Use of whole-exome sequencing for diagnosis of limb-girdle muscular dystrophy: Outcomes and lessons learned

JAMA Neurology

Volumn 72, Issue 12, 2015, Pages 1424-1432

  Ghaoui, Roula ^a,b   Cooper, Sandra T ^a,b   Lek, Monkol ^c   Jones, Kristi ^a,b   Corbett, Alastair ^d   Reddel, Stephen W ^d   Needham, Merrilee ^e   Liang, Christina ^f   Waddell, Leigh B ^a,b   Nicholson, Garth ^g   O'Grady, Gina ^a,b   Kaur, Simranpreet ^a,b   Ong, Royston ^e   Davis, Mark ^h   Sue, Carolyn M ^f   Laing, Nigel G ^e   North, Kathryn N ⁱ   MacArthur, Daniel G ^c   Clarke, Nigel F ^a,b  

^a CHILDREN S HOSPITAL AT WESTMEAD   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

^d Department of Microbiology and Infectious Diseases   (Australia)

^e UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^f ROYAL NORTH SHORE HOSPITAL   (Australia)

^g UNIVERSITY OF SYDNEY   (Australia)

^h PATHWEST LABORATORY MEDICINE   (Australia)

ⁱ ROYAL CHILDREN'S HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACTA1 GENE; ADULT; ARTICLE; AUSTRALIA; AUSTRALIAN; BIOINFORMATICS; CHD7 GENE; COHORT ANALYSIS; COLLAGEN MYOPATHY; COLVI GENE; CONGENITAL MYASTHENIC SYNDROME; CONGENITAL MYOPATHY; CONTROLLED STUDY; CPT2 GENE; DNA SEQUENCE; DOK7 GENE; DYSTROPHY; FEMALE; FLNC GENE; FOLLOW UP; GENE; GENE MUTATION; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; LIMB GIRDLE MUSCULAR DYSTROPHY; MAJOR CLINICAL STUDY; MALE; METABOLIC MYOPATHY; MUSCLE BIOPSY; MUSCLE WEAKNESS; MUSCULAR DYSTROPHY; MYOFIBRILLAR MYOPATHY; MYOPATHY; PRIORITY JOURNAL; RETROSPECTIVE STUDY; SANGER SEQUENCING; STIM1 GENE; SYNDROME CHARGE; TUBULAR AGGREGATE MYOPATHY; WHOLE GENOME SEQUENCING; BIOLOGY; EXOME; FAMILY HEALTH; GENETIC SCREENING; GENETICS; MUSCULAR DYSTROPHIES, LIMB-GIRDLE; MUTATION; PROCEDURES;

AUSTRALIA; COMPUTATIONAL BIOLOGY; EXOME; FAMILY HEALTH; FEMALE; GENETIC TESTING; HUMANS; MALE; MUSCULAR DYSTROPHIES, LIMB-GIRDLE; MUTATION; RETROSPECTIVE STUDIES; SEQUENCE ANALYSIS, DNA;

EID: 84950259881     PISSN: 21686149     EISSN: None     Source Type: Journal    
DOI: 10.1001/jamaneurol.2015.2274     Document Type: Article

References (40)

