinical Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK
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Gorman KM, Meyer E, Grozeva D, Spinelli E, McTague A, Sanchis-Juan A, Carss KJ, Bryant E, Reich A, Schneider AL, Pressler RM, Simpson MA, Debelle GD, Wassmer E, Morton J, Sieciechowicz D, Jan-Kamsteeg E, Paciorkowski AR, King MD, Cross JH, Poduri A, Mefford HC, Scheffer IE, Haack TB, McCullagh G, Millichap JJ, Carvill GL, Clayton-Smith J, Maher ER, Raymond FL, Kurian MA, McRae JF, Clayton S, Fitzgerald TW, Kaplanis J, Prigmore E, Rajan D, Sifrim A, Aitken S, Akawi N, Alvi M, Ambridge K, Barrett DM, Bayzetinova T, Jones P, Jones WD, King D, Krishnappa N, Mason LE, Singh T, Tivey AR, Ahmed M, Anjum U, Archer H, Armstrong R, Awada J, Balasubramanian M, Banka S, Baralle D, Barnicoat A, Batstone P, Baty D, Bennett C, Berg J, Bernhard B, Bevan AP, Bitner-Glindzicz M, Blair E, Blyth M, Bohanna D, Bourdon L, Bourn D, Bradley L, Brady A, Brent S, Brewer C, Brunstrom K, Bunyan DJ, Burn J, Canham N, Castle B, Chandler K, Chatzimichali E, Cilliers D, Clarke A, Clasper S, Clayton-Smith J, Clowes V, Coates A, Cole T, Colgiu I, Collins A, Collinson MN, Connell F, Cooper N, Cox H, Cresswell L, Cross G, Crow Y, D’Alessandro M, Dabir T, Davidson R, Davies S, de Vries D, Dean J, Deshpande C, Devlin G, Dixit A, Dobbie A, Donaldson A, Donnai D, Donnelly D, Donnelly C, Douglas A, Douzgou S, Duncan A, Eason J, Ellard S, Ellis I, Elmslie F, Evans K, Everest S, Fendick T, Fisher R, Flinter F, Foulds N, Fry A, Fryer A, Gardiner C, Gaunt L, Ghali N, Gibbons R, Gill H, Goodship J, Goudie D, Gray E, Green A, Greene P, Greenhalgh L, Gribble S, Harrison R, Harrison L, Harrison V, Hawkins R, He L, Hellens S, Henderson A, Hewitt S, Hildyard L, Hobson E, Holden S, Holder M, Holder S, Hollingsworth G, Homfray T, Humphreys M, Hurst J, Hutton B, Ingram S, Irving M, Islam L, Jackson A, Jarvis J, Jenkins L, Johnson D, Jones E, Josifova D, Joss S, Kaemba B, Kazembe S, Kelsell R, Kerr B, Kingston H, Kini U, Kinning E, Kirby G, Kirk C, Kivuva E, Kraus A, Kumar D, Kumar VKA, Lachlan K, Lam W, Lampe A, Langman C, Lees M, Lim D, Longman C, Lowther G, Lynch SA, Magee A, Maher E, Male A, Mansour S, Marks K, Martin K, Maye U, McCann E, McConnell V, McEntagart M, McGowan R, McKay K, McKee S, McMullan DJ, McNerlan S, McWilliam C, Mehta S, Metcalfe K, Middleton A, Miedzybrodzka Z, Miles E, Mohammed S, Montgomery T, Moore D, Morgan S, Morton J, Mugalaasi H, Murday V, Murphy H, Naik S, Nemeth A, Nevitt L, Newbury-Ecob R, Norman A, O’Shea R, Ogilvie C, Ong KR, Park SM, Parker MJ, Patel C, Paterson J, Payne S, Perrett D, Phipps J, Pilz DT, Pollard M, Pottinger C, Poulton J, Pratt N, Prescott K, Price S, Pridham A, Procter A, Purnell H, Quarrell O, Ragge N, Rahbari R, Randall J, Rankin J, Raymond L, Rice D, Robert L, Roberts E, Roberts J, Roberts P, Roberts G, Ross A, Rosser E, Saggar A, Samant S, Sampson J, Sandford R, Sarkar A, Schweiger S, Scott R, Scurr I, Selby A, Seller A, Sequeira C, Shannon N, Sharif S, Shaw-Smith C, Shearing E, Shears D, Sheridan E, Simonic I, Singzon R, Skitt Z, Smith A, Smith K, Smithson S, Sneddon L, Splitt M, Squires M, Stewart F, Stewart H, Straub V, Suri M, Sutton V, Swaminathan GJ, Sweeney E, Tatton-Brown K, Taylor C, Taylor R, Tein M, Temple IK, Thomson J, Tischkowitz M, Tomkins S, Torokwa A, Treacy B, Turner C, Turnpenny P, Tysoe C, Vandersteen A, Varghese V, Vasudevan P, Vijayarangakannan P, Vogt J, Wakeling E, Wallwark S, Waters J, Weber A, Wellesley D, Whiteford M, Widaa S, Wilcox S, Wilkinson E, Williams D, Williams N, Wilson L, Woods G, Wragg C, Wright M, Yates L, Yau M, Nellåker C, Parker M, Firth HV, Wright CF, FitzPatrick DR, Barrett JC, Hurles ME, Al Turki S, Anderson C, Anney R, Antony D, Artigas MS, Ayub M, Balasubramaniam S, Barrett JC, Barroso I, Beales P, Bentham J, Bhattacharya S, Birney E, Blackwood D, Bobrow M, Bochukova E, Bolton P, Bounds R, Boustred C, Breen G, Calissano M, Carss K, Chatterjee K, Chen L, Ciampi A, Cirak S, Clapham P, Clement G, Coates G, Collier D, Cosgrove C, Cox T, Craddock N, Crooks L, Curran S, Curtis D, Daly A, Day-Williams A, Day IN, Down T, Du Y, Dunham I, Edkins S, Ellis P, Evans D, Faroogi S, Fatemifar G, Fitzpatrick DR, Flicek P, Flyod J, Foley AR, Franklin CS, Futema M, Gallagher L, Geihs M, Geschwind D, Griffin H, Grozeva D, Guo X, Guo X, Gurling H, Hart D, Hendricks A, Holmans P, Howie B, Huang L, Hubbard T, Humphries SE, Hurles ME, Hysi P, Jackson DK, Jamshidi Y, Jing T, Joyce C, Kaye J, Keane T, Keogh J, Kemp J, Kennedy K, Kolb-Kokocinski A, Lachance G, Langford C, Lawson D, Lee I, Lek M, Liang J, Lin H, Li R, Li Y, Liu R, Lönnqvist J, Lopes M, Iotchkova V, MacArthur D, Marchini J, Maslen J, Massimo M, Mathieson I, Marenne G, McGuffin P, McIntosh A, McKechanie AG, McQuillin A, Metrustry S, Mitchison H, Moayyeri A, Morris J, Muntoni F, Northstone K, O'Donnovan M, Onoufriadis A, O'Rahilly S, Oualkacha K, Owen MJ, Palotie A, Panoutsopoulou K, Parker V, Parr JR, Paternoster L, Paunio T, Payne F, Pietilainen O, Plagnol V, Quaye L, Quail MA, Raymond L, Rehnström K, Ring S, Ritchie GR, Roberts N, Savage DB, Scambler P, Schiffels S, Schmidts M, Schoenmakers N, Semple RK, Serra E, Sharp SI, Shin SY, Skuse D, Small K, Southam L, Spasic-Boskovic O, St Clair D, Stalker J, Stevens E, St Pourcian B, Sun J, Suvisaari J, Tachmazidou I, Tobin MD, Valdes A, Van Kogelenberg M, Vijayarangakannan P, Visscher PM, Wain LV, Walters JT, Wang G, Wang J, Wang Y, Ward K, Wheeler E, Whyte T, Williams H, Williamson KA, Wilson C, Wong K, Xu C, Yang J, Zhang F, Zhang P, Aitman T, Alachkar H, Ali S, Allen L, Allsup D, Ambegaonkar G, Anderson J, Antrobus R, Armstrong R, Arno G, Arumugakani G, Ashford S, 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, Carss K, Caulfield M, Chalmers E, Chandra A, Chinnery P, Chitre M, Church C, Clement E, Clements-Brod N, Clowes V, Coghlan G, Collins P, Cooper N, Creaser-Myers A, DaCosta R, Daugherty L, Davies S, Davis J, De Vries M, Deegan P, Deevi SV, Deshpande C, Devlin L, Dewhurst E, Doffinger R, Dormand N, Drewe E, Edgar D, Egner W, Erber WN, Erwood M, Everington T, Favier R, Firth H, Fletcher D, Flinter F, Fox JC, 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, 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 JW, Henderson R, Hensiek A, Henskens Y, Herwadkar A, Holden S, Holder M, Holder S, Hu F, 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, Kumararatne D, Kurian M, Laffan MA, Lambert MP, Allen HL, Lawrie A, Lear S, Lees M, Lentaigne C, Liesner R, Linger R, Longhurst H, Lorenzo L, Machado R, Mackenzie R, MacLaren R, Maher E, Maimaris J, Mangles S, Manson A, Mapeta R, Markus HS, Martin J, Masati L, Mathias M, Matser V, Maw A, McDermott E, McJannet C, Meacham S, Meehan S, Megy K, 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, Ouwehand WH, Papadia S, Park SM, Parker A, Pasi J, Patch C, Paterson J, Payne J, Peacock A, Peerlinck K, Penkett CJ, Pepke-Zaba J, Perry DJ, Pollock V, Polwarth G, Ponsford M, Qasim W, Quinti I, Rankin S, Rankin J, Raymond FL, Rehnstrom K, Reid E, Rhodes CJ, Richards M, Richardson S, Richter A, Roberts I, Rondina M, Rosser E, Roughley C, Rue-Albrecht K, Samarghitean C, Sanchis-Juan A, Sandford R, Santra S, Sargur R, Savic S, Schulman S, Schulze H, Scott R, Scully M, Seneviratne S, Sewell C, Shamardina O, Shipley D, Simeoni I, Sivapalaratnam S, Smith K, Sohal A, Southgate L, Staines S, Staples E, Stauss H, Stein P, Stephens J, Stirrups K, Stock S, Suntharalingam J, Tait RC, Talks K, Tan Y, Thachil J, Thaventhiran J, Thomas E, Thomas M, Thompson D, Thrasher A, Tischkowitz M, Titterton C, Toh CH, Toshner M, Treacy C, Trembath R, Tuna S, Turek W, Turro E, Van Geet C, Veltman M, Vogt J, von Ziegenweldt J, Vonk Noordegraaf A, Wakeling E, Wanjiku I, Warner TQ, Wassmer E, Watkins H, Webster A, Welch S, Westbury S, Wharton J, Whitehorn D, Wilkins M, Willcocks L, Williamson C, Woods G, Wort J, Yeatman N, Yong P, Young T, Yu P. Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia. Am J Hum Genet 2019; 104:948-956. [PMID: 30982612 DOI: 10.1016/j.ajhg.2019.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/04/2019] [Indexed: 12/11/2022] Open
Abstract
The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.
