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Wojcik MH, Lemire G, Zaki MS, Wissman M, Win W, White S, Weisburd B, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Okur V, Oja KT, O'Leary M, O'Heir E, Morel C, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gazda HT, Ganesh VS, Ganapathy M, Gallacher L, Fu J, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bonnemann C, Beggs AH, Baxter SM, Agrawal PB, Talkowski M, Austin-Tse C, Rehm HL, O'Donnell-Luria A. Unique Capabilities of Genome Sequencing for Rare Disease Diagnosis. medRxiv 2023:2023.08.08.23293829. [PMID: 38328047 PMCID: PMC10849673 DOI: 10.1101/2023.08.08.23293829] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Background Causal variants underlying rare disorders may remain elusive even after expansive gene panels or exome sequencing (ES). Clinicians and researchers may then turn to genome sequencing (GS), though the added value of this technique and its optimal use remain poorly defined. We therefore investigated the advantages of GS within a phenotypically diverse cohort. Methods GS was performed for 744 individuals with rare disease who were genetically undiagnosed. Analysis included review of single nucleotide, indel, structural, and mitochondrial variants. Results We successfully solved 218/744 (29.3%) cases using GS, with most solves involving established disease genes (157/218, 72.0%). Of all solved cases, 148 (67.9%) had previously had non-diagnostic ES. We systematically evaluated the 218 causal variants for features requiring GS to identify and 61/218 (28.0%) met these criteria, representing 8.2% of the entire cohort. These included small structural variants (13), copy neutral inversions and complex rearrangements (8), tandem repeat expansions (6), deep intronic variants (15), and coding variants that may be more easily found using GS related to uniformity of coverage (19). Conclusion We describe the diagnostic yield of GS in a large and diverse cohort, illustrating several types of pathogenic variation eluding ES or other techniques. Our results reveal a higher diagnostic yield of GS, supporting the utility of a genome-first approach, with consideration of GS as a secondary or tertiary test when higher-resolution structural variant analysis is needed or there is a strong clinical suspicion for a condition and prior targeted genetic testing has been negative.
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Butters A, Do J, Stafford F, Krishnan N, Brown J, Hespe S, Richardson E, Bagnall R, Bhaskaran A, Burns C, Driscoll T, Fatkin D, Gray B, Iglesias C, Isbister J, Jabbour A, Johnson R, Kumar S, Leslie F, MacArthur D, Nowak N, Pouliopoulos J, Puranik R, Semsarian C, Sweeting J, Sy R, Ugander M, Yeates L, Ingles J. NSW HEARTS: The NSW Inherited Cardiomyopathy Cohort Study protocol. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Richardson E, Krishnan N, Stafford F, Yeates L, Nowak N, McGaughran J, Wildschutt J, Smith J, Turner C, Kevin L, Davis A, Macciocca I, Connell V, Ma A, Semsarian C, Bagnall R, Siggs O, Skinner J, MacArthur D, Ingles J. The Elusive Hearts Study: Seeking Genetic Diagnoses in Gene-elusive Cases of Rare Monogenic Cardiovascular Diseases. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.04.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Dworschak GC, Punetha J, Kalanithy JC, Mingardo E, Erdem HB, Akdemir ZC, Karaca E, Mitani T, Marafi D, Fatih JM, Jhangiani SN, Hunter JV, Dakal TC, Dhabhai B, Dabbagh O, Alsaif HS, Alkuraya FS, Maroofian R, Houlden H, Efthymiou S, Dominik N, Salpietro V, Sultan T, Haider S, Bibi F, Thiele H, Hoefele J, Riedhammer KM, Wagner M, Guella I, Demos M, Keren B, Buratti J, Charles P, Nava C, Héron D, Heide S, Valkanas E, Waddell LB, Jones KJ, Oates EC, Cooper ST, MacArthur D, Syrbe S, Ziegler A, Platzer K, Okur V, Chung WK, O'Shea SA, Alcalay R, Fahn S, Mark PR, Guerrini R, Vetro A, Hudson B, Schnur RE, Hoganson GE, Burton JE, McEntagart M, Lindenberg T, Yilmaz Ö, Odermatt B, Pehlivan D, Posey JE, Lupski JR, Reutter H. Biallelic and monoallelic variants in PLXNA1 are implicated in a novel neurodevelopmental disorder with variable cerebral and eye anomalies. Genet Med 2021; 23:1715-1725. [PMID: 34054129 PMCID: PMC8460429 DOI: 10.1038/s41436-021-01196-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 09/02/2020] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To investigate the effect of PLXNA1 variants on the phenotype of patients with autosomal dominant and recessive inheritance patterns and to functionally characterize the zebrafish homologs plxna1a and plxna1b during development. METHODS We assembled ten patients from seven families with biallelic or de novo PLXNA1 variants. We describe genotype-phenotype correlations, investigated the variants by structural modeling, and used Morpholino knockdown experiments in zebrafish to characterize the embryonic role of plxna1a and plxna1b. RESULTS Shared phenotypic features among patients include global developmental delay (9/10), brain anomalies (6/10), and eye anomalies (7/10). Notably, seizures were predominantly reported in patients with monoallelic variants. Structural modeling of missense variants in PLXNA1 suggests distortion in the native protein. Our zebrafish studies enforce an embryonic role of plxna1a and plxna1b in the development of the central nervous system and the eye. CONCLUSION We propose that different biallelic and monoallelic variants in PLXNA1 result in a novel neurodevelopmental syndrome mainly comprising developmental delay, brain, and eye anomalies. We hypothesize that biallelic variants in the extracellular Plexin-A1 domains lead to impaired dimerization or lack of receptor molecules, whereas monoallelic variants in the intracellular Plexin-A1 domains might impair downstream signaling through a dominant-negative effect.
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Affiliation(s)
- Gabriel C Dworschak
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany.
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany.
- Department of Pediatrics, University Hospital Bonn, Bonn, Germany.
