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Kaplanis J, Samocha KE, Wiel L, Zhang Z, Arvai KJ, Eberhardt RY, Gallone G, Lelieveld SH, Martin HC, McRae JF, Short PJ, Torene RI, de Boer E, Danecek P, Gardner EJ, Huang N, Lord J, Martincorena I, Pfundt R, Reijnders MRF, Yeung A, Yntema HG, Vissers LELM, Juusola J, Wright CF, Brunner HG, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME, Gilissen C, Retterer K. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 2020; 586:757-762. [PMID: 33057194 PMCID: PMC7116826 DOI: 10.1038/s41586-020-2832-5] [Citation(s) in RCA: 253] [Impact Index Per Article: 63.3] [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: 10/08/2019] [Accepted: 07/17/2020] [Indexed: 01/28/2023]
Abstract
De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.
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Affiliation(s)
- Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jeremy F McRae
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick J Short
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jenny Lord
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Iñigo Martincorena
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Alison Yeung
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, UK
| | - Han G Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
- MHENS School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jeffrey C Barrett
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Kaplanis J, Akawi N, Gallone G, McRae JF, Prigmore E, Wright CF, Fitzpatrick DR, Firth HV, Barrett JC, Hurles ME. Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations. Genome Res 2019; 29:1047-1056. [PMID: 31227601 PMCID: PMC6633265 DOI: 10.1101/gr.239756.118] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/24/2019] [Indexed: 01/25/2023]
Abstract
Approximately 2% of de novo single-nucleotide variants (SNVs) appear as part of clustered mutations that create multinucleotide variants (MNVs). MNVs are an important source of genomic variability as they are more likely to alter an encoded protein than a SNV, which has important implications in disease as well as evolution. Previous studies of MNVs have focused on their mutational origins and have not systematically evaluated their functional impact and contribution to disease. We identified 69,940 MNVs and 91 de novo MNVs in 6688 exome-sequenced parent–offspring trios from the Deciphering Developmental Disorders Study comprising families with severe developmental disorders. We replicated the previously described MNV mutational signatures associated with DNA polymerase zeta, an error-prone translesion polymerase, and the APOBEC family of DNA deaminases. We estimate the simultaneous MNV germline mutation rate to be 1.78 × 10−10 mutations per base pair per generation. We found that most MNVs within a single codon create a missense change that could not have been created by a SNV. MNV-induced missense changes were, on average, more physicochemically divergent, were more depleted in highly constrained genes (pLI ≥ 0.9), and were under stronger purifying selection compared with SNV-induced missense changes. We found that de novo MNVs were significantly enriched in genes previously associated with developmental disorders in affected children. This shows that MNVs can be more damaging than SNVs even when both induce missense changes, and are an important variant type to consider in relation to human disease.
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Affiliation(s)
- Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Jeremy F McRae
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, United Kingdom
| | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, United Kingdom
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
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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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Jaganathan K, Kyriazopoulou Panagiotopoulou S, McRae JF, Darbandi SF, Knowles D, Li YI, Kosmicki JA, Arbelaez J, Cui W, Schwartz GB, Chow ED, Kanterakis E, Gao H, Kia A, Batzoglou S, Sanders SJ, Farh KKH. Predicting Splicing from Primary Sequence with Deep Learning. Cell 2019; 176:535-548.e24. [DOI: 10.1016/j.cell.2018.12.015] [Citation(s) in RCA: 464] [Impact Index Per Article: 92.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/31/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022]
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Lord J, Gallone G, Short PJ, McRae JF, Ironfield H, Wynn EH, Gerety SS, He L, Kerr B, Johnson DS, McCann E, Kinning E, Flinter F, Temple IK, Clayton-Smith J, McEntagart M, Lynch SA, Joss S, Douzgou S, Dabir T, Clowes V, McConnell VPM, Lam W, Wright CF, FitzPatrick DR, Firth HV, Barrett JC, Hurles ME. Pathogenicity and selective constraint on variation near splice sites. Genome Res 2018; 29:159-170. [PMID: 30587507 PMCID: PMC6360807 DOI: 10.1101/gr.238444.118] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [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: 04/13/2018] [Accepted: 12/20/2018] [Indexed: 12/29/2022]
Abstract
Mutations that perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7833 probands with developmental disorders (DDs) and their unaffected parents, as well as more than 60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice sites and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects, and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. By using mutational burden analyses in this large cohort of proband–parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking noncanonical positions (27%), and calculate the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at noncanonical positions in splice sites. We estimate 35%–40% of pathogenic variants in noncanonical splice site positions are missing from public databases.