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Hartill VL, van de Hoek G, Patel MP, Little R, Watson CM, Berry IR, Shoemark A, Abdelmottaleb D, Parkes E, Bacchelli C, Szymanska K, Knoers NV, Scambler PJ, Ueffing M, Boldt K, Yates R, Winyard PJ, Adler B, Moya E, Hattingh L, Shenoy A, Hogg C, Sheridan E, Roepman R, Norris D, Mitchison HM, Giles RH, Johnson CA. DNAAF1 links heart laterality with the AAA+ ATPase RUVBL1 and ciliary intraflagellar transport. Hum Mol Genet 2019; 27:529-545. [PMID: 29228333 PMCID: PMC5886296 DOI: 10.1093/hmg/ddx422] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 01/11/2023] Open
Abstract
DNAAF1 (LRRC50) is a cytoplasmic protein required for dynein heavy chain assembly and cilia motility, and DNAAF1 mutations cause primary ciliary dyskinesia (PCD; MIM 613193). We describe four families with DNAAF1 mutations and complex congenital heart disease (CHD). In three families, all affected individuals have typical PCD phenotypes. However, an additional family demonstrates isolated CHD (heterotaxy) in two affected siblings, but no clinical evidence of PCD. We identified a homozygous DNAAF1 missense mutation, p.Leu191Phe, as causative for heterotaxy in this family. Genetic complementation in dnaaf1-null zebrafish embryos demonstrated the rescue of normal heart looping with wild-type human DNAAF1, but not the p.Leu191Phe variant, supporting the conserved pathogenicity of this DNAAF1 missense mutation. This observation points to a phenotypic continuum between CHD and PCD, providing new insights into the pathogenesis of isolated CHD. In further investigations of the function of DNAAF1 in dynein arm assembly, we identified interactions with members of a putative dynein arm assembly complex. These include the ciliary intraflagellar transport protein IFT88 and the AAA+ (ATPases Associated with various cellular Activities) family proteins RUVBL1 (Pontin) and RUVBL2 (Reptin). Co-localization studies support these findings, with the loss of RUVBL1 perturbing the co-localization of DNAAF1 with IFT88. We show that RUVBL1 orthologues have an asymmetric left-sided distribution at both the mouse embryonic node and the Kupffer's vesicle in zebrafish embryos, with the latter asymmetry dependent on DNAAF1. These results suggest that DNAAF1-RUVBL1 biochemical and genetic interactions have a novel functional role in symmetry breaking and cardiac development.
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Affiliation(s)
- Verity L Hartill
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Glenn van de Hoek
- Department of Nephrology and Hypertension.,Department of Medical Genetics, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Mitali P Patel
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Rosie Little
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Christopher M Watson
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - Ian R Berry
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - Amelia Shoemark
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK.,School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Dina Abdelmottaleb
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK.,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Emma Parkes
- Manchester Royal Infirmary, Manchester M13 9WL, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Katarzyna Szymanska
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Nine V Knoers
- Department of Medical Genetics, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Peter J Scambler
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.,Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Marius Ueffing
- Department for Ophthalmology, Institute for Ophthalmic Research and Medical Bioanalytics Core, University of Tübingen, 72074 Tübingen, Germany
| | - Karsten Boldt
- Department for Ophthalmology, Institute for Ophthalmic Research and Medical Bioanalytics Core, University of Tübingen, 72074 Tübingen, Germany
| | - Robert Yates
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.,Paediatric Cardiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Paul J Winyard
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Beryl Adler
- Department of Paediatrics, Luton and Dunstable Hospital NHS Trust, Luton LU4 0DZ, UK
| | - Eduardo Moya
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Louise Hattingh
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Anil Shenoy
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Claire Hogg
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK
| | - Eamonn Sheridan
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, The Netherlands
| | - Dominic Norris
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | | | - Colin A Johnson
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
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5
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Mestek-Boukhibar L, Clement E, Jones WD, Drury S, Ocaka L, Gagunashvili A, Le Quesne Stabej P, Bacchelli C, Jani N, Rahman S, Jenkins L, Hurst JA, Bitner-Glindzicz M, Peters M, Beales PL, Williams HJ. Rapid Paediatric Sequencing (RaPS): comprehensive real-life workflow for rapid diagnosis of critically ill children. J Med Genet 2018; 55:721-728. [PMID: 30049826 PMCID: PMC6252361 DOI: 10.1136/jmedgenet-2018-105396] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/22/2018] [Accepted: 06/10/2018] [Indexed: 11/13/2022]
Abstract
Background Rare genetic conditions are frequent risk factors for, or direct causes of, paediatric intensive care unit (PICU) admission. Such conditions are frequently suspected but unidentified at PICU admission. Compassionate and effective care is greatly assisted by definitive diagnostic information. There is therefore a need to provide a rapid genetic diagnosis to inform clinical management. To date, whole genome sequencing (WGS) approaches have proved successful in diagnosing a proportion of children with rare diseases, but results may take months to report. Our aim was to develop an end-to-end workflow for the use of rapid WGS for diagnosis in critically ill children in a UK National Health Service (NHS) diagnostic setting. Methods We sought to establish a multidisciplinary Rapid Paediatric Sequencing team for case selection, trio WGS, rapid bioinformatics sequence analysis and a phased analysis and reporting system to prioritise genes with a high likelihood of being causal. Results Trio WGS in 24 critically ill children led to a molecular diagnosis in 10 (42%) through the identification of causative genetic variants. In 3 of these 10 individuals (30%), the diagnostic result had an immediate impact on the individual’s clinical management. For the last 14 trios, the shortest time taken to reach a provisional diagnosis was 4 days (median 8.5 days). Conclusion Rapid WGS can be used to diagnose and inform management of critically ill children within the constraints of an NHS clinical diagnostic setting. We provide a robust workflow that will inform and facilitate the rollout of rapid genome sequencing in the NHS and other healthcare systems globally.
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Affiliation(s)
- Lamia Mestek-Boukhibar
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Emma Clement
- Department of Clinical Genetics, North East Thames RegionalGenetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Wendy D Jones
- Department of Clinical Genetics, North East Thames RegionalGenetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Suzanne Drury
- Congenica Ltd, Bioinnovation Data Centre, Wellcome Genome Campus, Cambridge, UK
| | - Louise Ocaka
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Andrey Gagunashvili
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Polona Le Quesne Stabej
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Chiara Bacchelli
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nital Jani
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Shamima Rahman
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lucy Jenkins
- NE Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Jane A Hurst
- Department of Clinical Genetics, North East Thames RegionalGenetics Service, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mark Peters
- Respiratory, Critical Care and Anaesthesia Unit, UCL Great Ormond Street Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, UK
| | - Philip L Beales
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Hywel J Williams
- GOSgene, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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6
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Whitworth J, Smith PS, Martin JE, 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 SM, Chen-Shtoyerman R, Searle C, Side L, Skytte AB, Snape K, Woodward ER, Tischkowitz MD, Maher ER, Aitman T, Alachkar H, Ali S, Allen L, Allsup D, Ambegaonkar G, Anderson J, Antrobus R, Armstrong R, Arno G, Arumugakani G, Ashford S, 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, Carss K, 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 SV, Deshpande C, Devlin L, Dewhurst E, Dixon P, Doffinger R, Dormand N, Drewe E, Edgar D, Egner W, Erber WN, Erwood M, 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 JW, Henderson R, Hensiek A, Henskens Y, Herwadkar A, Holden S, Holder M, Holder S, Hu F, Huis in’t 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, Mapeta R, Markus HS, Martin J, Masati L, Mathias M, Matser V, Maw A, McDermott E, McJannet C, Meacham S, Meehan S, Megy K, 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, Ouwehand WH, Papadia S, Park SM, Parker A, Pasi J, Patch C, Paterson J, 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 KG, Sohal A, Southgate L, Staines S, Staples E, Stark H, Stauss H, Stein P, Stephens J, Stirrups K, 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 CH, Toshner M, Treacy C, Trembath R, Tuna S, Turek W, Turro E, Van Geet C, Veltman M, Vogt J, von Ziegenweldt J, Vonk Noordegraaf A, 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, Woods G, Wort J, Yeatman N, Yong P, Young T, Yu P. Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. Am J Hum Genet 2018; 103:3-18. [PMID: 29909963 PMCID: PMC6037202 DOI: 10.1016/j.ajhg.2018.04.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/25/2018] [Indexed: 12/17/2022] Open
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.
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Abstract
Bardet-Biedl syndrome is a rare autosomal recessive multisystem disorder caused by defects in genes encoding for proteins that localize to the primary cilium/basal body complex. Twenty-one disease-causing genes have been identified to date. It is one of the most well-studied conditions in the family of diseases caused by defective cilia collectively known as ciliopathies. In this review, we provide an update on diagnostic developments, clinical features, and progress in the management of Bardet-Biedl syndrome. Advances in diagnostic technologies including exome and whole genome sequencing are expanding the spectrum of patients who are diagnosed with Bardet-Biedl syndrome and increasing the number of cases with diagnostic uncertainty. As a result of the diagnostic developments, a small number of patients with only one or two clinical features of Bardet-Biedl syndrome are being diagnosed. Our understanding of the syndrome-associated renal disease has evolved and is reviewed here. Novel interventions are developing at a rapid pace and are explored in this review including genetic therapeutics such as gene therapy, exon skipping therapy, nonsense suppression therapy, and gene editing. Other non-genetic therapies such as gene repurposing, targeted therapies, and non-pharmacological interventions are also discussed.
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Affiliation(s)
- Elizabeth Forsythe
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Joanna Kenny
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chiara Bacchelli
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Philip L Beales
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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Antony D, Nampoory N, Bacchelli C, Melhem M, Wu K, James CT, Beales PL, Hubank M, Thomas D, Mashankar A, Behbehani K, Schmidts M, Alsmadi O. Exome sequencing for the differential diagnosis of ciliary chondrodysplasias: Example of a WDR35 mutation case and review of the literature. Eur J Med Genet 2017; 60:658-666. [DOI: 10.1016/j.ejmg.2017.08.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 08/17/2017] [Accepted: 08/29/2017] [Indexed: 12/30/2022]
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Abstract
Personalized medicine is becoming routine in the treatment of common diseases such as cancer, but has lagged behind in the field of rare diseases. It is currently in the early stages for the treatment of Bardet–Biedl syndrome. Advances in the understanding of ciliary biology and diagnostic techniques have opened up the prospect of treating BBS in a patient-specific manner. Owing to their structure and function, cilia provide an attractive therapeutic target and genetic therapies are being explored in ciliopathy treatment. Promising avenues include gene therapy, gene editing techniques and splice-correcting and read-through therapies. Targeted drug design has been successful in the treatment of genetic disease and research is underway in the discovery of known and novel drugs to treat Bardet–Biedl syndrome.