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeshurun C Kalanithy
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Enrico Mingardo
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Haktan B Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, TX, USA
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Bhanupriya Dhabhai
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
| | - Omar Dabbagh
- Department of Neuroscience, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health, The Children's Hospital Lahore, Lahore, Pakistan
| | - Shahzad Haider
- Department of Paediatric Medicine, Wah Medical College, Rawalpindi, Pakistan
| | - Farah Bibi
- University Institute of Biochemistry & Biotechnology, PMAS - Arid Agriculture University, Rawalpindi, Pakistan
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ilaria Guella
- Department of Medical Genetics, Centre for Applied Neurogenetics, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Boris Keren
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Julien Buratti
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Perrine Charles
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Caroline Nava
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
- Institut du Cerveau et de la Moelle épinière, Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, Paris, France
| | - Delphine Héron
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Solveig Heide
- AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Elise Valkanas
- Center for Mendelian Genomics, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Leigh B Waddell
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Emily C Oates
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Children's Medical Research Institute, Westmead, NSW, Australia
| | - Daniel MacArthur
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steffen Syrbe
- Division of Pediatric Epileptology, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Ziegler
- Division of Pediatric Neurology and Metabolic Medicine, Centre for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Volkan Okur
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Sarah A O'Shea
- Department of Neurology, Columbia University, New York, NY, USA
| | - Roy Alcalay
- Department of Neurology, Columbia University, New York, NY, USA
| | - Stanley Fahn
- Department of Neurology, Columbia University, New York, NY, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital Grand Rapids, New York, MI, USA
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Annalisa Vetro
- Neuroscience Department, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | | | | | - George E Hoganson
- Department of Pediatrics, University of Illinois, College of Medicine, Chicago, IL, USA
| | - Jennifer E Burton
- Department of Pediatrics, University of Illinois, College of Medicine, Peoria, IL, USA
| | - Meriel McEntagart
- South West Thames Regional Genetics Centre, St. George's Healthcare NHS Trust, St. George's, University of London, London, United Kingdom
| | - Tobias Lindenberg
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Öznur Yilmaz
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin Odermatt
- Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, Bonn, Germany
- Institute of Neuroanatomy, Medical Faculty, University of Bonn, Bonn, Germany
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Heiko Reutter
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany
- Department of Neonatology and Pediatric Intensive Care, University Hospital Bonn, Bonn, Germany
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Natera-de Benito D, Zaharieva I, Pini V, Manzur A, Munot P, DiTroia SP, Gioia SD, Jurgens J, Barry B, England E, Ledoux D, O´Donell-Luria A, MacArthur D, Feng L, Phadke R, Sarkozy A, Engle E, Muntoni F. CONGENITAL MUSCULAR DYSTROPHIES. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mroczek M, Töpf A, Specht S, Johnson K, Philips L, England E, Chao K, MacArthur D, Straub V. LIMB GIRDLE MUSCULAR DYSTROPHIES. Neuromuscul Disord 2020. [DOI: 10.1016/j.nmd.2020.08.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bolduc V, Foley A, Solomon Degefa H, Sarathy A, Donkervoort S, Hu Y, Zhou H, Cummings B, Lek M, Regev O, Jimenez-Mallebrera C, Allamand V, Ferlini A, Wilton S, Hanssen E, Lamandé S, MacArthur D, Wagener R, Muntoni F, Bönnemann C. O.10A novel target for splice-modulating therapies: a common pseudoexon-inducing mutation that causes a severe collagen VI-related muscular dystrophy. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Topf A, Johnson K, Mroczek M, Phillips L, Duff J, Valkanas E, England E, MacArthur D, Straub V, MYO-SEQ consortium. E-POSTERS – NEXT GENERATION SEQUENCING. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Topf A, Casasus A, Barresi R, Johnson K, Mroczek M, Duff J, Phillips L, England E, Xu L, Valkanas E, MacArthur D, Straub V, MYO-SEQ consortium. P.175Detection and interpretation of variants in dystroglycanopathy-causing genes in a cohort of 1,566 patients with unexplained limb-girdle muscle weakness. Neuromuscul Disord 2019. [DOI: 10.1016/j.nmd.2019.06.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Donkervoort S, Dowling JJ, Laporte J, MacArthur D, Bönnemann CG. 214th ENMC International Workshop: Establishing an international consortium for gene discovery and clinical research for Congenital Muscle Disease, Heemskerk, the Netherlands, 6-18 October 2015. Neuromuscul Disord 2019; 29:644-650. [PMID: 31400830 DOI: 10.1016/j.nmd.2019.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - James J Dowling
- Division of Neurology, Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, Illkirch, France
| | | | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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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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Marks P, Garcia S, Barrio AM, Belhocine K, Bernate J, Bharadwaj R, Bjornson K, Catalanotti C, Delaney J, Fehr A, Fiddes IT, Galvin B, Heaton H, Herschleb J, Hindson C, Holt E, Jabara CB, Jett S, Keivanfar N, Kyriazopoulou-Panagiotopoulou S, Lek M, Lin B, Lowe A, Mahamdallie S, Maheshwari S, Makarewicz T, Marshall J, Meschi F, O'Keefe CJ, Ordonez H, Patel P, Price A, Royall A, Ruark E, Seal S, Schnall-Levin M, Shah P, Stafford D, Williams S, Wu I, Xu AW, Rahman N, MacArthur D, Church DM. Resolving the full spectrum of human genome variation using Linked-Reads. Genome Res 2019; 29:635-645. [PMID: 30894395 PMCID: PMC6442396 DOI: 10.1101/gr.234443.118] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [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: 01/09/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023]
Abstract
Large-scale population analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short-read whole-genome sequencing. However, these short-read approaches fail to give a complete picture of a genome. They struggle to identify structural events, cannot access repetitive regions, and fail to resolve the human genome into haplotypes. Here, we describe an approach that retains long range information while maintaining the advantages of short reads. Starting from ∼1 ng of high molecular weight DNA, we produce barcoded short-read libraries. Novel informatic approaches allow for the barcoded short reads to be associated with their original long molecules producing a novel data type known as "Linked-Reads". This approach allows for simultaneous detection of small and large variants from a single library. In this manuscript, we show the advantages of Linked-Reads over standard short-read approaches for reference-based analysis. Linked-Reads allow mapping to 38 Mb of sequence not accessible to short reads, adding sequence in 423 difficult-to-sequence genes including disease-relevant genes STRC, SMN1, and SMN2 Both Linked-Read whole-genome and whole-exome sequencing identify complex structural variations, including balanced events and single exon deletions and duplications. Further, Linked-Reads extend the region of high-confidence calls by 68.9 Mb. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adrian Fehr
- 10x Genomics, Pleasanton, California 94566, USA
| | | | | | | | | | | | - Esty Holt
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London SM2 5NG, United Kingdom
| | | | | | | | | | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Bill Lin
- 10x Genomics, Pleasanton, California 94566, USA
| | - Adam Lowe
- 10x Genomics, Pleasanton, California 94566, USA
| | - Shazia Mahamdallie
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London SM2 5NG, United Kingdom
| | | | | | - Jamie Marshall
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | | | | | | | | | - Elise Ruark
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London SM2 5NG, United Kingdom
| | - Sheila Seal
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London SM2 5NG, United Kingdom
| | | | - Preyas Shah
- 10x Genomics, Pleasanton, California 94566, USA
| | | | | | - Indira Wu
- 10x Genomics, Pleasanton, California 94566, USA
| | | | - Nazneen Rahman
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London SM2 5NG, United Kingdom
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Donkervoort S, Foley A, Saade D, Neuhaus S, Mohassel P, Bharucha-Goebel D, Chao K, Cummings B, Lek M, MacArthur D, Bönnemann C. NEXT GENERATION SEQUENCING AND EXPERIMENTAL MYOLOGY. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Donkervoort S, Hu Y, Shieh P, Koliwer J, Tsai L, Cummings B, Snyder M, Chao K, Kaur R, Bharucha-Goebel D, Iannaccone S, MacArthur D, Foley A, Schwake M, Bönnemann C. NEW GENES, FUNCTIONS AND BIOMARKERS. Neuromuscul Disord 2018. [DOI: 10.1016/j.nmd.2018.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Jamshidi F, Place EM, Mehrotra S, Navarro-Gomez D, Maher M, Branham KE, Valkanas E, Cherry TJ, Lek M, MacArthur D, Pierce EA, Bujakowska KM. Contribution of noncoding pathogenic variants to RPGRIP1-mediated inherited retinal degeneration. Genet Med 2018; 21:694-704. [PMID: 30072743 PMCID: PMC6399075 DOI: 10.1038/s41436-018-0104-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 04/03/2018] [Accepted: 06/15/2018] [Indexed: 11/22/2022] Open
Abstract
Purpose: With the advent of gene therapies for inherited retinal degenerations (IRDs), genetic diagnostics will have an increasing role in clinical decision-making. Yet the genetic cause of disease cannot be identified using exon-based sequencing for a significant portion of patients. We hypothesized that non-coding mutations contribute significantly to the genetic causality of IRDs and evaluated patients with single coding mutations in RPGRIP1 to test this hypothesis. Methods: IRD families underwent targeted panel sequencing. Unsolved cases were explored by whole exome and genome sequencing looking for additional mutations. Candidate mutations were then validated by Sanger sequencing, quantitative PCR, and in vitro splicing assays in two cell lines analyzed through amplicon sequencing. Results: Among 1722 families, three had biallelic loss of function mutations in RPGRIP1 while seven had a single disruptive coding mutation. Whole exome and genome sequencing revealed potential non-coding mutations in these seven families. In six, the non-coding mutations were shown to lead to loss of function in vitro. Conclusion: Non-coding mutations were identified in 6 of 7 families with single coding mutations in RPGRIP1. The results suggest that non-coding mutations contribute significantly to the genetic causality of IRDs and RPGRIP1–mediated IRDs are more common than previously thought.