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Affiliation(s)
- Jenny Lord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Patrick J Short
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jeremy F McRae
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Holly Ironfield
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Elizabeth H Wynn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sebastian S Gerety
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Liu He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, United Kingdom
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, OPD2, Northern General Hospital, Sheffield S5 7AU, United Kingdom
| | - Emma McCann
- Liverpool Women's Hospital Foundation Trust, Liverpool L8 7SS, United Kingdom
| | - Esther Kinning
- West of Scotland Regional Genetics Service, NHS Greater Glasgow and Clyde, Institute of Medical Genetics, Yorkhill Hospital, Glasgow G3 8SJ, United Kingdom
| | - Frances Flinter
- South East Thames Regional Genetics Centre, Guy's and St Thomas' NHS Foundation Trust, Guy's Hospital, London SE1 9RT, United Kingdom
| | - I Karen Temple
- Faculty of Medicine, University of Southampton, Institute of Developmental Sciences, Southampton SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, University Hospital Southampton, Princess Anne Hospital, Southampton SO16 5YA, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, United Kingdom
| | - Meriel McEntagart
- South West Thames Regional Genetics Centre, St. George's Healthcare NHS Trust, St. George's, University of London, London SW17 0RE, United Kingdom
| | | | - Shelagh Joss
- West of Scotland Regional Genetics Service, NHS Greater Glasgow and Clyde, Queen Elizabeth University Hospital, Glasgow G51 4TF, United Kingdom
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester M13 9NT, United Kingdom
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast BT9 7AB, United Kingom
| | - Virginia Clowes
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Northwick Park and St. Mark's Hospitals, Harrow HA1 3UJ, United Kingdom
| | - Vivienne P M McConnell
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast BT9 7AB, United Kingom
| | - Wayne Lam
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, United Kingdom
| | - David R FitzPatrick
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
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6
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Martin HC, Jones WD, McIntyre R, Sanchez-Andrade G, Sanderson M, Stephenson JD, Jones CP, Handsaker J, Gallone G, Bruntraeger M, McRae JF, Prigmore E, Short P, Niemi M, Kaplanis J, Radford EJ, Akawi N, Balasubramanian M, Dean J, Horton R, Hulbert A, Johnson DS, Johnson K, Kumar D, Lynch SA, Mehta SG, Morton J, Parker MJ, Splitt M, Turnpenny PD, Vasudevan PC, Wright M, Bassett A, Gerety SS, Wright CF, FitzPatrick DR, Firth HV, Hurles ME, Barrett JC. Quantifying the contribution of recessive coding variation to developmental disorders. Science 2018; 362:1161-1164. [PMID: 30409806 DOI: 10.1126/science.aar6731] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/10/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022]
Abstract
We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.
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Affiliation(s)
- Hilary C Martin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Great Ormond Street Hospital for Children, National Health Service (NHS) Foundation Trust, Great Ormond Street Hospital, Great Ormond Street, London WC1N 3JH, UK
| | - Rebecca McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Mark Sanderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James D Stephenson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Carla P Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Juliet Handsaker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Giuseppe Gallone
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Patrick Short
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mari Niemi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Joanna Kaplanis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Elizabeth J Radford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Paediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - John Dean
- Department of Genetics, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Rachel Horton
- Wessex Clinical Genetics Service, G Level, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - Alice Hulbert
- Cheshire and Merseyside Clinical Genetic Service, Liverpool Women's NHS Foundation Trust, Crown Street, Liverpool L8 7SS, UK
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, OPD2, Northern General Hospital, Herries Rd., Sheffield, S5 7AU, UK
| | - Katie Johnson
- Department of Clinical Genetics, City Hospital Campus, Hucknall Road, Nottingham NG5 1PB, UK
| | - Dhavendra Kumar
- Institute of Cancer and Genetics, University Hospital of Wales, Cardiff, UK
| | | | - Sarju G Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women's Hospital, Edgbaston, Birmingham B15 2TG, UK
| | - Michael J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Miranda Splitt
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter D Turnpenny
- Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Pradeep C Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester LE1 5WW, UK
| | - Michael Wright