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Affiliation(s)
- Joanna Kenny
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford St, London WC1N 1EH, UK
| | - Elizabeth Forsythe
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford St, London WC1N 1EH, UK
| | - Philip Beales
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford St, London WC1N 1EH, UK
| | - Chiara Bacchelli
- NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guildford St, London WC1N 1EH, UK
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10
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Munye MM, Diaz-Font A, Ocaka L, Henriksen ML, Lees M, Brady A, Jenkins D, Morton J, Hansen SW, Bacchelli C, Beales PL, Hernandez-Hernandez V. COLEC10 is mutated in 3MC patients and regulates early craniofacial development. PLoS Genet 2017; 13:e1006679. [PMID: 28301481 PMCID: PMC5373641 DOI: 10.1371/journal.pgen.1006679] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/30/2017] [Accepted: 03/09/2017] [Indexed: 12/24/2022] Open
Abstract
3MC syndrome is an autosomal recessive heterogeneous disorder with features linked to developmental abnormalities. The main features include facial dysmorphism, craniosynostosis and cleft lip/palate; skeletal structures derived from cranial neural crest cells (cNCC). We previously reported that lectin complement pathway genes COLEC11 and MASP1/3 are mutated in 3MC syndrome patients. Here we define a new gene, COLEC10, also mutated in 3MC families and present novel mutations in COLEC11 and MASP1/3 genes in a further five families. The protein products of COLEC11 and COLEC10, CL-K1 and CL-L1 respectively, form heteromeric complexes. We show COLEC10 is expressed in the base membrane of the palate during murine embryo development. We demonstrate how mutations in COLEC10 (c.25C>T; p.Arg9Ter, c.226delA; p.Gly77Glufs*66 and c.528C>G p.Cys176Trp) impair the expression and/or secretion of CL-L1 highlighting their pathogenicity. Together, these findings provide further evidence linking the lectin complement pathway and complement factors COLEC11 and COLEC10 to morphogenesis of craniofacial structures and 3MC etiology. The 3MC syndrome is a unifying term amalgamating four rare recessive genetic disorders with overlapping features namely; Mingarelli, Malpuech, Michels and Carnevale syndromes. It is characterised by facial malformations including, high-arched eyebrows, cleft lip/palate, hypertelorism, developmental delay and hearing loss. We previously reported that lectin complement pathway genes COLEC11 and MASP1/3 were mutated in 3MC syndrome patients. Here we describe a new gene from the same pathway, COLEC10, mutated in 3MC patients. Our results show that COLEC10 is expressed in craniofacial tissues during development. We demonstrate how CL-L1, the protein expressed by COLEC10, can act as a cellular chemoattractant in vitro, controlling cell movement and migration. We overexpressed constructs carrying COLEC10 non-sense mutations found in our patients, CL-L1 failed to be expressed and secreted. Moreover, when we expressed a missense COLEC10 construct, CL-L1 was expressed but failed to be secreted. In sum, we discovered a new gene, COLEC10, mutated in 3MC syndrome and we propose a pathogenic mechanism for 3MC relating to the failure of CL-L1 function and its craniofacial developmental consequences.
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Affiliation(s)
- Mustafa M. Munye
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Anna Diaz-Font
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Louise Ocaka
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Maiken L. Henriksen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital, London, United Kingdom
| | - Angela Brady
- North West Thames Regional Genetics Service, Kennedy-Galton Centre, Northwick Park Hospital, London, United Kingdom
| | - Dagan Jenkins
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Jenny Morton
- Department of Clinical Genetics, Birmingham Women’s Hospital, Birmingham, United Kingdom
| | - Soren W. Hansen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Chiara Bacchelli
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Philip L. Beales
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- * E-mail: (PLB); (VHH)
| | - Victor Hernandez-Hernandez
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
- * E-mail: (PLB); (VHH)
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11
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Oud MM, Tuijnenburg P, Hempel M, van Vlies N, Ren Z, Ferdinandusse S, Jansen MH, Santer R, Johannsen J, Bacchelli C, Alders M, Li R, Davies R, Dupuis L, Cale CM, Wanders RJA, Pals ST, Ocaka L, James C, Müller I, Lehmberg K, Strom T, Engels H, Williams HJ, Beales P, Roepman R, Dias P, Brunner HG, Cobben JM, Hall C, Hartley T, Le Quesne Stabej P, Mendoza-Londono R, Davies EG, de Sousa SB, Lessel D, Arts HH, Kuijpers TW. Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome. Am J Hum Genet 2017; 100:281-296. [PMID: 28132690 DOI: 10.1016/j.ajhg.2017.01.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 12/16/2022] Open
Abstract
EXTL3 regulates the biosynthesis of heparan sulfate (HS), important for both skeletal development and hematopoiesis, through the formation of HS proteoglycans (HSPGs). By whole-exome sequencing, we identified homozygous missense mutations c.1382C>T, c.1537C>T, c.1970A>G, and c.2008T>G in EXTL3 in nine affected individuals from five unrelated families. Notably, we found the identical homozygous missense mutation c.1382C>T (p.Pro461Leu) in four affected individuals from two unrelated families. Affected individuals presented with variable skeletal abnormalities and neurodevelopmental defects. Severe combined immunodeficiency (SCID) with a complete absence of T cells was observed in three families. EXTL3 was most abundant in hematopoietic stem cells and early progenitor T cells, which is in line with a SCID phenotype at the level of early T cell development in the thymus. To provide further support for the hypothesis that mutations in EXTL3 cause a neuro-immuno-skeletal dysplasia syndrome, and to gain insight into the pathogenesis of the disorder, we analyzed the localization of EXTL3 in fibroblasts derived from affected individuals and determined glycosaminoglycan concentrations in these cells as well as in urine and blood. We observed abnormal glycosaminoglycan concentrations and increased concentrations of the non-sulfated chondroitin disaccharide D0a0 and the disaccharide D0a4 in serum and urine of all analyzed affected individuals. In summary, we show that biallelic mutations in EXTL3 disturb glycosaminoglycan synthesis and thus lead to a recognizable syndrome characterized by variable expression of skeletal, neurological, and immunological abnormalities.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands.
| | - Paul Tuijnenburg
- Department of Experimental Immunology, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands; Department of Pediatric Hematology, Immunology, and Infectious disease, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Naomi van Vlies
- Laboratory Genetic Metabolic Diseases, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Zemin Ren
- Department of Pathology, Academic Medical Center, University of Amsterdam, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Machiel H Jansen
- Department of Experimental Immunology, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands; Department of Pediatric Hematology, Immunology, and Infectious disease, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Chiara Bacchelli
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Rosalind Davies
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Catherine M Cale
- Department of Immunology, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Steven T Pals
- Department of Pathology, Academic Medical Center, University of Amsterdam, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Louise Ocaka
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Chela James
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Ingo Müller
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kai Lehmberg
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 München, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Hywel J Williams
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Phil Beales
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Patricia Dias
- Serviςo de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, 1640-035 Lisboa, Portugal
| | - Han G Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Jan-Maarten Cobben
- Department of Pediatrics, Academic Medical Center University Hospital, PO Box 22660, 1100 DD Amsterdam, the Netherlands; Department of Clinical Genetics, St. George's University Hospital, SW19 0ER London, UK
| | - Christine Hall
- Emerita, Department of Radiology, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8 L1, Canada
| | - Polona Le Quesne Stabej
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada
| | - E Graham Davies
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK; Department of Immunology, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Sérgio B de Sousa
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK; Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Heleen H Arts
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands; Department of Pathology and Molecular Medicine, McMaster University Medical Centre, Hamilton, ON L8S 4J9, Canada
| | - Taco W Kuijpers
- Department of Experimental Immunology, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands.
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Melhem M, Abu-Farha M, Antony D, Madhoun AA, Bacchelli C, Alkayal F, AlKhairi I, John S, Alomari M, Beales PL, Alsmadi O. Novel G6B gene variant causes familial autosomal recessive thrombocytopenia and anemia. Eur J Haematol 2017; 98:218-227. [PMID: 27743390 DOI: 10.1111/ejh.12819] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2016] [Indexed: 12/25/2022]
Abstract
OBJECTIVE To characterize the underlying genetic and molecular defects in a consanguineous family with lifelong blood disorder manifested with thrombocytopenia (low platelets count) and anemia. METHODS Genetic linkage analysis, exome sequencing, and functional genomics were carried out to identify and characterize the defective gene. RESULTS We identified a novel truncation mutation (p.C108*) in chromosome 6 open reading frame 25 (C6orf25) gene in this family. We also showed the p.C108* mutation was responsible for destabilizing the encoded truncated G6B protein. Unlike the truncated form, wild-type G6B expression resulted in enhanced K562 differentiation into megakaryocytes and erythrocytes. C6orf25, also known as G6B, is an effector protein for the key hematopoiesis regulators, Src homology region 2 domain-containing phosphatases SHP-1 and SHP-2. CONCLUSION G6B seems to act through an autosomal recessive mode of disease transmission in this family and regarded as the gene responsible for the observed hematological disorder. This inference is well supported further by in vivo evidence where similar outcomes were reported from G6b-/- and SHP1/2 DKO mouse models.
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Affiliation(s)
- Motasem Melhem
- Genetics and Genomics Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Dinu Antony
- Genetics and Genomics Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Ashraf Al Madhoun
- Genetics and Genomics Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Chiara Bacchelli
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Fadi Alkayal
- Pancreatic Islet Biology & Transplantation Unit, Dasman Diabetes Institute, Dasman, Kuwait
| | - Irina AlKhairi
- Biochemistry and Molecular Biology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Sumi John
- Integrative Informatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Mohamad Alomari
- Department of Pathology, Windsor Regional Hospital, Windsor, ON, Canada
| | - Phillip L Beales
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Osama Alsmadi
- Genetics and Genomics Department, Dasman Diabetes Institute, Dasman, Kuwait
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Kammermeier J, Dziubak R, Pescarin M, Drury S, Godwin H, Reeve K, Chadokufa S, Huggett B, Sider S, James C, Acton N, Cernat E, Gasparetto M, Noble-Jamieson G, Kiparissi F, Elawad M, Beales PL, Sebire NJ, Gilmour K, Uhlig HH, Bacchelli C, Shah N. Phenotypic and Genotypic Characterisation of Inflammatory Bowel Disease Presenting Before the Age of 2 years. J Crohns Colitis 2017; 11:60-69. [PMID: 27302973 PMCID: PMC5885808 DOI: 10.1093/ecco-jcc/jjw118] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Inflammatory bowel disease [IBD] presenting in early childhood is extremely rare. More recently, progress has been made to identify children with monogenic forms of IBD predominantly presenting very early in life. In this study, we describe the heterogeneous phenotypes and genotypes of patients with IBD presenting before the age of 2 years and establish phenotypic features associated with underlying monogenicity. METHODS Phenotype data of 62 children with disease onset before the age of 2 years presenting over the past 20 years were reviewed. Children without previously established genetic diagnosis were prospectively recruited for next-generation sequencing. RESULTS In all, 62 patients [55% male] were identified. The median disease onset was 3 months of age (interquartile range [IQR]: 1 to 11). Conventional IBD classification only applied to 15 patients with Crohn's disease [CD]-like [24%] and three with ulcerative colitis [UC]-like [5%] phenotype; 44 patients [71%] were diagnosed with otherwise unclassifiable IBD. Patients frequently required parenteral nutrition [40%], extensive immunosuppression [31%], haematopoietic stem-cell transplantation [29%], and abdominal surgery [19%]. In 31% of patients, underlying monogenic diseases were established [EPCAM, IL10, IL10RA, IL10RB, FOXP3, LRBA, SKIV2L, TTC37, TTC7A]. Phenotypic features significantly more prevalent in monogenic IBD were: consanguinity, disease onset before the 6th month of life, stunting, extensive intestinal disease and histological evidence of epithelial abnormalities. CONCLUSIONS IBD in children with disease onset before the age of 2 years is frequently unclassifiable into Crohn's disease and ulcerative colitis, particularly treatment resistant, and can be indistinguishable from monogenic diseases with IBD-like phenotype.