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Affiliation(s)
- Farzad Jamshidi
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily M Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathew Maher
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elise Valkanas
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Timothy J Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute and University of Washington, Department of Pediatrics, Seattle, Washington, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA.
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA.
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Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D. A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat Methods 2018; 15:595-597. [PMID: 30013044 PMCID: PMC6341484 DOI: 10.1038/s41592-018-0054-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [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: 11/22/2017] [Accepted: 05/14/2018] [Indexed: 12/30/2022]
Abstract
Existing benchmark datasets for use in evaluating variant-calling accuracy are constructed from a consensus of known short-variant callers, and they are thus biased toward easy regions that are accessible by these algorithms. We derived a new benchmark dataset from the de novo PacBio assemblies of two fully homozygous human cell lines, which provides a relatively more accurate and less biased estimate of small-variant-calling error rates in a realistic context.
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Affiliation(s)
- Heng Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | | | - Yossi Farjoun
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mark Fleharty
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Benjamin Neale
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
| | - Daniel MacArthur
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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18
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Ganna A, Satterstrom FK, Zekavat SM, Das I, Kurki MI, Churchhouse C, Alfoldi J, Martin AR, Havulinna AS, Byrnes A, Thompson WK, Nielsen PR, Karczewski KJ, Saarentaus E, Rivas MA, Gupta N, Pietiläinen O, Emdin CA, Lescai F, Bybjerg-Grauholm J, Flannick J, Mercader JM, Udler M, Laakso M, Salomaa V, Hultman C, Ripatti S, Hämäläinen E, Moilanen JS, Körkkö J, Kuismin O, Nordentoft M, Hougaard DM, Mors O, Werge T, Mortensen PB, MacArthur D, Daly MJ, Sullivan PF, Locke AE, Palotie A, Børglum AD, Kathiresan S, Neale BM, Palotie A, Børglum AD, Kathiresan S, Neale BM. Quantifying the Impact of Rare and Ultra-rare Coding Variation across the Phenotypic Spectrum. Am J Hum Genet 2018; 102:1204-1211. [PMID: 29861106 DOI: 10.1016/j.ajhg.2018.05.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/02/2018] [Indexed: 10/14/2022] Open
Abstract
There is a limited understanding about the impact of rare protein-truncating variants across multiple phenotypes. We explore the impact of this class of variants on 13 quantitative traits and 10 diseases using whole-exome sequencing data from 100,296 individuals. Protein-truncating variants in genes intolerant to this class of mutations increased risk of autism, schizophrenia, bipolar disorder, intellectual disability, and ADHD. In individuals without these disorders, there was an association with shorter height, lower education, increased hospitalization, and reduced age at enrollment. Gene sets implicated from GWASs did not show a significant protein-truncating variants burden beyond what was captured by established Mendelian genes. In conclusion, we provide a thorough investigation of the impact of rare deleterious coding variants on complex traits, suggesting widespread pleiotropic risk.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Aarno Palotie
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki 00290, Finland
| | - Anders D Børglum
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus 8210, Denmark; Department of Biomedicine - Human Genetics, Aarhus University, Aarhus 8210, Denmark
| | - Sekar Kathiresan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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19
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Harris E, Marini-Bettolo C, Töpf A, Barresi R, Polvikoski T, Bailey G, Charlton R, Tellez J, MacArthur D, Guglieri M, Lochmüller H, Bushby K, Straub V. MEGF10 related myopathies: A new case with adult onset disease with prominent respiratory failure and review of reported phenotypes. Neuromuscul Disord 2018; 28:48-53. [DOI: 10.1016/j.nmd.2017.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/21/2017] [Accepted: 09/28/2017] [Indexed: 11/25/2022]
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20
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Mercader JM, Liao RG, Bell AD, Dymek Z, Estrada K, Tukiainen T, Huerta-Chagoya A, Moreno-Macías H, Jablonski KA, Hanson RL, Walford GA, Moran I, Chen L, Agarwala V, Ordoñez-Sánchez ML, Rodríguez-Guillen R, Rodríguez-Torres M, Segura-Kato Y, García-Ortiz H, Centeno-Cruz F, Barajas-Olmos F, Caulkins L, Puppala S, Fontanillas P, Williams AL, Bonàs-Guarch S, Hartl C, Ripke S, Tooley K, Lane J, Zerrweck C, Martínez-Hernández A, Córdova EJ, Mendoza-Caamal E, Contreras-Cubas C, González-Villalpando ME, Cruz-Bautista I, Muñoz-Hernández L, Gómez-Velasco D, Alvirde U, Henderson BE, Wilkens LR, Le Marchand L, Arellano-Campos O, Riba L, Harden M, Gabriel S, Abboud HE, Cortes ML, Revilla-Monsalve C, Islas-Andrade S, Soberon X, Curran JE, Jenkinson CP, DeFronzo RA, Lehman DM, Hanis CL, Bell GI, Boehnke M, Blangero J, Duggirala R, Saxena R, MacArthur D, Ferrer J, McCarroll SA, Torrents D, Knowler WC, Baier LJ, Burtt N, González-Villalpando C, Haiman CA, Aguilar-Salinas CA, Tusié-Luna T, Flannick J, Jacobs SBR, Orozco L, Altshuler D, Florez JC. A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. Diabetes 2017; 66:2903-2914. [PMID: 28838971 PMCID: PMC5652606 DOI: 10.2337/db17-0187] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/13/2017] [Indexed: 12/12/2022]
Abstract
Type 2 diabetes (T2D) affects more than 415 million people worldwide, and its costs to the health care system continue to rise. To identify common or rare genetic variation with potential therapeutic implications for T2D, we analyzed and replicated genome-wide protein coding variation in a total of 8,227 individuals with T2D and 12,966 individuals without T2D of Latino descent. We identified a novel genetic variant in the IGF2 gene associated with ∼20% reduced risk for T2D. This variant, which has an allele frequency of 17% in the Mexican population but is rare in Europe, prevents splicing between IGF2 exons 1 and 2. We show in vitro and in human liver and adipose tissue that the variant is associated with a specific, allele-dosage-dependent reduction in the expression of IGF2 isoform 2. In individuals who do not carry the protective allele, expression of IGF2 isoform 2 in adipose is positively correlated with both incidence of T2D and increased plasma glycated hemoglobin in individuals without T2D, providing support that the protective effects are mediated by reductions in IGF2 isoform 2. Broad phenotypic examination of carriers of the protective variant revealed no association with other disease states or impaired reproductive health. These findings suggest that reducing IGF2 isoform 2 expression in relevant tissues has potential as a new therapeutic strategy for T2D, even beyond the Latin American population, with no major adverse effects on health or reproduction.