- Northern Genetics Service, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew Bassett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sebastian S Gerety
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Research, Innovation, Learning and Development (RILD), Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
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7
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Sundaram L, Gao H, Padigepati SR, McRae JF, Li Y, Kosmicki JA, Fritzilas N, Hakenberg J, Dutta A, Shon J, Xu J, Batzoglou S, Li X, Farh KKH. Predicting the clinical impact of human mutation with deep neural networks. Nat Genet 2018; 50:1161-1170. [PMID: 30038395 PMCID: PMC6237276 DOI: 10.1038/s41588-018-0167-z] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [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: 01/29/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
Abstract
Millions of human genomes and exomes have been sequenced, but their clinical applications remain limited due to the difficulty of distinguishing disease-causing mutations from benign genetic variation. Here we demonstrate that common missense variants in other primate species are largely clinically benign in human, enabling pathogenic mutations to be systematically identified by the process of elimination. Using hundreds of thousands of common variants from population sequencing of six non-human primate species, we train a deep neural network that identifies pathogenic mutations in rare disease patients with 88% accuracy and enables the discovery of 14 new candidate genes in intellectual disability at genome-wide significance. Cataloging common variation from additional primate species would improve interpretation for millions of variants of uncertain significance, further advancing the clinical utility of human genome sequencing.
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Affiliation(s)
- Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Samskruthi Reddy Padigepati
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
- National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA
| | - Jeremy F McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Yanjun Li
- National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA
| | - Jack A Kosmicki
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
- Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nondas Fritzilas
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Jörg Hakenberg
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Anindita Dutta
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - John Shon
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Xiaolin Li
- National Science Foundation Center for Big Learning, University of Florida, Gainesville, FL, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA.
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8
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Short PJ, McRae JF, Gallone G, Sifrim A, Won H, Geschwind DH, Wright CF, Firth HV, FitzPatrick DR, Barrett JC, Hurles ME. De novo mutations in regulatory elements in neurodevelopmental disorders. Nature 2018; 555:611-616. [PMID: 29562236 PMCID: PMC5912909 DOI: 10.1038/nature25983] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [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: 02/24/2017] [Accepted: 01/24/2018] [Indexed: 12/23/2022]
Abstract
We previously estimated that 42% of patients with severe developmental disorders carry pathogenic de novo mutations in coding sequences. The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant twofold enrichment of recurrently mutated elements. We estimate that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasize the importance of combining functional and evolutionary evidence to identify regulatory causes of genetic disorders.
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Affiliation(s)
- Patrick J Short
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Giuseppe Gallone
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alejandro Sifrim
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Hyejung Won
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Center for Autism Research and Treatment, Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Caroline F Wright
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Level 4, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - David R FitzPatrick
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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9
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Wright CF, Fitzgerald TW, Jones WD, Clayton S, McRae JF, van Kogelenberg M, King DA, Ambridge K, Barrett DM, Bayzetinova T, Bevan AP, Bragin E, Chatzimichali EA, Gribble S, Jones P, Krishnappa N, Mason LE, Miller R, Morley KI, Parthiban V, Prigmore E, Rajan D, Sifrim A, Swaminathan GJ, Tivey AR, Middleton A, Parker M, Carter NP, Barrett JC, Hurles ME, FitzPatrick DR, Firth HV. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet 2015; 385:1305-14. [PMID: 25529582 PMCID: PMC4392068 DOI: 10.1016/s0140-6736(14)61705-0] [Citation(s) in RCA: 527] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount. METHODS The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team. FINDINGS Around 80,000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation. INTERPRETATION Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene-phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial. FUNDING Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health.