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Affiliation(s)
- Jochen Kammermeier
- Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK,Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Robert Dziubak
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Matilde Pescarin
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Suzanne Drury
- Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK,NE Thames Regional Genetics Laboratory, Great Ormond Street Hospital, London, UK
| | - Heather Godwin
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Kate Reeve
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | | | - Bonita Huggett
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Sara Sider
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Chela James
- Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK
| | - Nikki Acton
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Elena Cernat
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Marco Gasparetto
- Department of Paediatric Gastroenterology, Addenbrookes Hospital, Cambridge, UK
| | - Gabi Noble-Jamieson
- Department of Paediatric Gastroenterology, Addenbrookes Hospital, Cambridge, UK
| | - Fevronia Kiparissi
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Mamoun Elawad
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
| | - Phil L. Beales
- Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK
| | - Neil J. Sebire
- Department of Histopathology, Great Ormond Street Hospital, London, UK
| | - Kimberly Gilmour
- Department of Immunology, Great Ormond Street Hospital, London, UK
| | - Holm H. Uhlig
- Transitional Gastroenterology Unit, Nuffield Department of Medicine and Department of Paediatrics, University of Oxford, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK
| | - Neil Shah
- Department of Gastroenterology, Great Ormond Street Hospital, London, UK
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Abstract
INTRODUCTION Rare pediatric diseases are clinically severe with high rates of mortality and morbidity. This paper outlines how next-generation sequencing (NGS) can be used to greatly advance identification of the underlying genetic causes. Areas covered: This manuscript is a blend of evidence obtained from literature searches from PubMed and rare disease related websites, laboratory experience and the author's opinions. The paper covers the current state of the field and identifies where the challenges lie and how they are being overcome, using up-to-date references. Expert commentary: The field of NGS is still relatively new but it has already transformed the field of rare disease research. Technological advances in instrumentation, computational hardware and software have resulted in the identification of many causative genes, but as sequencing moves into population-scale initiatives standardisation and data sharing is going to be of paramount importance to ensure we derive the maximum benefit for patients.
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Affiliation(s)
- Chiara Bacchelli
- a Head of Experimental & Personalised Medicine Section , Genetics and Genomic Medicine Programme, UCL GOS Institute of Child Health , London , England
| | - Hywel J Williams
- b GOSgene, Genetics and Genomic Medicine Programme , UCL GOS Institute of Child Health , London , England
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15
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Bacchelli C, Moretti FA, Carmo M, Adams S, Stanescu HC, Pearce K, Madkaikar M, Gilmour KC, Nicholas AK, Woods CG, Kleta R, Beales PL, Qasim W, Gaspar HB. Mutations in linker for activation of T cells (LAT) lead to a novel form of severe combined immunodeficiency. J Allergy Clin Immunol 2016; 139:634-642.e5. [PMID: 27522155 DOI: 10.1016/j.jaci.2016.05.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/17/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Signaling through the T-cell receptor (TCR) is critical for T-cell development and function. Linker for activation of T cells (LAT) is a transmembrane adaptor signaling molecule that is part of the TCR complex and essential for T-cell development, as demonstrated by LAT-deficient mice, which show a complete lack of peripheral T cells. OBJECTIVE We describe a pedigree affected by a severe combined immunodeficiency phenotype with absent T cells and normal B-cell and natural killer cell numbers. A novel homozygous frameshift mutation in the gene encoding for LAT was identified in this kindred. METHODS Genetic, molecular, and functional analyses were used to identify and characterize the LAT defect. Clinical and immunologic analysis of patients was also performed and reported. RESULTS Homozygosity mapping was used to identify potential defective genes. Sanger sequencing of the LAT gene showed a mutation that resulted in a premature stop codon and protein truncation leading to complete loss of function and loss of expression of LAT in the affected family members. We also demonstrate loss of LAT expression and lack of TCR signaling restoration in LAT-deficient cell lines reconstituted with a synthetic LAT gene bearing this severe combined immunodeficiency mutation. CONCLUSION For the first time, the results of this study show that inherited LAT deficiency should be considered in patients with combined immunodeficiency with T-cell abnormalities.
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Affiliation(s)
- Chiara Bacchelli
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Federico A Moretti
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Marlene Carmo
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Stuart Adams
- Bone Marrow Transplantation, Great Ormond Street Hospital NHS Trust, London, United Kingdom
| | - Horia C Stanescu
- Centre for Nephrology, University College London Royal Free Hospital, London, United Kingdom
| | - Kerra Pearce
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Manisha Madkaikar
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, United Kingdom; Department of Pediatric Immunology and Leukocyte Biology, National Institute of Immunohematology, ICMR, Mumbai, India
| | - Kimberly C Gilmour
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, United Kingdom; Department of Clinical Immunology, Great Ormond Street Hospital NHS Trust, London, United Kingdom
| | - Adeline K Nicholas
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - C Geoffrey Woods
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Robert Kleta
- Centre for Nephrology, University College London Royal Free Hospital, London, United Kingdom
| | - Phil L Beales
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Waseem Qasim
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, United Kingdom; Department of Clinical Immunology, Great Ormond Street Hospital NHS Trust, London, United Kingdom
| | - H Bobby Gaspar
- Infection, Immunity, Inflammation and Physiological Medicine, UCL Institute of Child Health, London, United Kingdom; Department of Clinical Immunology, Great Ormond Street Hospital NHS Trust, London, United Kingdom.
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16
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De Nes LCF, Bacchelli C, Montorsi M, Spinelli A. Single-port laparoscopic Hartmann reversal through the stoma site - a video vignette. Colorectal Dis 2016; 18:215. [PMID: 26588201 DOI: 10.1111/codi.13217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 02/08/2023]
Affiliation(s)
- L C F De Nes
- Colon and Rectal Surgery Unit, Department of General Surgery, Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy.
| | - C Bacchelli
- Colon and Rectal Surgery Unit, Department of General Surgery, Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - M Montorsi
- Colon and Rectal Surgery Unit, Department of General Surgery, Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - A Spinelli
- Colon and Rectal Surgery Unit, Department of General Surgery, Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy
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17
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Reid ES, Williams H, Stabej PLQ, James C, Ocaka L, Bacchelli C, Footitt EJ, Boyd S, Cleary MA, Mills PB, Clayton PT. Seizures Due to a KCNQ2 Mutation: Treatment with Vitamin B6. JIMD Rep 2015; 27:79-84. [PMID: 26446091 DOI: 10.1007/8904_2015_460] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/13/2015] [Accepted: 05/19/2015] [Indexed: 12/13/2022] Open
Abstract
There is increasing evidence that vitamin B6, given either as pyridoxine or pyridoxal 5'-phosphate, can sometimes result in improved seizure control in idiopathic epilepsy. Whole-exome sequencing was used to identify a de novo mutation (c.629G>A; p.Arg210His) in KCNQ2 in a 7-year-old patient whose neonatal seizures showed a response to pyridoxine and who had a high plasma to CSF pyridoxal 5'-phosphate ratio, usually indicative of an inborn error of vitamin B6 metabolism. This mutation has been described in three other patients with neonatal epileptic encephalopathy. A review of the literature was performed to assess the effectiveness of vitamin B6 treatment in patients with a KCNQ2 channelopathy. Twenty-three patients have been reported to have been trialled with B6; in three of which B6 treatment was used alone or in combination with other antiepileptic drugs to control seizures. The anticonvulsant effect of B6 vitamers may be propagated by multiple mechanisms including direct antagonist action on ion channels, antioxidant action on excess reactive oxygen species generated by increased neuronal firing and replenishing the pool of pyridoxal 5'-phosphate needed for the synthesis of some inhibitory neurotransmitters. Vitamin B6 may be a promising adjunctive treatment for patients with channelopathies and the wider epileptic population. This report also demonstrates that an abnormal plasma to CSF pyridoxal 5'-phosphate ratio may not be exclusive to inborn errors of vitamin B6 metabolism.
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Affiliation(s)
- Emma S Reid
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Hywel Williams
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Polona Le Quesne Stabej
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Chela James
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Louise Ocaka
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Chiara Bacchelli
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Emma J Footitt
- Metabolic Medicine Department, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, UK, WC1N 3JH
| | - Stewart Boyd
- Electrophysiology Department, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, UK, WC1N 3JH
| | - Maureen A Cleary
- Metabolic Medicine Department, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, UK, WC1N 3JH
| | - Philippa B Mills
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH
| | - Peter T Clayton
- Centre for Translational Omics, Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK, WC1N 1EH.
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18
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Le Quesne Stabej P, Williams HJ, James C, Tekman M, Stanescu HC, Kleta R, Ocaka L, Lescai F, Storr HL, Bitner-Glindzicz M, Bacchelli C, Conway GS. STAG3 truncating variant as the cause of primary ovarian insufficiency. Eur J Hum Genet 2015; 24:135-8. [PMID: 26059840 PMCID: PMC4795223 DOI: 10.1038/ejhg.2015.107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/09/2015] [Accepted: 04/03/2015] [Indexed: 12/30/2022] Open
Abstract
Primary ovarian insufficiency (POI) is a distressing cause of infertility in young women. POI is heterogeneous with only a few causative genes having been discovered so far. Our objective was to determine the genetic cause of POI in a consanguineous Lebanese family with two affected sisters presenting with primary amenorrhoea and an absence of any pubertal development. Multipoint parametric linkage analysis was performed. Whole-exome sequencing was done on the proband. Linkage analysis identified a locus on chromosome 7 where exome sequencing successfully identified a homozygous two base pair duplication (c.1947_48dupCT), leading to a truncated protein p.(Y650Sfs*22) in the STAG3 gene, confirming it as the cause of POI in this family. Exome sequencing combined with linkage analyses offers a powerful tool to efficiently find novel genetic causes of rare, heterogeneous disorders, even in small single families. This is only the second report of a STAG3 variant; the first STAG3 variant was recently described in a phenotypically similar family with extreme POI. Identification of an additional family highlights the importance of STAG3 in POI pathogenesis and suggests it should be evaluated in families affected with POI.