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Affiliation(s)
- Josep M Mercader
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Rachel G Liao
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Avery D Bell
- Department of Genetics, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Zachary Dymek
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Karol Estrada
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Taru Tukiainen
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Alicia Huerta-Chagoya
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Universidad Autónoma Metropolitana, Mexico City, Mexico
| | | | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ
| | - Geoffrey A Walford
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Ignasi Moran
- Department of Medicine, Imperial College London, London, U.K
| | - Ling Chen
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Vineeta Agarwala
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - María Luisa Ordoñez-Sánchez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rosario Rodríguez-Guillen
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Maribel Rodríguez-Torres
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Yayoi Segura-Kato
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | | | - Lizz Caulkins
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Sobha Puppala
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Pierre Fontanillas
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Amy L Williams
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY
| | - Sílvia Bonàs-Guarch
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona, Spain
| | - Chris Hartl
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Stephan Ripke
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katherine Tooley
- Department of Genetics, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Jacqueline Lane
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Carlos Zerrweck
- Clínica Integral de Cirugía para la Obesidad y Enfermedades Metabólicas, Hospital General Tláhuac, Mexico City, Mexico
| | | | | | | | | | - María E González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | - Ivette Cruz-Bautista
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Liliana Muñoz-Hernández
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Donaji Gómez-Velasco
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Ulises Alvirde
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Loic Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI
| | - Olimpia Arellano-Campos
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Laura Riba
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Maegan Harden
- The Genomics Platform, Broad Institute, Cambridge, MA
| | | | | | | | - Hanna E Abboud
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | | | - Cristina Revilla-Monsalve
- Unidad de Investigación Médica en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Sergio Islas-Andrade
- Unidad de Investigación Médica en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Xavier Soberon
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX
| | - Christopher P Jenkinson
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX
| | - Ralph A DeFronzo
- Division of Diabetes, Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Donna M Lehman
- Departments of Medicine and Cellular & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Craig L Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | - Graeme I Bell
- Department of Medicine, The University of Chicago, Chicago, IL
- Department of Human Genetics, The University of Chicago, Chicago, IL
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI
| | - John Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX
| | - Ravindranath Duggirala
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Edinburg, TX
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Daniel MacArthur
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Jorge Ferrer
- Department of Medicine, Imperial College London, London, U.K
- Genomic Programming of Beta Cells and Diabetes, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- CIBERDEM, Barcelona, Spain
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - David Torrents
- Barcelona Supercomputing Center, Joint BSC-CRG-IRB Research Programme in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ
| | - Noel Burtt
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Clicerio González-Villalpando
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Pública, Mexico City, Mexico
| | | | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jason Flannick
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Molecular Biology, Harvard Medical School, Boston, MA
| | - Suzanne B R Jacobs
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - David Altshuler
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Molecular Biology, Harvard Medical School, Boston, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jose C Florez
- Broad Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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Oates E, Yau K, Jones K, Smith J, Cummings B, Farrar M, Cooper S, Lek M, Hoffman E, Straub V, Ferreiro A, Udd B, Beggs A, Bönnemann C, North K, MacArthur D, Granzier H, Muntoni F, Davis M, Laing N. Do titin developmental isoforms contribute to the pathogenesis of congenital titinopathy? Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Reghan Foley A, Donkervoort S, Bolduc V, Hu Y, Cummings B, Lek M, Sarkozy A, Jimenez-Mallebrera C, Butterfield R, Lamande S, Kirschner J, Allamand V, Stojkovic T, Quijano-Roy S, Gualandi F, Ferlini A, Bertini E, MacArthur D, Muntoni F, Bönnemann C. A common COL6A1 deep-intronic pseudo-exon inserting mutation causes a distinct phenotype of Ullrich congenital muscular dystrophy. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Johnson K, Töpf A, Bertoli M, Phillips L, De Ridder W, Baets J, De Jonghe P, Deconinck T, Rakocevic Stojanovic V, Perić S, Durmus H, Jamal-Omidi S, Nafissi S, Łusakowska A, Mongini T, Lek M, Valkanas E, Mullen T, Xu L, MacArthur D, Straub V. Detection of TRIM32 variants associated with LGMD2H in a large cohort of patients with unexplained limb-girdle weakness. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Harris E, Topf A, Barresi R, Hudson J, Powell H, Tellez J, Hicks D, Porter A, Bertoli M, Evangelista T, Marini-Betollo C, Magnússon Ó, Lek M, MacArthur D, Bushby K, Lochmüller H, Straub V. Exome sequences versus sequential gene testing in the UK highly specialised Service for Limb Girdle Muscular Dystrophy. Orphanet J Rare Dis 2017; 12:151. [PMID: 28877744 PMCID: PMC5588739 DOI: 10.1186/s13023-017-0699-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 06/01/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Limb girdle muscular dystrophies are a group of rare and genetically heterogeneous diseases that share proximal weakness as a common feature; however they are often lacking very specific phenotypic features to allow an accurate differential diagnosis based on the clinical signs only, limiting the diagnostic rate using phenotype driven genetic testing. Next generation sequencing provides an opportunity to obtain molecular diagnoses for undiagnosed patients, as well as identifying novel genetic causes of muscle diseases. We performed whole exome sequencing (WES) on 104 affected individuals from 75 families in who standard gene by gene testing had not yielded a diagnosis. For comparison we also evaluated the diagnostic rate using sequential gene by gene testing for 91 affected individuals from 84 families over a 2 year period. RESULTS Patients selected for WES had undergone more extensive prior testing than those undergoing standard genetic testing and on average had had 8 genes screened already. In this extensively investigated cohort WES identified the genetic diagnosis in 28 families (28/75, 37%), including the identification of the novel gene ZAK and two unpublished genes. WES of a single affected individual with sporadic disease yielded a diagnosis in 13/38 (34%) of cases. In comparison, conventional gene by gene testing provided a genetic diagnosis in 28/84 (33%) families. Titinopathies and collagen VI related dystrophy were the most frequent diagnoses made by WES. Reasons why mutations in known genes were not identified previously included atypical phenotypes, reassignment of pathogenicity of variants, and in one individual mosaicism for a COL6A1 mutation which was undetected by prior direct sequencing. CONCLUSION WES was able to overcome many limitations of standard testing and achieved a higher rate of diagnosis than standard testing even in this cohort of extensively investigated patients. Earlier application of WES is therefore likely to yield an even higher diagnostic rate. We obtained a high diagnosis rate in simplex cases and therefore such individuals should be included in exome or genome sequencing projects. Disease due to somatic mosaicism may be increasingly recognised due to the increased sensitivity of next generation sequencing techniques to detect low level mosaicism.