1. Bushby K. Report on the 12th ENMC sponsored international workshop-the "limb-girdle" muscular dystrophies. Neuromuscul Disord. 1992;2(1): 3-5.
2. Bushby KM. Making sense of the limb-girdle muscular dystrophies. Brain. 1999; 122(pt 8): 1403-1420.
3. Zatz M, Vainzof M, Passos-Bueno MR. Limb-girdle muscular dystrophy: one gene with different phenotypes, one phenotype with different genes. Curr Opin Neurol. 2000;13(5): 511-517.
4. Walton JN, Nattrass FJ On the classification, natural history and treatment of the myopathies. Brain. 1954;77(2): 169-231.
5. Stevenson AC. Muscular dystrophy in Northern Ireland, I: an account of the condition in fifty-one families. Ann Eugen. 1953;18(1): 50-93.
6. Kaplan JC, Hamroun D. The 2014 version of the gene table of monogenic neuromuscular disorders (nuclear genome). Neuromuscul Disord. 2013;23 (12): 1081-1111.
7. Narayanaswami P, Weiss M, Selcen D., et al; Guideline Development Subcommittee of the American Academy of Neurology; Practice Issues Review Panel of the American Association of Neuromuscular & Electrodiagnostic Medicine. Evidence-based guideline summary: diagnosis and treatment of limb-girdle and distal dystrophies: report of the guideline development subcommittee of the American Academy of Neurology and the practice issues review panel of the American Association of Neuromuscular & Electrodiagnostic Medicine. Neurology. 2014;83(16): 1453-1463.
8. Lo HP, Cooper ST, Evesson F.J., et al. Limb-girdle muscular dystrophy: diagnostic evaluation, frequency and clues to pathogenesis. Neuromuscul Disord. 2008;18(1): 34-44.
9. Yau K, Allcock R, Mina K., et al. Neurogenetic disease diagnostics by targeted capture and next generation sequencing. Neuromuscul Disord. 2014; 24(9-10): 799-800. doi:10.1016/j.nmd.2014.06.032.
10. Cabrera-Serrano M., Ghaoui R, Ravenscroft G., et al. Expanding the phenotype of GMPPB mutations. Brain. 2015; 138(pt 4): 836-844.
11. Ku CS, Cooper DN, Polychronakos C, Naidoo N., Wu M, Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol. 2012;71 (1): 5-14.
12. Ng SB, Turner EH, Robertson P.D., et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009; 461(7261): 272-276.
13. Waddell LB, Evesson FJ, North K.N., Cooper ST, Clarke NF. Diagnosis of the muscular dystrophies. In: Hegde M, Ankala A, eds. Muscular Dystrophy. Rijeka, Croatia: InTech; 2012: 261-288.
14. Peat RA, Smith JM, Compton A.G., et al. Diagnosis and etiology of congenital muscular dystrophy. Neurology. 2008;71(5): 312-321.
15. Liquori CL, Ricker K, Moseley M.L., et al. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science. 2001; 293 (5531): 864-867.
16. Bushby K, Norwood F, Straub V. The limb-girdle muscular dystrophies-diagnostic strategies. Biochem Biophys Acta. 2007;1772(2): 238-242.
17. Menezes MP, Waddell L, Lenk GM, et al. Whole exome sequencing identifies three recessive FIG4 mutations in an apparently dominant pedigree with Charcot-Marie-Tooth disease. Neuromuscul Disord. 2014;24(8): 666-670.
18. Abecasis GR, Auton A, Brooks LD, et al; 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422): 56-65.
19. Shin JY, Méndez-López I, Wang Y, et al. Lamina-associated polypeptide-1 interacts with the muscular dystrophy protein emerin and is essential for skeletal muscle maintenance. Dev Cell. 2013;26 (6): 591-603.
20. Kayman-Kurekci G, Talim B, Korkusuz P, et al. Mutation in TOR1AIP1 encoding LAP1B in a form of muscular dystrophy: a novel gene related to nuclear envelopathies. Neuromuscul Disord. 2014;24(7): 624-633.
21. Manzini MC, Tambunan DE, Hill RS, et al. Exome sequencing and functional validation in zebrafish identify GTDC2 mutations as a cause of Walker-Warburg syndrome. Am J Hum Genet. 2012; 91(3): 541-547.
22. Carss KJ, Stevens E, Foley AR, et al; UK10K Consortium. Mutations in GDP-mannose pyrophosphorylase B cause congenital and limb-girdle muscular dystrophies associated with hypoglycosylation of α-dystroglycan. Am J Hum Genet. 2013;93(1): 29-41.
23. Geranmayeh F, Clement E, Feng LH, et al. Genotype-phenotype correlation in a large population of muscular dystrophy patients with LAMA2 mutations. Neuromuscul Disord. 2010;20 (4): 241-250.
24. Jöbsis GJ, Keizers H, Vreijling JP, et al. Type VI collagen mutations in Bethlem myopathy, an autosomal dominant myopathy with contractures. Nat Genet. 1996;14(1): 113-115.
25. Bönnemann CG, Brockmann K, Hanefeld F. Muscle ultrasound in Bethlem myopathy. Neuropediatrics. 2003;34(6): 335-336.
26. Wolfe GI, Baker NS, Haller RG, Burns DK, Barohn RJ. McArdle's disease presenting with asymmetric, late-onset arm weakness. Muscle Nerve. 2000;23(4): 641-645.
27. Nadaj-Pakleza AA, Vincitorio CM, Laforêt P, et al. Permanent muscle weakness in McArdle disease. Muscle Nerve. 2009;40(3): 350-357.
28. Deschauer M, Wieser T, Zierz S. Muscle carnitine palmitoyltransferase II deficiency: clinical and molecular genetic features and diagnostic aspects. Arch Neurol. 2005;62(1): 37-41.
29. Anichini A, Fanin M, Vianey-Saban C, et al. Genotype-phenotype correlations in a large series of patients with muscle type CPT II deficiency. Neurol Res. 2011;33(1): 24-32.
30. Ryan MM, Schnell C, Strickland CD, et al. Nemaline myopathy: a clinical study of 143 cases. Ann Neurol. 2001;50(3): 312-320.
31. Misceo D, Holmgren A, Louch WE, et al. A dominant STIM1 mutation causes Stormorken syndrome. Hum Mutat. 2014;35(5): 556-564.
32. Verloes A. Updated diagnostic criteria for CHARGE syndrome: a proposal. Am J Med Genet A. 2005;133A(3): 306-308.
33. Bergman JEH, Janssen N, Hoefsloot LH, Jongmans MC, Hofstra RM, van Ravenswaaij-Arts CM. CHD7 mutations and CHARGE syndrome: the clinical implications of an expanding phenotype. J Med Genet. 2011;48(5): 334-342.
34. Schuelke M, Wagner KR, Stolz LE, et al. Myostatin mutation associated with gross muscle hypertrophy in a child. N Engl J Med. 2004;350 (26): 2682-2688.
35. Hoischen A, Gilissen C, Arts P, et al. Massively parallel sequencing of ataxia genes after array-based enrichment. Hum Mutat. 2010;31(4): 494-499.
36. Ng SB, Bigham AW, Buckingham KJ, et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet. 2010;42(9): 790-793.
37. Ng SB, Buckingham AW, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010;42(1): 30-35.
38. Sacconi S, Lemmers RJ, Balog J, et al. The FSHD2 gene SMCHD1 is a modifier of disease severity in families affected by FSHD1. Am J Hum Genet. 2013;93(4): 744-751.
39. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1): 57-63.
40. Foo JN, Liu JJ, Tan EK. Whole-genome and whole-exome sequencing in neurological diseases. Nat Rev Neurol. 2012;8(9): 508-517.