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Affiliation(s)
| | - Hywel J Williams
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Chela James
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | | | | | - Robert Kleta
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK.,Division of Medicine, UCL, London, UK
| | - Louise Ocaka
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Francesco Lescai
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Chiara Bacchelli
- Department of Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Gerard S Conway
- Reproductive Medicine Unit, Institute for Women's Health, University College London Hospitals, London, UK
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19
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Williams HJ, Hurst JR, Ocaka L, James C, Pao C, Chanudet E, Lescai F, Stanescu HC, Kleta R, Rosser E, Bacchelli C, Beales P. The use of whole-exome sequencing to disentangle complex phenotypes. Eur J Hum Genet 2015; 24:298-301. [PMID: 26059842 PMCID: PMC4717198 DOI: 10.1038/ejhg.2015.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 03/11/2015] [Accepted: 04/24/2015] [Indexed: 12/30/2022] Open
Abstract
The success of whole-exome sequencing to identify mutations causing single-gene disorders has been well documented. In contrast whole-exome sequencing has so far had limited success in the identification of variants causing more complex phenotypes that seem unlikely to be due to the disruption of a single gene. We describe a family where two male offspring of healthy first cousin parents present a complex phenotype consisting of peripheral neuropathy and bronchiectasis that has not been described previously in the literature. Due to the fact that both children had the same problems in the context of parental consanguinity we hypothesised illness resulted from either X-linked or autosomal recessive inheritance. Through the use of whole-exome sequencing we were able to simplify this complex phenotype and identified a causative mutation (p.R1070*) in the gene periaxin (PRX), a gene previously shown to cause peripheral neuropathy (Dejerine-Sottas syndrome) when this mutation is present. For the bronchiectasis phenotype we were unable to identify a causal single mutation or compound heterozygote, reflecting the heterogeneous nature of this phenotype. In conclusion, in this study we show that whole-exome sequencing has the power to disentangle complex phenotypes through the identification of causative genetic mutations for distinct clinical disorders that were previously masked.
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Affiliation(s)
- Hywel J Williams
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - John R Hurst
- UCL Respiratory Medicine, UCL Medical School, London, UK
| | - Louise Ocaka
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Chela James
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Caroline Pao
- Paediatric Respiratory Medicine, Royal London Hospital, Whitechapel, London, UK
| | - Estelle Chanudet
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Francesco Lescai
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | | | - Robert Kleta
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK.,UCL Respiratory Medicine, UCL Medical School, London, UK
| | | | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond St Hospital, London, UK
| | - Chiara Bacchelli
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
| | - Philip Beales
- Centre for Translational Omics - GOSgene, UCL Institute of Child Health, University College London, London, UK
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20
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Waters AM, Asfahani R, Carroll P, Bicknell L, Lescai F, Bright A, Chanudet E, Brooks A, Christou-Savina S, Osman G, Walsh P, Bacchelli C, Chapgier A, Vernay B, Bader DM, Deshpande C, O' Sullivan M, Ocaka L, Stanescu H, Stewart HS, Hildebrandt F, Otto E, Johnson CA, Szymanska K, Katsanis N, Davis E, Kleta R, Hubank M, Doxsey S, Jackson A, Stupka E, Winey M, Beales PL. The kinetochore protein, CENPF, is mutated in human ciliopathy and microcephaly phenotypes. J Med Genet 2015; 52:147-56. [PMID: 25564561 PMCID: PMC4345935 DOI: 10.1136/jmedgenet-2014-102691] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Mutations in microtubule-regulating genes are associated with disorders of neuronal migration and microcephaly. Regulation of centriole length has been shown to underlie the pathogenesis of certain ciliopathy phenotypes. Using a next-generation sequencing approach, we identified mutations in a novel centriolar disease gene in a kindred with an embryonic lethal ciliopathy phenotype and in a patient with primary microcephaly. Methods and results Whole exome sequencing data from a non-consanguineous Caucasian kindred exhibiting mid-gestation lethality and ciliopathic malformations revealed two novel non-synonymous variants in CENPF, a microtubule-regulating gene. All four affected fetuses showed segregation for two mutated alleles [IVS5-2A>C, predicted to abolish the consensus splice-acceptor site from exon 6; c.1744G>T, p.E582X]. In a second unrelated patient exhibiting microcephaly, we identified two CENPF mutations [c.1744G>T, p.E582X; c.8692 C>T, p.R2898X] by whole exome sequencing. We found that CENP-F colocalised with Ninein at the subdistal appendages of the mother centriole in mouse inner medullary collecting duct cells. Intraflagellar transport protein-88 (IFT-88) colocalised with CENP-F along the ciliary axonemes of renal epithelial cells in age-matched control human fetuses but did not in truncated cilia of mutant CENPF kidneys. Pairwise co-immunoprecipitation assays of mitotic and serum-starved HEKT293 cells confirmed that IFT88 precipitates with endogenous CENP-F. Conclusions Our data identify CENPF as a new centriolar disease gene implicated in severe human ciliopathy and microcephaly related phenotypes. CENP-F has a novel putative function in ciliogenesis and cortical neurogenesis.
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Affiliation(s)
- Aoife M Waters
- Institute of Child Health, University College London, London, UK Department of Nephrology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Rowan Asfahani
- Institute of Child Health, University College London, London, UK
| | - Paula Carroll
- Institute of Genetics & Molecular Medicine, Edinburgh, UK
| | | | - Francesco Lescai
- Institute of Child Health, University College London, London, UK
| | | | - Estelle Chanudet
- Institute of Child Health, University College London, London, UK
| | - Anthony Brooks
- Institute of Child Health, University College London, London, UK
| | | | - Guled Osman
- Institute of Child Health, University College London, London, UK
| | - Patrick Walsh
- Institute of Child Health, University College London, London, UK
| | - Chiara Bacchelli
- Institute of Child Health, University College London, London, UK
| | - Ariane Chapgier
- Institute of Child Health, University College London, London, UK
| | - Bertrand Vernay
- Institute of Child Health, University College London, London, UK
| | - David M Bader
- Department of Cell and Developmental Biology, Vanderbilt University, USA
| | - Charu Deshpande
- Department of Clinical Genetics, Evelina Children's Hospital, London, UK
| | - Mary O' Sullivan
- Institute of Child Health, University College London, London, UK
| | - Louise Ocaka
- Institute of Child Health, University College London, London, UK
| | - Horia Stanescu
- Centre for Nephrology, Royal Free Hospital, University College London, London, UK
| | - Helen S Stewart
- Department of Clinical Genetics, Oxford Radcliffe Hospitals NHS Trust, Churchill Hospital, Oxford, UK
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, USA
| | - Edgar Otto
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Colin A Johnson
- Department of Pediatrics, Leeds Institute of Biomedical and Clinical Sciences, Leeds, UK
| | - Katarzyna Szymanska
- Department of Pediatrics, Leeds Institute of Biomedical and Clinical Sciences, Leeds, UK
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center
| | - Erica Davis
- Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center
| | - Robert Kleta
- Centre for Nephrology, Royal Free Hospital, University College London, London, UK
| | - Mike Hubank
- Institute of Child Health, University College London, London, UK
| | | | - Andrew Jackson
- Institute of Genetics & Molecular Medicine, Edinburgh, UK MRC Human Genetics, University of Edinburgh, Edinburgh, UK
| | - Elia Stupka
- Institute of Child Health, University College London, London, UK
| | - Mark Winey
- Molecular, Ceullular, and Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Philip L Beales
- Institute of Child Health, University College London, London, UK
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21
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Affiliation(s)
- E D L Urso
- 1^ Surgical Department, University of Padova, Padova, Italy
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22
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Karda R, Buckley SMK, Mattar CN, Ng J, Massaro G, Hughes MP, Kurian MA, Baruteau J, Gissen P, Chan JKY, Bacchelli C, Waddington SN, Rahim AA. Perinatal systemic gene delivery using adeno-associated viral vectors. Front Mol Neurosci 2014; 7:89. [PMID: 25452713 PMCID: PMC4231876 DOI: 10.3389/fnmol.2014.00089] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/29/2014] [Indexed: 01/26/2023] Open
Abstract
Neurodegenerative monogenic diseases often affect tissues and organs beyond the nervous system. An effective treatment would require a systemic approach. The intravenous administration of novel therapies is ideal but is hampered by the inability of such drugs to cross the blood–brain barrier (BBB) and precludes efficacy in the central nervous system. A number of these early lethal intractable diseases also present devastating irreversible pathology at birth or soon after. Therefore, any therapy would ideally be administered during the perinatal period to prevent, stop, or ameliorate disease progression. The concept of perinatal gene therapy has moved a step further toward being a feasible approach to treating such disorders. This has primarily been driven by the recent discoveries that particular serotypes of adeno-associated virus (AAV) gene delivery vectors have the ability to cross the BBB following intravenous administration. Furthermore, safety has been demonstrated after perinatal administration mice and non-human primates. This review focuses on the progress made in using AAV to achieve systemic transduction and what this means for developing perinatal gene therapy for early lethal neurodegenerative diseases.