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Affiliation(s)
- Elizabeth Harris
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ana Topf
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rita Barresi
- Muscle Immunoanalysis Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4AZ, UK
| | - Judith Hudson
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Powell
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - James Tellez
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Debbie Hicks
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Anna Porter
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Marta Bertoli
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Teresinha Evangelista
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Chiara Marini-Betollo
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | | | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Kate Bushby
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Hanns Lochmüller
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. .,Newcastle University John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
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Harris E, Töpf A, Vihola A, Evilä A, Barresi R, Hudson J, Hackman P, Herron B, MacArthur D, Lochmüller H, Bushby K, Udd B, Straub V. A 'second truncation' in TTN causes early onset recessive muscular dystrophy. Neuromuscul Disord 2017; 27:1009-1017. [PMID: 28716623 DOI: 10.1016/j.nmd.2017.06.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/14/2017] [Accepted: 06/19/2017] [Indexed: 11/24/2022]
Abstract
Mutations in the gene encoding the giant skeletal muscle protein titin are associated with a variety of muscle disorders, including recessive congenital myopathies ±cardiomyopathy, limb girdle muscular dystrophy (LGMD) and late onset dominant distal myopathy. Heterozygous truncating mutations have also been linked to dilated cardiomyopathy. The phenotypic spectrum of titinopathies is emerging and expanding, as next generation sequencing techniques make this large gene amenable to sequencing. We undertook whole exome sequencing in four individuals with LGMD. An essential splice site mutation, previously reported in dilated cardiomyopathy, was identified in all families in combination with a second truncating mutation. Affected individuals presented with childhood onset proximal weakness associated with joint contractures and elevated CK. Cardiac dysfunction was present in two individuals. Muscle biopsy showed increased internal nuclei and immunoblotting identified reduction or absence of calpain-3 and demonstrated a marked reduction of C-terminal titin fragments. We confirm the co-occurrence of cardiac and skeletal myopathies associated with recessive truncating titin mutations. Compound heterozygosity of a truncating mutation previously associated with dilated cardiomyopathy and a 'second truncation' in TTN was identified as causative in our skeletal myopathy patients. These findings add to the complexity of interpretation and genetic counselling for titin mutations.
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Affiliation(s)
- Elizabeth Harris
- Newcastle University, John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Ana Töpf
- Newcastle University, John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Anna Vihola
- Folkhälsan Institute of Genetics, Helsinki University, Helsinki, Finland
| | - Anni Evilä
- Folkhälsan Institute of Genetics, Helsinki University, Helsinki, Finland
| | - Rita Barresi
- Newcastle University, John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle upon Tyne, UK; Muscle Immunoanalysis Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4AZ, UK
| | - Judith Hudson
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Peter Hackman
- Folkhälsan Institute of Genetics, Helsinki University, Helsinki, Finland
| | - Brian Herron
- Department of Pathology, Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Hanns Lochmüller
- Newcastle University, John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Kate Bushby
- Newcastle University, John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle upon Tyne, UK
| | - Bjarne Udd
- Folkhälsan Institute of Genetics, Helsinki University, Helsinki, Finland; Tampere Neuromuscular Center, Tampere University and University Hospital, Tampere, Finland; Neurology Department, Vaasa Central Hospital, Vaasa, Finland
| | - Volker Straub
- Newcastle University, John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
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Whiffin N, Minikel E, Walsh R, O'Donnell-Luria AH, Karczewski K, Ing AY, Barton PJR, Funke B, Cook SA, MacArthur D, Ware JS. Using high-resolution variant frequencies to empower clinical genome interpretation. Genet Med 2017; 19:1151-1158. [PMID: 28518168 PMCID: PMC5563454 DOI: 10.1038/gim.2017.26] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [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: 11/07/2016] [Accepted: 02/02/2017] [Indexed: 02/06/2023] Open
Abstract
Purpose Whole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants. Methods We present a statistical framework for the frequency-based filtering of candidate disease-causing variants, accounting for disease prevalence, genetic and allelic heterogeneity, inheritance mode, penetrance, and sampling variance in reference datasets. Results Using the example of cardiomyopathy, we show that our approach reduces by two-thirds the number of candidate variants under consideration in the average exome, without removing true pathogenic variants (false-positive rate<0.001). Conclusion We outline a statistically robust framework for assessing whether a variant is “too common” to be causative for a Mendelian disorder of interest. We present precomputed allele frequency cutoffs for all variants in the ExAC dataset.
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Affiliation(s)
- Nicola Whiffin
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK
| | - Eric Minikel
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA
| | - Roddy Walsh
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK
| | - Anne H O'Donnell-Luria
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA
| | - Konrad Karczewski
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA
| | - Alexander Y Ing
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Paul J R Barton
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart A Cook
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK.,National Heart Centre Singapore, Singapore, Singapore.,Duke-National University of Singapore, Singapore, Singapore
| | - Daniel MacArthur
- Analytic &Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - James S Ware
- Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK.,NIHR Royal Brompton Cardiovascular Biomedical Research Unit, Royal Brompton &Harefield Hospitals &Imperial College London, London, UK.,Program in Medical and Population Genetics, Broad Institute of MIT &Harvard, Cambridge, Massachusetts, USA.,MRC London Institute of Medical Sciences, Imperial College London, London, UK
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27
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Johnson K, Bertoli M, Phillips L, Töpf A, Lek M, Xu L, MacArthur D, Straub V. The MYO-SEQ project: Application of exome sequencing technologies to 1000 patients affected by limb-girdle weakness of unknown origin. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Van den Bergh P, Sznajer Y, Van Parijs V, van Tol W, Wevers R, Lefeber D, Xu L, Lek M, MacArthur D, Xu L, Lek M, MacArthur D, Johnson K, Phillips L, Topf A, Straub V. A homozygous DPM3 mutation in a patient with alpha-dystroglycan-related limb girdle muscular dystrophy. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Phillips L, Töpf A, Johnson K, Bertoli M, Xu L, Lek M, Claeys K, Van den Bergh P, Vissing J, Colomer J, Wallgren-Patterson C, Lopez de Munain A, Vilchez J, Kostera-Pruszczyk A, MacArthur D, Straub V. Identification of sequence variants in eight genes associated with dystroglycanopathies using whole exome sequencing. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Hydrochlorofluorocarbons (HCFCs) have been widely adopted as an interim blowing agent in urethane insulations. Due to their scheduled phase-out, research efforts are being devoted to the identification and development of alternatives with zero ozone depletion potential. Physical blowing agents identified have included hydrocarbons, fluorocarbons, hydrofluoroethers, and more predominantly, hydrofluorocarbons (HFCs). The majority of the HFC evaluations have focused on the more readily available, low boiling candidates such as HFC 134a. Higher boiling HFC candidates that could be handled at ambient conditions and use current processing equipment would be more desirable. This paper will describe results from a research program of two such candidate HFCs performed as a cooperative effort between the Environmental Protection Agency, Oak Ridge National Laboratory and Martin Marietta Manned Space Systems. The purpose of this effort was to perform a limited evaluation of the developmental HFCs 245ca and 236ea as blowing agents in urethane based insulations. These two materials were selected from screening tests of 37 C2, C3 and C4 isomers based on physical properties, atmospheric lifetime, flammability, estimated toxicity, difficulty of synthesis, suitability for dual use as a refrigerant and other factors. Solubility of the two materials in typical foam components was tested, pour foaming trials were performed and preliminary data were gathered regarding foam insulation performance.