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Affiliation(s)
- Caroline F Wright
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
| | - Tomas W Fitzgerald
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Wendy D Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Stephen Clayton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Jeremy F McRae
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Daniel A King
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Kirsty Ambridge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Daniel M Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Tanya Bayzetinova
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - A Paul Bevan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Eugene Bragin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Susan Gribble
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Philip Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Laura E Mason
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ray Miller
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Katherine I Morley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Institute of Psychiatry, King's College London, London, UK; Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Vijaya Parthiban
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Diana Rajan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Alejandro Sifrim
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Adrian R Tivey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Anna Middleton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Michael Parker
- The Ethox Centre, Nuffield Department of Population Health University of Oxford, Old Road Campus, Oxford, UK
| | - Nigel P Carter
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, WGH, Edinburgh, UK
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK; Cambridge University Hospitals Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
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10
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Jaeger SR, McRae JF, Bava CM, Beresford MK, Hunter D, Jia Y, Chheang SL, Jin D, Peng M, Gamble JC, Atkinson KR, Axten LG, Paisley AG, Tooman L, Pineau B, Rouse SA, Newcomb RD. A Mendelian trait for olfactory sensitivity affects odor experience and food selection. Curr Biol 2013; 23:1601-5. [PMID: 23910657 DOI: 10.1016/j.cub.2013.07.030] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/27/2013] [Accepted: 07/03/2013] [Indexed: 11/25/2022]
Abstract
Humans vary in acuity to many odors [1-4], with variation within olfactory receptor (OR) genes contributing to these differences [5-9]. How such variation also affects odor experience and food selection remains uncertain [10], given that such effects occur for taste [11-15]. Here we investigate β-ionone, which shows extreme sensitivity differences [4, 16, 17]. β-ionone is a key aroma in foods and beverages [18-21] and is added to products in order to give a pleasant floral note [22, 23]. Genome-wide and in vitro assays demonstrate rs6591536 as the causal variant for β-ionone odor sensitivity. rs6591536 encodes a N183D substitution in the second extracellular loop of OR5A1 and explains >96% of the observed phenotypic variation, resembling a monogenic Mendelian trait. Individuals carrying genotypes for β-ionone sensitivity can more easily differentiate between food and beverage stimuli with and without added β-ionone. Sensitive individuals typically describe β-ionone in foods and beverages as "fragrant" and "floral," whereas less-sensitive individuals describe these stimuli differently. rs6591536 genotype also influences emotional associations and explains differences in food and product choices. These studies demonstrate that an OR variant that influences olfactory sensitivity can affect how people experience and respond to foods, beverages, and other products.
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Affiliation(s)
- Sara R Jaeger
- New Zealand Institute for Plant and Food Research, Auckland 1025, New Zealand
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11
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McRae JF, Mainland JD, Jaeger SR, Adipietro KA, Matsunami H, Newcomb RD. Genetic variation in the odorant receptor OR2J3 is associated with the ability to detect the "grassy" smelling odor, cis-3-hexen-1-ol. Chem Senses 2012; 37:585-93. [PMID: 22714804 DOI: 10.1093/chemse/bjs049] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The ability to detect many odors varies among individuals; however, the contribution of genotype to this variation has been assessed for relatively few compounds. We have identified a genetic basis for the ability to detect the flavor compound cis-3-hexen-1-ol. This compound is typically described as "green grassy" or the smell of "cut grass," with variation in the ability to detect it linked to single nucleotide polymorphisms (SNPs) in a region on human chromosome 6 containing 25 odorant receptor genes. We have sequenced the coding regions of all 25 receptors across an ethnically mixed population of 52 individuals and identified 147 sequence variants. We tested these for association with cis-3-hexen-1-ol detection thresholds and found 3 strongly associated SNPs, including one found in a functional odorant receptor (rs28757581 in OR2J3). In vitro assays of 13 odorant receptors from the region identified 3 receptors that could respond to cis-3-hexen-1-ol, including OR2J3. This gene contained 5 predicted haplotypes across the 52 individuals. We tested all 5 haplotypes in vitro and several amino acid substitutions on their own, such as rs28757581 (T113A). Two amino acid substitutions, T113A and R226Q, impaired the ability of OR2J3 to respond to cis-3-hexen-1-ol, and together these two substitutions effectively abolished the response to the compound. The haplotype of OR2J3 containing both T113A and R226Q explains 26.4% of the variation in cis-3-hexen-1-ol detection in our study cohort. Further research is required to examine whether OR2J3 haplotypes explain variation in perceived flavor experience and the consumption of foods containing cis-3-hexen-1-ol.
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Affiliation(s)
- Jeremy F McRae
- Food Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
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12
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Jaeger SR, McRae JF, Salzman Y, Williams L, Newcomb RD. A preliminary investigation into a genetic basis for cis-3-hexen-1-ol odour perception: A genome-wide association approach. Food Qual Prefer 2010. [DOI: 10.1016/j.foodqual.2009.08.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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