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Affiliation(s)
- Rajvinder Karda
- Gene Transfer Technology Group, UCL EGA Institute for Women's Health, University College London London, UK
| | - Suzanne M K Buckley
- Gene Transfer Technology Group, UCL EGA Institute for Women's Health, University College London London, UK
| | - Citra N Mattar
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, National University of Singapore Singapore, Singapore
| | - Joanne Ng
- Gene Transfer Technology Group, UCL EGA Institute for Women's Health, University College London London, UK
| | - Giulia Massaro
- Department of Pharmacology, UCL School of Pharmacy, University College London London, UK
| | - Michael P Hughes
- Department of Pharmacology, UCL School of Pharmacy, University College London London, UK
| | - Manju A Kurian
- Neurosciences Unit, UCL Institute of Child Health, University College London London, UK
| | - Julien Baruteau
- Gene Transfer Technology Group, UCL EGA Institute for Women's Health, University College London London, UK
| | - Paul Gissen
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health, University College London London, UK
| | - Jerry K Y Chan
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, National University of Singapore Singapore, Singapore
| | - Chiara Bacchelli
- Centre for Translational Research - GOSgene, UCL Institute of Child Health, University College London London, UK
| | - Simon N Waddington
- Gene Transfer Technology Group, UCL EGA Institute for Women's Health, University College London London, UK ; School of Pathology, University of the Witwatersrand Johannesburg, South Africa
| | - Ahad A Rahim
- Department of Pharmacology, UCL School of Pharmacy, University College London London, UK
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23
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Thomas AC, Williams H, Setó-Salvia N, Bacchelli C, Jenkins D, O'Sullivan M, Mengrelis K, Ishida M, Ocaka L, Chanudet E, James C, Lescai F, Anderson G, Morrogh D, Ryten M, Duncan AJ, Pai YJ, Saraiva JM, Ramos F, Farren B, Saunders D, Vernay B, Gissen P, Straatmaan-Iwanowska A, Baas F, Wood NW, Hersheson J, Houlden H, Hurst J, Scott R, Bitner-Glindzicz M, Moore GE, Sousa SB, Stanier P. Mutations in SNX14 cause a distinctive autosomal-recessive cerebellar ataxia and intellectual disability syndrome. Am J Hum Genet 2014; 95:611-21. [PMID: 25439728 DOI: 10.1016/j.ajhg.2014.10.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/13/2014] [Indexed: 12/30/2022] Open
Abstract
Intellectual disability and cerebellar atrophy occur together in a large number of genetic conditions and are frequently associated with microcephaly and/or epilepsy. Here we report the identification of causal mutations in Sorting Nexin 14 (SNX14) found in seven affected individuals from three unrelated consanguineous families who presented with recessively inherited moderate-severe intellectual disability, cerebellar ataxia, early-onset cerebellar atrophy, sensorineural hearing loss, and the distinctive association of progressively coarsening facial features, relative macrocephaly, and the absence of seizures. We used homozygosity mapping and whole-exome sequencing to identify a homozygous nonsense mutation and an in-frame multiexon deletion in two families. A homozygous splice site mutation was identified by Sanger sequencing of SNX14 in a third family, selected purely by phenotypic similarity. This discovery confirms that these characteristic features represent a distinct and recognizable syndrome. SNX14 encodes a cellular protein containing Phox (PX) and regulator of G protein signaling (RGS) domains. Weighted gene coexpression network analysis predicts that SNX14 is highly coexpressed with genes involved in cellular protein metabolism and vesicle-mediated transport. All three mutations either directly affected the PX domain or diminished SNX14 levels, implicating a loss of normal cellular function. This manifested as increased cytoplasmic vacuolation as observed in cultured fibroblasts. Our findings indicate an essential role for SNX14 in neural development and function, particularly in development and maturation of the cerebellum.
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Affiliation(s)
- Anna C Thomas
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Hywel Williams
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Núria Setó-Salvia
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Dagan Jenkins
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Mary O'Sullivan
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Miho Ishida
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Louise Ocaka
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Estelle Chanudet
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Chela James
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Francesco Lescai
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Centre for Translational Omics-GOSgene, UCL Institute of Child Health, London WC1N 1EH, UK; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Deborah Morrogh
- NE Thames Regional Genetics Laboratory Service, London WC1N 3BH, UK
| | - Mina Ryten
- UCL Institute of Neurology, London WC1N 3BG, UK; Department of Clinical Genetics, Guy's Hospital, London SE1 9RT, UK
| | - Andrew J Duncan
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Yun Jin Pai
- Developmental Biology and Cancer, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Jorge M Saraiva
- Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, 3000-602 Coimbra, Portugal
| | - Fabiana Ramos
- Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal
| | - Bernadette Farren
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Dawn Saunders
- Radiology, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Bertrand Vernay
- Developmental Biology and Cancer, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Paul Gissen
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | | | - Frank Baas
- Department of Genome Analysis, Academic Medical Center, University of Amsterdam, 1105AZ Amsterdam, the Netherlands
| | | | | | | | - Jane Hurst
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Richard Scott
- Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Maria Bitner-Glindzicz
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Clinical Genetics, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK
| | - Sérgio B Sousa
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK; Serviço de Genética Médica, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal.
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL Institute of Child Health, London WC1N 1EH, UK.
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24
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Kammermeier J, Drury S, James CT, Dziubak R, Ocaka L, Elawad M, Beales P, Lench N, Uhlig HH, Bacchelli C, Shah N. Targeted gene panel sequencing in children with very early onset inflammatory bowel disease--evaluation and prospective analysis. J Med Genet 2014; 51:748-55. [PMID: 25194001 DOI: 10.1136/jmedgenet-2014-102624] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Multiple monogenetic conditions with partially overlapping phenotypes can present with inflammatory bowel disease (IBD)-like intestinal inflammation. With novel genotype-specific therapies emerging, establishing a molecular diagnosis is becoming increasingly important. DESIGN We have introduced targeted next-generation sequencing (NGS) technology as a prospective screening tool in children with very early onset IBD (VEOIBD). We evaluated the coverage of 40 VEOIBD genes in two separate cohorts undergoing targeted gene panel sequencing (TGPS) (n=25) and whole exome sequencing (WES) (n=20). RESULTS TGPS revealed causative mutations in four genes (IL10RA, EPCAM, TTC37 and SKIV2L) discovered unexpected phenotypes and directly influenced clinical decision making by supporting as well as avoiding haematopoietic stem cell transplantation. TGPS resulted in significantly higher median coverage when compared with WES, fewer coverage deficiencies and improved variant detection across established VEOIBD genes. CONCLUSIONS Excluding or confirming known VEOIBD genotypes should be considered early in the disease course in all cases of therapy-refractory VEOIBD, as it can have a direct impact on patient management. To combine both described NGS technologies would compensate for the limitations of WES for disease-specific application while offering the opportunity for novel gene discovery in the research setting.
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Affiliation(s)
- Jochen Kammermeier
- Department of Gastroenterology, Great Ormond Street Hospital for Children, London, UK Experimental & Personalised Medicine Section, Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Suzanne Drury
- North East Thames Regional Genetics Service, Hospital for Children, London, UK
| | - Chela T James
- Centre for Translational Omics-GOSgene, Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Robert Dziubak
- Department of Gastroenterology, Great Ormond Street Hospital for Children, London, UK
| | - Louise Ocaka
- Centre for Translational Omics-GOSgene, Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Mamoun Elawad
- Department of Gastroenterology, Great Ormond Street Hospital for Children, London, UK
| | - Philip Beales
- Experimental & Personalised Medicine Section, Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Nicholas Lench
- North East Thames Regional Genetics Service, Hospital for Children, London, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK Department of Pediatrics, University of Oxford, Oxford, UK
| | - Chiara Bacchelli
- Experimental & Personalised Medicine Section, Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Neil Shah
- Department of Gastroenterology, Great Ormond Street Hospital for Children, London, UK Katholic University Leuven, Leuven, Belgium
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25
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Kelberman D, Islam L, Lakowski J, Bacchelli C, Chanudet E, Lescai F, Patel A, Stupka E, Buck A, Wolf S, Beales PL, Jacques TS, Bitner-Glindzicz M, Liasis A, Lehmann OJ, Kohlhase J, Nischal KK, Sowden JC. Mutation of SALL2 causes recessive ocular coloboma in humans and mice. Hum Mol Genet 2014; 23:2511-26. [PMID: 24412933 PMCID: PMC3990155 DOI: 10.1093/hmg/ddt643] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ocular coloboma is a congenital defect resulting from failure of normal closure of the optic fissure during embryonic eye development. This birth defect causes childhood blindness worldwide, yet the genetic etiology is poorly understood. Here, we identified a novel homozygous mutation in the SALL2 gene in members of a consanguineous family affected with non-syndromic ocular coloboma variably affecting the iris and retina. This mutation, c.85G>T, introduces a premature termination codon (p.Glu29*) predicted to truncate the SALL2 protein so that it lacks three clusters of zinc-finger motifs that are essential for DNA-binding activity. This discovery identifies SALL2 as the third member of the Drosophila homeotic Spalt-like family of developmental transcription factor genes implicated in human disease. SALL2 is expressed in the developing human retina at the time of, and subsequent to, optic fissure closure. Analysis of Sall2-deficient mouse embryos revealed delayed apposition of the optic fissure margins and the persistence of an anterior retinal coloboma phenotype after birth. Sall2-deficient embryos displayed correct posterior closure toward the optic nerve head, and upon contact of the fissure margins, dissolution of the basal lamina occurred and PAX2, known to be critical for this process, was expressed normally. Anterior closure was disrupted with the fissure margins failing to meet, or in some cases misaligning leading to a retinal lesion. These observations demonstrate, for the first time, a role for SALL2 in eye morphogenesis and that loss of function of the gene causes ocular coloboma in humans and mice.
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26
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Onoufriadis A, Shoemark A, Munye MM, James CT, Schmidts M, Patel M, Rosser EM, Bacchelli C, Beales PL, Scambler PJ, Hart SL, Danke-Roelse JE, Sloper JJ, Hull S, Hogg C, Emes RD, Pals G, Moore AT, Chung EMK, Mitchison HM. Combined exome and whole-genome sequencing identifies mutations in ARMC4 as a cause of primary ciliary dyskinesia with defects in the outer dynein arm. J Med Genet 2013; 51:61-7. [PMID: 24203976 PMCID: PMC3888613 DOI: 10.1136/jmedgenet-2013-101938] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Background Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous ciliopathy disorder affecting cilia and sperm motility. A range of ultrastructural defects of the axoneme underlie the disease, which is characterised by chronic respiratory symptoms and obstructive lung disease, infertility and body axis laterality defects. We applied a next-generation sequencing approach to identify the gene responsible for this phenotype in two consanguineous families. Methods and results Data from whole-exome sequencing in a consanguineous Turkish family, and whole-genome sequencing in the obligate carrier parents of a consanguineous Pakistani family was combined to identify homozygous loss-of-function mutations in ARMC4, segregating in all five affected individuals from both families. Both families carried nonsense mutations within the highly conserved armadillo repeat region of ARMC4: c.2675C>A; pSer892* and c.1972G>T; p.Glu658*. A deficiency of ARMC4 protein was seen in patient's respiratory cilia accompanied by loss of the distal outer dynein arm motors responsible for generating ciliary beating, giving rise to cilia immotility. ARMC4 gene expression is upregulated during ciliogenesis, and we found a predicted interaction with the outer dynein arm protein DNAI2, mutations in which also cause PCD. Conclusions We report the first use of whole-genome sequencing to identify gene mutations causing PCD. Loss-of-function mutations in ARMC4 cause PCD with situs inversus and cilia immotility, associated with a loss of the distal outer (but not inner) dynein arms. This addition of ARMC4 to the list of genes associated with ciliary outer dynein arm defects expands our understanding of the complexities of PCD genetics.