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Affiliation(s)
- J. Sharpe
- Martin Marietta Manned Space Systems, MSFC Operations, P.O. Box 9008, Marshall Space Flight Center, AL 35812
| | - D. MacArthur
- Martin Marietta Manned Space Systems, MSFC Operations, P.O. Box 9008, Marshall Space Flight Center, AL 35812
| | - M. Liu
- Martin Marietta Manned Space Systems, New Orleans, LA
| | - T. Kollie
- Oak Ridge National Laboratory, Metals and Ceramics Division, Oak Ridge, TN
| | - R. Graves
- Oak Ridge National Laboratory, Metals and Ceramics Division, Oak Ridge, TN
| | - R. Hendriks
- U.S. Environmental Protection Agency, Air and Energy Engineering Research Laboratory, Research Triangle Park, NC
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Mégarbané A, Al-Ali R, Choucair N, Lek M, Wang E, Ladjimi M, Rose CM, Hobeika R, Macary Y, Temanni R, Jithesh PV, Chouchane A, Sastry KS, Thomas R, Tomei S, Liu W, Marincola FM, MacArthur D, Chouchane L. Temple-Baraitser Syndrome and Zimmermann-Laband Syndrome: one clinical entity? BMC Med Genet 2016; 17:42. [PMID: 27282200 PMCID: PMC4901505 DOI: 10.1186/s12881-016-0304-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/02/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND KCNH1 encodes a voltage-gated potassium channel that is predominantly expressed in the central nervous system. Mutations in this gene were recently found to be responsible for Temple-Baraitser Syndrome (TMBTS) and Zimmermann-Laband syndrome (ZLS). METHODS Here, we report a new case of TMBTS diagnosed in a Lebanese child. Whole genome sequencing was carried out on DNA samples of the proband and his parents to identify mutations associated with this disease. Sanger sequencing was performed to confirm the presence of detected variants. RESULTS Whole genome sequencing revealed three missense mutations in TMBTS patient: c.1042G > A in KCNH1, c.2131 T > C in STK36, and c.726C > A in ZNF517. According to all predictors, mutation in KCNH1 is damaging de novo mutation that results in substitution of Glycine by Arginine, i.e., p.(Gly348Arg). This mutation was already reported in a patient with ZLS that could affect the connecting loop between helices S4-S5 of KCNH1 with a gain of function effect. CONCLUSIONS Our findings demonstrate that KCNH1 mutations cause TMBTS and expand the mutational spectrum of KCNH1 in TMBTS. In addition, all cases of TMBTS were reviewed and compared to ZLS. We suggest that the two syndromes are a continuum and that the variability in the phenotypes is the result of the involvement of genetic modifiers.
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Affiliation(s)
| | - Rashid Al-Ali
- Bioinformatics Division, Sidra Medical & Research Center, Doha, Qatar
| | | | - Monko Lek
- Medical and Population Genetics, Broad Institute of Harvard Medical School, Boston, USA
| | - Ena Wang
- Genomics Core Laboratory, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | - Moncef Ladjimi
- Laboratory of Protein Chemistry, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Catherine M Rose
- POSSUMweb, Victorian Clinical Genetics Service and Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, VIC, Australia
| | | | | | - Ramzi Temanni
- Bioinformatics Division, Sidra Medical & Research Center, Doha, Qatar
| | - Puthen V Jithesh
- Bioinformatics Division, Sidra Medical & Research Center, Doha, Qatar
| | - Aouatef Chouchane
- Dermatology Research Group, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | - Konduru S Sastry
- Dermatology Research Group, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | - Remy Thomas
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Sara Tomei
- Genomics Core Laboratory, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | - Wei Liu
- Genomics Core Laboratory, Translational Medicine Division, Sidra Medical & Research Center, Doha, Qatar
| | | | - Daniel MacArthur
- Medical and Population Genetics, Broad Institute of Harvard Medical School, Boston, USA
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar.
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Gonorazky H, Liang M, Cummings B, Lek M, Micallef J, Hawkins C, Basran R, Cohn R, Wilson MD, MacArthur D, Marshall CR, Ray PN, Dowling JJ. RNAseq analysis for the diagnosis of muscular dystrophy. Ann Clin Transl Neurol 2015; 3:55-60. [PMID: 26783550 PMCID: PMC4704476 DOI: 10.1002/acn3.267] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 10/25/2015] [Indexed: 12/19/2022] Open
Abstract
The precise genetic cause remains elusive in nearly 50% of patients with presumed neurogenetic disease, representing a significant barrier for clinical care. This is despite significant advances in clinical genetic diagnostics, including the application of whole‐exome sequencing and next‐generation sequencing‐based gene panels. In this study, we identify a deep intronic mutation in the DMD gene in a patient with muscular dystrophy using both conventional and RNAseq‐based transcriptome analyses. The implications of our data are that noncoding mutations likely comprise an important source of unresolved genetic disease and that RNAseq is a powerful platform for detecting such mutations.
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Affiliation(s)
- Hernan Gonorazky
- Division of Neurology Hospital for Sick Children Toronto Ontario Canada M5G A04; Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4
| | - Minggao Liang
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Beryl Cummings
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Monkol Lek
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Johann Micallef
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Cynthia Hawkins
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Raveen Basran
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Ronald Cohn
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Michael D Wilson
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit Massachusetts General Hospital Boston Massachusetts 02114; Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge Massachusetts
| | - Christian R Marshall
- Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - Peter N Ray
- Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4; Pediatric Laboratory Medicine Hospital for Sick Children Toronto Ontario Canada M5G A04
| | - James J Dowling
- Division of Neurology Hospital for Sick Children Toronto Ontario Canada M5G A04; Program of Genetics and Genome Biology Hospital for Sick Children Toronto Ontario Canada M5G A04; Department of Paediatrics University of Toronto Toronto Ontario Canada M5G AO4; Department of Molecular Genetics University of Toronto Toronto Ontario Canada M5G AO4
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33
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MacArthur D, Van Allen E. Advancing the promise of genomic medicine. Science 2015. [DOI: 10.1126/science.348.6235.715-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Genomic technologies present powerful tools with the potential to diagnose, treat, and elucidate the underpinnings of human disease. Technological advances have allowed researchers and clinicians to apply novel approaches and gain statistical power to delve more deeply and broadly into our genomes than ever before, enabling them to discover associations between genomic variants and disease phenotypes that were previously beyond our reach. In this webinar, we will explore how genomics is currently being applied to characterize rare disease and cancer, highlight recent advances in these respective areas, and look toward the future to predict what is needed to positively impact human health.