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Affiliation(s)
- Alexandros Onoufriadis
- Molecular Medicine Unit, Birth Defects Research Centre, Institute of Child Health, University College London, London, UK
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27
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Lescai F, Marasco E, Bacchelli C, Stanier P, Mantovani V, Beales P. Identification and validation of loss of function variants in clinical contexts. Mol Genet Genomic Med 2013; 2:58-63. [PMID: 24498629 PMCID: PMC3907911 DOI: 10.1002/mgg3.42] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/05/2013] [Indexed: 12/20/2022] Open
Abstract
The choice of an appropriate variant calling pipeline for exome sequencing data is becoming increasingly more important in translational medicine projects and clinical contexts. Within GOSgene, which facilitates genetic analysis as part of a joint effort of the University College London and the Great Ormond Street Hospital, we aimed to optimize a variant calling pipeline suitable for our clinical context. We implemented the GATK/Queue framework and evaluated the performance of its two callers: the classical UnifiedGenotyper and the new variant discovery tool HaplotypeCaller. We performed an experimental validation of the loss-of-function (LoF) variants called by the two methods using Sequenom technology. UnifiedGenotyper showed a total validation rate of 97.6% for LoF single-nucleotide polymorphisms (SNPs) and 92.0% for insertions or deletions (INDELs), whereas HaplotypeCaller was 91.7% for SNPs and 55.9% for INDELs. We confirm that GATK/Queue is a reliable pipeline in translational medicine and clinical context. We conclude that in our working environment, UnifiedGenotyper is the caller of choice, being an accurate method, with a high validation rate of error-prone calls like LoF variants. We finally highlight the importance of experimental validation, especially for INDELs, as part of a standard pipeline in clinical environments.
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Affiliation(s)
- Francesco Lescai
- University College London, Institute of Child Health, GOSgene team London, U.K ; Department of Biomedicine, Human Genetics, Aarhus University Aarhus, Denmark
| | - Elena Marasco
- CRBA Centro Ricerca Biomedica Applicata, Azienda Ospedaliero-Universitaria Policlinico S. Orsola - Malpighi Bologna, Italy
| | - Chiara Bacchelli
- University College London, Institute of Child Health, GOSgene team London, U.K
| | - Philip Stanier
- University College London, Institute of Child Health, GOSgene team London, U.K
| | - Vilma Mantovani
- Department of Biomedicine, Human Genetics, Aarhus University Aarhus, Denmark
| | - Philip Beales
- University College London, Institute of Child Health, GOSgene team London, U.K
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28
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Webb EA, AlMutair A, Kelberman D, Bacchelli C, Chanudet E, Lescai F, Andoniadou CL, Banyan A, Alsawaid A, Alrifai MT, Alahmesh MA, Balwi M, Mousavy-Gharavy SN, Lukovic B, Burke D, McCabe MJ, Kasia T, Kleta R, Stupka E, Beales PL, Thompson DA, Chong WK, Alkuraya FS, Martinez-Barbera JP, Sowden JC, Dattani MT. ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies. ACTA ACUST UNITED AC 2013; 136:3096-105. [PMID: 24022475 DOI: 10.1093/brain/awt218] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We describe a previously unreported syndrome characterized by secondary (post-natal) microcephaly with fronto-temporal lobe hypoplasia, multiple pituitary hormone deficiency, seizures, severe visual impairment and abnormalities of the kidneys and urinary tract in a highly consanguineous family with six affected children. Homozygosity mapping and exome sequencing revealed a novel homozygous frameshift mutation in the basic helix-loop-helix transcription factor gene ARNT2 (c.1373_1374dupTC) in affected individuals. This mutation results in absence of detectable levels of ARNT2 transcript and protein from patient fibroblasts compared with controls, consistent with nonsense-mediated decay of the mutant transcript and loss of ARNT2 function. We also show expression of ARNT2 within the central nervous system, including the hypothalamus, as well as the renal tract during human embryonic development. The progressive neurological abnormalities, congenital hypopituitarism and post-retinal visual pathway dysfunction in affected individuals demonstrates for the first time the essential role of ARNT2 in the development of the hypothalamo-pituitary axis, post-natal brain growth, and visual and renal function in humans.
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Affiliation(s)
- Emma A Webb
- 1 Developmental Endocrinology Research Group, UCL Institute of Child Health and Department of Endocrinology, Great Ormond Street Hospital for Children, London, WC1N 1EH, UK
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29
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Iacono C, Verlato G, Ruzzenente A, Campagnaro T, Bacchelli C, Valdegamberi A, Bortolasi L, Guglielmi A. Systematic review of central pancreatectomy and meta-analysis of central versus distal pancreatectomy. Br J Surg 2013; 100:873-85. [PMID: 23640664 DOI: 10.1002/bjs.9136] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND Central pancreatectomy (CP) is a parenchyma-sparing surgical procedure that enables the removal of benign and/or low-grade malignant lesions from the neck and proximal body of the pancreas. The aim of this review was to evaluate the short- and long-term surgical results of CP from all published studies, and the results of comparative studies of CP versus distal pancreatectomy (DP). METHODS Eligible studies published between 1988 and 2010 were reviewed systematically. Comparisons between CP and DP were pooled and analysed by meta-analytical techniques using random- or fixed-effects models, as appropriate. RESULTS Ninety-four studies, involving 963 patients undergoing CP, were identified. Postoperative morbidity and pancreatic fistula rates were 45·3 and 40·9 per cent respectively. Endocrine and exocrine pancreatic insufficiency was reported in 5·0 and 9·9 per cent of patients. The overall mortality rate was 0·8 per cent. Compared with DP, CP had a higher postoperative morbidity rate and a higher incidence of pancreatic fistula, but a lower risk of endocrine insufficiency (relative risk (RR) 0·22, 95 per cent confidence interval 0·14 to 0·35; P < 0·001). The risk of exocrine failure was also lower after CP, although this was not significant (RR 0·59, 0·32 to 1·07; P = 0·082). CONCLUSION CP is a safe procedure with good long-term functional reserve. In situations where DP represents an alternative, CP is associated with a slightly higher risk of early complications.
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Affiliation(s)
- C Iacono
- Department of Surgery, Unit of Hepato-Biliary-Pancreatic Surgery, Verona, Italy.
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30
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Lescai F, Bonfiglio S, Bacchelli C, Chanudet E, Waters A, Sisodiya SM, Kasperavičiūtė D, Williams J, Harold D, Hardy J, Kleta R, Cirak S, Williams R, Achermann JC, Anderson J, Kelsell D, Vulliamy T, Houlden H, Wood N, Sheerin U, Tonini GP, Mackay D, Hussain K, Sowden J, Kinsler V, Osinska J, Brooks T, Hubank M, Beales P, Stupka E. Characterisation and validation of insertions and deletions in 173 patient exomes. PLoS One 2012; 7:e51292. [PMID: 23251486 PMCID: PMC3522676 DOI: 10.1371/journal.pone.0051292] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/01/2012] [Indexed: 01/01/2023] Open
Abstract
Recent advances in genomics technologies have spurred unprecedented efforts in genome and exome re-sequencing aiming to unravel the genetic component of rare and complex disorders. While in rare disorders this allowed the identification of novel causal genes, the missing heritability paradox in complex diseases remains so far elusive. Despite rapid advances of next-generation sequencing, both the technology and the analysis of the data it produces are in its infancy. At present there is abundant knowledge pertaining to the role of rare single nucleotide variants (SNVs) in rare disorders and of common SNVs in common disorders. Although the 1,000 genome project has clearly highlighted the prevalence of rare variants and more complex variants (e.g. insertions, deletions), their role in disease is as yet far from elucidated.We set out to analyse the properties of sequence variants identified in a comprehensive collection of exome re-sequencing studies performed on samples from patients affected by a broad range of complex and rare diseases (N = 173). Given the known potential for Loss of Function (LoF) variants to be false positive, we performed an extensive validation of the common, rare and private LoF variants identified, which indicated that most of the private and rare variants identified were indeed true, while common novel variants had a significantly higher false positive rate. Our results indicated a strong enrichment of very low-frequency insertion/deletion variants, so far under-investigated, which might be difficult to capture with low coverage and imputation approaches and for which most of study designs would be under-powered. These insertions and deletions might play a significant role in disease genetics, contributing specifically to the underlining rare and private variation predicted to be discovered through next generation sequencing.
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Affiliation(s)
- Francesco Lescai
- UCL Genomics, University College London, London, United Kingdom
- Division of Research Strategy, University College London, London, United Kingdom
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Silvia Bonfiglio
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bacchelli
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Estelle Chanudet
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Aoife Waters
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Sanjay M. Sisodiya
- UCL Institute of Neurology, University College London, London, United Kingdom
| | | | - Julie Williams
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - Denise Harold
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - John Hardy
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Robert Kleta
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Sebahattin Cirak
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Richard Williams
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - John C. Achermann
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - John Anderson
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - David Kelsell
- Blizard Institute of Cell and Molecular Science, Barts and The London, London, United Kingdom
| | - Tom Vulliamy
- Blizard Institute of Cell and Molecular Science, Barts and The London, London, United Kingdom
| | - Henry Houlden
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Nicholas Wood
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Una Sheerin
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Gian Paolo Tonini
- Translational Oncopathology, National Cancer Research Institute (IST), Genova, Italy
| | - Donna Mackay
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Khalid Hussain
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Jane Sowden
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Veronica Kinsler
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Justyna Osinska
- UCL Genomics, University College London, London, United Kingdom
| | - Tony Brooks
- UCL Genomics, University College London, London, United Kingdom
| | - Mike Hubank
- UCL Genomics, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Philip Beales
- GOSgene, UCL Institute of Child Health, University College London, London, United Kingdom
- UCL Institute of Child Health, University College London, London, United Kingdom
| | - Elia Stupka
- UCL Genomics, University College London, London, United Kingdom
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
- Cancer Institute, University College London, London, United Kingdom
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31
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Slade I, Bacchelli C, Davies H, Murray A, Abbaszadeh F, Hanks S, Barfoot R, Burke A, Chisholm J, Hewitt M, Jenkinson H, King D, Morland B, Pizer B, Prescott K, Saggar A, Side L, Traunecker H, Vaidya S, Ward P, Futreal PA, Vujanic G, Nicholson AG, Sebire N, Turnbull C, Priest JR, Pritchard-Jones K, Houlston R, Stiller C, Stratton MR, Douglas J, Rahman N. DICER1 syndrome: clarifying the diagnosis, clinical features and management implications of a pleiotropic tumour predisposition syndrome. J Med Genet 2011; 48:273-8. [DOI: 10.1136/jmg.2010.083790] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bacchelli C, Buckridge S, Thrasher AJ, Gaspar HB. Translational mini-review series on immunodeficiency: molecular defects in common variable immunodeficiency. Clin Exp Immunol 2007; 149:401-9. [PMID: 17697196 PMCID: PMC2219326 DOI: 10.1111/j.1365-2249.2007.03461.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Common variable immunodeficiency (CVID) is a primary immunodeficiency that typically affects adults and is characterized by abnormalities of quantative and qualitative humoral function that are heterogeneous in their immunological profile and clinical manifestations. The recent identification of four monogenic defects that result in the CVID phenotype also demonstrates that the genetic basis of CVID is highly variable. Mutations in the genes encoding the tumour necrosis factor (TNF) superfamily receptors transmembrane activator and calcium-modulating ligand interactor (TACI) and B cell activation factor of the TNF family receptor (BAFF-R), CD19 and the co-stimulatory molecule inducible co-stimulator molecule (ICOS) all lead to CVID and illustrate the complex interplay required to co-ordinate an effective humoral immune response. The molecular mechanisms leading to the immune defect are still not understood clearly and particularly in the case of TACI, where a number of heterozygous mutations have been found in affected individuals, the molecular pathogenesis of disease requires further elucidation. Together these defects account for perhaps 10-15% of all cases of CVID and it is highly likely that further genetic defects will be identified.