View the Webinar
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34
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MacArthur D. Managing complications of liver biopsy. J Vasc Interv Radiol 2015. [DOI: 10.1016/j.jvir.2014.12.524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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35
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Sivananthan G, Menashe L, MacArthur D, Marcus R, Halin N. Cephalic arch stenosis in hemodialysis patients: what is the cephalic arch and does the precise location of stenosis effect patency? J Vasc Interv Radiol 2014. [DOI: 10.1016/j.jvir.2013.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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36
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Lek M, MacArthur D. The Challenge of Next Generation Sequencing in the Context of Neuromuscular Diseases. J Neuromuscul Dis 2014; 1:135-149. [PMID: 27858772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
New genomic technologies, such as exome, whole-genome and transcriptome sequencing, are transforming the genetic diagnosis of neuromuscular diseases and dramatically accelerating the discovery of new disease-associated genes. The increasingly widespread availability of these technologies creates both opportunities and challenges for neuromuscular disease researchers. Here we survey the current literature on the application of new genomic technologies to the diagnosis of severe muscle diseases, with a focus on assessment of the approaches used for data processing, analysis and interpretation. We also highlight several key areas requiring improvement.
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Affiliation(s)
- Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
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37
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Affiliation(s)
- Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Paediatrics and Child Health, University of Sydney, Sydney, NSW, Australia
- Institute for Neuroscience and Muscle Research, Sydney, NSW, Australia
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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Ammoun S, Zhou L, Barczyk M, Hilton D, Hafizi S, Hanemann C, Lehnus KS, Donovan LK, Pilkington GJ, An Q, Anderson IA, Thomson S, Bailey M, Lekka E, Law J, Davis C, Banfill K, Loughrey C, Hatfield P, Bax D, Elliott R, Bishop R, Taylor K, Marshall L, Gaspar N, Viana-Pereira M, Reis R, Renshaw J, Ashworth A, Lord C, Jones C, Bellamy C, Shaw L, Alder J, Shorrocks A, Lea R, Birks S, Burnet M, Pilkington G, Bruch JD, Ho J, Watts C, Price SJ, Camp S, Apostolopoulos V, Mehta A, Roncaroli F, Nandi D, Clark B, Mackinnon M, MacLeod N, Stewart W, Chalmers A, Cole A, Hanna G, Bailie K, Conkey D, Harney J, Darlow C, Chapman S, Mohsen L, Price S, Donovan L, Birks S, Pilkington G, Dyer H, Lord H, Fletcher K, das Nair R, MacNiven J, Basu S, Byrne P, Glancz L, Critchley G, Grech-Sollars M, Saunders D, Phipps K, Clayden J, Clark C, Greco A, Acquati S, Marino S, Hammouche S, Wilkins SP, Smith T, Brodbelt A, Hammouche S, Clark S, Wong AHL, Eldridge P, Farah JO, Ho J, Bruch J, Watts C, Price S, Lamb G, Smith S, James A, Glegg M, Jeffcote T, Boulos S, Robbins P, Knuckey N, Banigo A, Brodbelt AR, Jenkinson MD, Jeyapalan JN, Mumin MA, Forshew T, Lawson AR, Tatevossian RG, Jacques TS, Sheer D, Kilday J, Wright K, Leavy S, Lowe J, Schwalbe E, Clifford S, Gilbertson R, Coyle B, Grundy R, Kinsella P, Clynes M, Amberger-Murphy V, Barron N, Lambert SR, Jones D, Pearson D, Ichimura I, Collins V, Steele L, Sinha P, Chumas P, Tyler J, Ogawa D, Chiocca E, DeLay M, Bronisz A, Nowicki M, Godlewski J, Lawler S, Lee MK, Javadpour M, Jenkinson MD, Lekka E, Abel P, Dawson T, Lea B, Davis C, Lim CSK, Grundy PL, Pendleton M, Lord H, Mackinnon M, Williamson A, James A, Stewart W, Clark B, Chalmers A, Merve A, Zhang X, Marino S, Miller S, Rogers HA, Lyon P, Rand V, Adamowicz-Brice M, Clifford SC, Hayden JT, Dyer S, Pfister S, Korshunov A, Brundler MA, Lowe J, Coyle B, Grundy RG, Nankivell M, Mulvenna P, Barton R, Wilson P, Faivre-Finn C, Pugh C, Langley R, Ngoga D, Tennant D, Williams A, Moss P, Cruickshank G, Owusu-Agyemang K, Bell S, Stewart W, St.George J, Piccirillo SG, Watts C, Qadri S, Pirola E, Jenkinson M, Brodbelt A, Rahman R, Rahman C, Smith S, MacArthur D, Rose F, Shakesheff K, Grundy R, Carroll C, Watson P, Hawkins M, Spoudeas H, Walker D, Holland T, Ring H, Rooney A, McNamara S, Mackinnon M, Fraser M, Rampling R, Carson A, Grant R, Royds J, Al Nadaf S, Ahn A, Chen YJ, Wiles A, Jellinek D, Braithwaite A, Baguley B, MacFarlane M, Hung N, Slatter T, Rusbridge S, Walmsley N, Griffiths S, Wilford P, Rees J, Ryan D, Watts C, Liu P, Galavotti S, Shaked-Rabi M, Tulchinsky E, Brandner S, Jones C, Salomoni P, Schulte A, Gunther HS, Zapf S, Riethdorf S, Westphal M, Lamszus K, Selvanathan SK, Hammouche S, Salminen HJ, Jenkinson MD, Setua S, Watts C, Welland ME, Shevtsov M, Khachatryan W, Kim A, Samochernych K, Pozdnyakov A, Guzhova IV, Romanova IV, Margulis B, Smith S, Rahman R, Rahman C, Barrow J, Macarthur D, Rose F, Grundy R, Smith S, Long A, Barrow J, Macarthur D, Coyle B, Grundy R, Maherally Z, Smith JR, Dickson L, Pilkington GJ, Prabhu S, Harris F, Lea R, Snape TJ, Sussman M, Wilne S, Whitehouse W, Chow G, Liu JF, Walker D, Snape T, Karakoula A, Rowther F, Warr T, Williamson A, Mackinnon M, Zisakis A, Varsos V, Panteli A, Karypidou O, Zampethanis A, Fotovati A, Abu-Ali S, Wang PS, Deleyrolle L, Lee C, Triscott J, Chen JY, Franciosi S, Nakamura Y, Sugita Y, Uchiumi T, Kuwano M, Leavitt BR, Singh SK, Jury A, Jones C, Wakimoto H, Reynolds BA, Pallen CJ, Dunn SE, Shepherd S, Scott S, Bowyer D, Wallace L, Hacking B, Mohsen L, Jena R, Gillard J, Price S, Lee C, Fotovati A, Verraeult M, Wakimoto H, Reynolds B, Dunham C, Bally M, Hukin J, Singhal S, Singh S, Dunn S. Abstracts from the 2011 BNOS Conference, June 29 - July 1, 2011, Homerton College, Cambridge. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Balasubramanian S, Habegger L, Frankish A, MacArthur D, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Defining the human reference protein-coding gene set. Genome Biol 2010. [PMCID: PMC3026232 DOI: 10.1186/gb-2010-11-s1-o5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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Abstract
Summary: We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data. We find that given a fixed coverage, longer reads (implying fewer of them) are preferable. Availability: The executable and user manual can be freely downloaded from ftp://ftp.sanger.ac.uk/pub/zn1/HI. Contact:ql2@sanger.ac.uk
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Affiliation(s)
- Quan Long
- The Wellcome Trust Sanger Institute, Hinxton, Cambs, UK.
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Clayton J, Vloeberghs M, Jaspan T, Walker D, MacArthur D, Grundy R. Intrathecal chemotherapy delivered by a lumbar-thecal catheter in metastatic medulloblastoma: a case illustration. Acta Neurochir (Wien) 2008; 150:709-12. [PMID: 18401539 DOI: 10.1007/s00701-008-1577-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 03/10/2008] [Indexed: 10/22/2022]
Abstract
BACKGROUND Medulloblastoma is the most common malignant brain tumour in children. Despite recent advances, the prognosis in high risk patients remains poor. Further improvement in survival is dependent upon the development of strategies to attack the tumour more effectively, but with less toxicity. Intrathecal chemotherapy, is an ideal but currently underused method of directly targeting residual tumour within the area of resection and the leptomeningeal disease commonly associated with this tumour. METHOD We describe the case of a 12 yr old child with metastatic medulloblastoma, who received intrathecal topotecan via a spinal catheter. CONCLUSION This method represents a simple, safe and effective method of delivering an even and widespread distribution of drug within the cerebrospinal fluid (CSF) of the neuroaxis. With new agents being identified and others in the early stages of development, intrathecal chemotherapy may emerge as an important therapeutic option to consider when faced with such challenging cases.
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Smith WE, Clark PF, MacArthur D, Allatt RD, Hayes KC, Cunningham DA. Oxygen costs using a reciprocating gait orthosis in a paraplegic (T9) patient with a bilateral below-knee amputation: case report. Spinal Cord 1997; 35:121-3. [PMID: 9044521 DOI: 10.1038/sj.sc.3100354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 02/03/2023]
Abstract
The Reciprocating Gait Orthosis (RGO) is a useful aid to ambulation for patients with paraplegia. Its use has been described previously though not in conjunction with limb prostheses. We report here the energy costs of ambulation of a patient, disabled by paraplegia at T9 and bilateral below-knee amputations, walking at her preferred rate using an RGO while gas exchange was measured by the Douglas bag method. Oxygen uptake (VO2) rose from 0.198 1 min-1 at rest to 0.582 1 min-1 in the last minute of exercise, representing a VO2 of 14.3 ml kg-1 min-1. During the fourth minute of ambulation, energy consumption was 30.44 J kg-1 s-1 with an energy cost of 4.17 J kg-1 m-1 at a velocity of 0.13 m s-1, Ambulation with this combination of disability is possible with the aid of limb prostheses and an RGO though it is slow and the energy expenditure as consumption per second and cost per metre are high.
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Affiliation(s)
- W E Smith
- Parkwood Hospital, London, Ontario, Canada
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Kennedy RL, Harrison RF, Burton AM, Fraser HS, Hamer WG, MacArthur D, McAllum R, Steedman DJ. An artificial neural network system for diagnosis of acute myocardial infarction (AMI) in the accident and emergency department: evaluation and comparison with serum myoglobin measurements. Comput Methods Programs Biomed 1997; 52:93-103. [PMID: 9034674 DOI: 10.1016/s0169-2607(96)01782-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Recent studies have confirmed that artificial neural networks (ANNs) are adept at recognising patterns in sets of clinical data. The diagnosis of acute myocardial infarction (AMI) in patients presenting with chest pain remains one of the greatest challenges in emergency medicine. The aim of this study was to evaluate the performance of an ANN trained to analyse clinical data from chest pain patients. The ANN was compared with serum myoglobin measurements--cardiac damage is associated with increased circulating myoglobin levels, and this is widely used as an early marker for evolving AMI. We used 39 items of clinical and ECG data from the time of presentation to derive 53 binary inputs to a back propagation network. On test data (200 cases), overall accuracy, sensitivity, specificity and positive predictive value (PPV) of the ANN were 91.8, 91.2, 90.2 and 84.9% respectively. Corresponding figures using linear discriminant analysis were 81.0, 77.9, 82.6 and 69.7% (P < 0.01). Using a further test set from a different centre (91 cases), the accuracy, sensitivity, specificity and PPV for the admitting physicians were 65.1, 28.5, 76.9 and 28.6% respectively compared with 73.6, 52.4, 80.0 and 44.0% for the ANN. Although myoglobin at presentation was highly specific, it was only 38.0% sensitive, compared with 85.7% at 3 h. Simple strategies to combine clinical opinion, ANN output and myoglobin at presentation could greatly improve sensitivity and specificity of AMI diagnosis. The ideal support for emergency room physicians may come from a combination of computer-aided analysis of clinical factors and biochemical markers such as myoglobin. This study demonstrates that the two approaches could be usefully combined, the major benefit of the decision support system being in the first 3 h before biochemical markers have become abnormal.
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Affiliation(s)
- R L Kennedy
- City Hospitals Sunderland, Department of Medicine, UK
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Abstract
The present study examined some of the problems involved in communication and learning processes when inexperienced subjects were presented with information supplied through unfamiliar types of instruction media. In the study, 110 Xhosa-speaking novices to the gold mining industry were instructed through the media of video-tape or lecture, in either Fanakalo or Xhosa, with repeated or non-repeated presentations. Results showed that those who received repeated instruction recalled more information. A significant interaction also occurred between language and instruction medium. Level of education also affected comprehension. It appeared that the more the presentation methods were tailored to the specific needs of the individuals — in this case presentation through a familiar language, using an empathie lecturer — the more effective the communication and learning was likely to be.
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Affiliation(s)
- N.R. Barnes
- Chamber of Mines, Human Resources Laboratory, P.O. Box 91230, Auckland Park 2006, Republic of South Africa
| | - D. MacArthur
- Chamber of Mines, Human Resources Laboratory, P.O. Box 91230, Auckland Park 2006, Republic of South Africa
| | - P.R. Ballantine
- Chamber of Mines, Human Resources Laboratory, P.O. Box 91230, Auckland Park 2006, Republic of South Africa
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