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Affiliation(s)
- C Bacchelli
- Molecular Immunology Unit, Institute of Child Health, London, UK
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33
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Pan-Hammarström Q, Salzer U, Du L, Björkander J, Cunningham-Rundles C, Nelson DL, Bacchelli C, Gaspar HB, Offer S, Behrens TW, Grimbacher B, Hammarström L. Reexamining the role of TACI coding variants in common variable immunodeficiency and selective IgA deficiency. Nat Genet 2007; 39:429-30. [PMID: 17392797 PMCID: PMC2931279 DOI: 10.1038/ng0407-429] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Beales PL, Bland E, Tobin JL, Bacchelli C, Tuysuz B, Hill J, Rix S, Pearson CG, Kai M, Hartley J, Johnson C, Irving M, Elcioglu N, Winey M, Tada M, Scambler PJ. IFT80, which encodes a conserved intraflagellar transport protein, is mutated in Jeune asphyxiating thoracic dystrophy. Nat Genet 2007; 39:727-9. [PMID: 17468754 DOI: 10.1038/ng2038] [Citation(s) in RCA: 268] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Accepted: 04/04/2007] [Indexed: 01/30/2023]
Abstract
Jeune asphyxiating thoracic dystrophy, an autosomal recessive chondrodysplasia, often leads to death in infancy because of a severely constricted thoracic cage and respiratory insufficiency; retinal degeneration, cystic renal disease and polydactyly may be complicating features. We show that IFT80 mutations underlie a subset of Jeune asphyxiating thoracic dystrophy cases, establishing the first association of a defective intraflagellar transport (IFT) protein with human disease. Knockdown of ift80 in zebrafish resulted in cystic kidneys, and knockdown in Tetrahymena thermophila produced shortened or absent cilia.
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Affiliation(s)
- Philip L Beales
- Molecular Medicine Unit, University College London (UCL) Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
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35
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Salzer U, Birmelin J, Bacchelli C, Witte T, Buchegger-Podbielski U, Buckridge S, Rzepka R, Gaspar HB, Thrasher AJ, Schmidt RE, Melchers I, Grimbacher B. Sequence Analysis of TNFRSF13b, Encoding TACI, in Patients with Systemic Lupus Erythematosus. J Clin Immunol 2007; 27:372-7. [PMID: 17464555 DOI: 10.1007/s10875-007-9094-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
B cell activating factor belonging to the TNF family (BAFF) and a proliferation inducing ligand (APRIL), and their receptors BAFF receptor (BAFFR), B cell maturation antigen (BCMA), and transmembrane activator and CAML interactor (TACI) are involved in the regulation of B cell homeostasis and differentiation. BAFF overexpression leads to systemic lupus erythematosus (SLE) in mice and elevated BAFF levels have been observed in human SLE and mouse models for SLE. Furthermore, genetic inactivation of TACI in mice results in a SLE-like phenotype. Based on our recent finding that TACI is mutated in patients with common variable immunodeficiency, of whom more than 30% suffer from autoimmune conditions, we analyzed TACI in humans with SLE. Sequence analysis of TNFRSF13b/TACI in 119 unrelated SLE patients revealed four variants: R20C in exon 1, R72H in exon 3, the silent variation c.327 G > A in exon 3, and A181E in exon 4. No significant association with any of these variants was found, when compared to the frequencies of the variants in a healthy control cohort. Furthermore, the mutated alleles R20C and R72H did not segregate with the SLE phenotype in familial cases of SLE. Thus, our evaluation of the coding region of TNFRSF13b/TACI did not reveal any deleterious or disease-associated mutations.
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Affiliation(s)
- Ulrich Salzer
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany
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36
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Bacchelli C, Wilson LC, Cook JA, Winter RM, Goodman FR. ROR2 is mutated in hereditary brachydactyly with nail dysplasia, but not in Sorsby syndrome. Clin Genet 2003; 64:263-5. [PMID: 12919145 DOI: 10.1034/j.1399-0004.2003.00139.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Morgan NV, Bacchelli C, Gissen P, Morton J, Ferrero GB, Silengo M, Labrune P, Casteels I, Hall C, Cox P, Kelly DA, Trembath RC, Scambler PJ, Maher ER, Goodman FR, Johnson CA. A locus for asphyxiating thoracic dystrophy, ATD, maps to chromosome 15q13. J Med Genet 2003; 40:431-5. [PMID: 12807964 PMCID: PMC1735497 DOI: 10.1136/jmg.40.6.431] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Asphyxiating thoracic dystrophy (ATD), or Jeune syndrome, is a multisystem autosomal recessive disorder associated with a characteristic skeletal dysplasia and variable renal, hepatic, pancreatic, and retinal abnormalities. We have performed a genome wide linkage search using autozygosity mapping in a cohort of four consanguineous families with ATD, three of which originate from Pakistan, and one from southern Italy. In these families, as well as in a fifth consanguineous family from France, we localised a novel ATD locus (ATD) to chromosome 15q13, with a maximum cumulative two point lod score at D15S1031 (Zmax=3.77 at theta=0.00). Five consanguineous families shared a 1.2 cM region of homozygosity between D15S165 and D15S1010. Investigation of a further four European kindreds, with no known parental consanguinity, showed evidence of marker homozygosity across a similar interval. Families with both mild and severe forms of ATD mapped to 15q13, but mutation analysis of two candidate genes, GREMLIN and FORMIN, did not show pathogenic mutations.
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Affiliation(s)
- N V Morgan
- Section of Medical and Molecular Genetics, Department of Paediatrics and Child Health, University of Birmingham Medical School, Birmingham B15 2TT, UK
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38
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Debeer P, Bacchelli C, Scambler PJ, De Smet L, Fryns JP, Goodman FR. Severe digital abnormalities in a patient heterozygous for both a novel missense mutation in HOXD13 and a polyalanine tract expansion in HOXA13. J Med Genet 2002; 39:852-6. [PMID: 12414828 PMCID: PMC1735011 DOI: 10.1136/jmg.39.11.852] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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Innis JW, Goodman FR, Bacchelli C, Williams TM, Mortlock DP, Sateesh P, Scambler PJ, McKinnon W, Guttmacher AE. A HOXA13 allele with a missense mutation in the homeobox and a dinucleotide deletion in the promoter underlies Guttmacher syndrome. Hum Mutat 2002; 19:573-4. [PMID: 11968094 DOI: 10.1002/humu.9036] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Guttmacher syndrome, a dominantly inherited combination of distal limb and genital tract abnormalities, has several features in common with hand-foot-genital syndrome (HFGS), including hypoplastic first digits and hypospadias. The presence of features not seen in HFGS, however, including postaxial polydactyly of the hands and uniphalangeal 2(nd) toes with absent nails, suggests that it represents a distinct entity. HFGS is caused by mutations in the HOXA13 gene. We have therefore re-investigated the original Guttmacher syndrome family, and have found that affected individuals are heterozygous for a novel missense mutation in the HOXA13 homeobox (c.1112A>T; homeodomain residue Q50L), which arose on an allele already carrying a novel 2-bp deletion (-78-79delGC) in the gene's highly conserved promoter region. This deletion produces no detectable abnormalities on its own, but may contribute to the phenotype in the affected individuals. The missense mutation, which alters a key residue in the recognition helix of the homeodomain, is likely to perturb HOXA13's DNA-binding properties, resulting in both a loss and a specific gain of function.
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Affiliation(s)
- Jeffrey W Innis
- Departments of Human Genetics and Pediatrics, University of Michigan, Ann Arbor, MI, USA.
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40
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41
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Goodman FR, Bacchelli C, Brady AF, Brueton LA, Fryns JP, Mortlock DP, Innis JW, Holmes LB, Donnenfeld AE, Feingold M, Beemer FA, Hennekam RC, Scambler PJ. Novel HOXA13 mutations and the phenotypic spectrum of hand-foot-genital syndrome. Am J Hum Genet 2000; 67:197-202. [PMID: 10839976 PMCID: PMC1287077 DOI: 10.1086/302961] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2000] [Accepted: 05/17/2000] [Indexed: 11/03/2022] Open
Abstract
Hand-foot-genital syndrome (HFGS) is a rare, dominantly inherited condition affecting the distal limbs and genitourinary tract. A nonsense mutation in the homeobox of HOXA13 has been identified in one affected family, making HFGS the second human syndrome shown to be caused by a HOX gene mutation. We have therefore examined HOXA13 in two new and four previously reported families with features of HFGS. In families 1, 2, and 3, nonsense mutations truncating the encoded protein N-terminal to or within the homeodomain produce typical limb and genitourinary abnormalities; in family 4, an expansion of an N-terminal polyalanine tract produces a similar phenotype; in family 5, a missense mutation, which alters an invariant domain, produces an exceptionally severe limb phenotype; and in family 6, in which limb abnormalities were atypical, no HOXA13 mutation could be detected. Mutations in HOXA13 can therefore cause more-severe limb abnormalities than previously suspected and may act by more than one mechanism.
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Affiliation(s)
- F R Goodman
- Molecular Medicine Unit, Institute of Child Health, London, United Kingdom.
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42
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Bacchelli C, Condom R, Patino N, Aubertin AM. Synthesis and biological activities of new carbaacyclonucleosides and 1'-oxaacyclonucleosides related to clitocine. Nucleosides Nucleotides Nucleic Acids 2000; 19:567-84. [PMID: 10843493 DOI: 10.1080/15257770008035008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
We describe the synthesis of two series of acyclonucleosides:carbaacyclonucleosides and 1'-oxaacyclonucleosides which possess the same aglycone as clitocine 3 which is a natural nucleoside exhibiting interesting biological properties. These compounds have been obtained by condensation of 4-aminobutanol or 3-silyloxypropoxyamine with 4,6-dichloro-5-nitropyrimidine. Structural modifications have been made on the heterocyclic base and the side chain to enhance their potential activity. All these compounds have been tested against different viruses: HIV-1, HSV-1, HSV-2, CMV, VZV, EBV. The carbaacyclonucleoside 10 was associated with an anti-EBV activity (EC50 = 0.86 microg/mL).
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Affiliation(s)
- C Bacchelli
- Laboratoire de Chimie Bio-Organique, CNRS ESA 6001, Université de Nice-Sophia Antipolis, Faculté des Sciences, France
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