Next generation sequencing for molecular diagnosis of neuromuscular diseases

Acta Neuropathologica

Volumn 124, Issue 2, 2012, Pages 273-283

  Vasli, Nasim ^a,b,c,d,e   Böhm, Johann ^a,b,c,d,e   Le Gras, Stéphanie ^a,b,c,d   Muller, Jean ^a,b,c,d,e   Pizot, Cécile ^a,b,c,d,e   Jost, Bernard ^a,b,c,d   Echaniz Laguna, Andoni ^f   Laugel, Vincent ^g   Tranchant, Christine ^f   Bernard, Rafaelle ^b   Plewniak, Frédéric ^a,b,c,d   Vicaire, Serge ^a,b,c,d   Levy, Nicolas ^b   Chelly, Jamel ^h   Mandel, Jean Louis ^a,b,c,d,e   Biancalana, Valérie ^a,b,c,d,e   Laporte, Jocelyn ^a,b,c,d,e  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^b INSERM   (France)

^c CNRS   (France)

^d UNIVERSITÉ DE STRASBOURG   (France)

^e Paris Sciences et Lettres   (France)

^f HÔPITAL CIVIL   (France)

^g UNIVERSITY HOSPITAL OF STRASBOURG   (France)

^h INSTITUT COCHIN   (France)

Author keywords

DNA barcoding; Molecular diagnosis; Myopathy; Neuromuscular disorder; Neuropathy; Sequencing

Indexed keywords

COLLAGEN TYPE 6; RYANODINE RECEPTOR 1;

ARTICLE; BIOINFORMATICS; CLINICAL ARTICLE; CLINICAL EVALUATION; COL6A3 GENE; COST EFFECTIVENESS ANALYSIS; DIAGNOSTIC KIT; DIAGNOSTIC VALUE; DNA DETERMINATION; DUCHENNE MUSCULAR DYSTROPHY; EXONIC MUTATION; FEMALE; GENE; GENE LOSS; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENETIC CODE; GENETIC PROCEDURES; GENETIC SCREENING; HUMAN; INDEL MUTATION; INHERITANCE; INTRONIC MUTATION; MALE; MOLECULAR DIAGNOSIS; MOLECULAR LIBRARY; MUTAGENESIS; NEUROMUSCULAR DISEASE; NEXT GENERATION SEQUENCING; PILOT STUDY; POINT MUTATION; PRIORITY JOURNAL; REPRODUCIBILITY; RYR1 GENE; SENSITIVITY ANALYSIS; TTN GENE; VALIDATION PROCESS;

DATABASES, GENETIC; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; NEUROMUSCULAR DISEASES; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84865861518     PISSN: 00016322     EISSN: 14320533     Source Type: Journal    
DOI: 10.1007/s00401-012-0982-8     Document Type: Article

References (32)

1. Bang ML, Centner T, Fornoff F et al (2001) The complete gene sequence of titin, expression of an unusual approximately 700-kDa titin isoform, and its interaction with obscurin identify a novel Z-line to I-band linking system. Circ Res 89:1065-1072 (Pubitemid 34640875)
2. Desmet FO, Hamroun D, Lalande M et al (2009) Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 37:e67
3. Emery AE (1991) Population frequencies of inherited neuromuscular diseases - a world survey. Neuromuscul Disord 1:19-29
4. Ge D, Ruzzo EK, Shianna KV et al (2011) SVA: software for annotating and visualizing sequenced human genomes. Bioinformatics 27:1998-2000
5. Hackman P, Vihola A, Haravuori H et al (2002) Tibial muscular dystrophy is a titinopathy caused by mutations in TTN, the gene encoding the giant skeletal-muscle protein titin. Am J Hum Genet 71:492-500 (Pubitemid 34970121)
6. Hoischen A, Gilissen C, Arts P et al (2010) Massively parallel sequencing of ataxia genes after array-based enrichment. Hum Mutat 31:494-499
7. Hubisz MJ, Pollard KS, Siepel A (2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform 12:41-51
8. Kaplan JC (2010) The 2011 version of the gene table of neuromuscular disorders. Neuromuscul Disord 20:852-873
9. Kingsmore SF, Saunders CJ (2011) Deep sequencing of patient genomes for disease diagnosis: when will it become routine? Sci Transl Med 3:87ps23
10. Levy S, Sutton G, Ng PC et al (2007) The diploid genome sequence of an individual human. PLoS Biol 5:e254
11. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760
12. Li H, Handsaker B, Wysoker A et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079
13. Lim BC, Lee S, Shin JY et al (2011) Genetic diagnosis of Duchenne and Becker muscular dystrophy using next-generation sequencing technology: comprehensive mutational search in a single platform. J Med Genet 48:731-736
14. Lupski JR, Reid JG, Gonzaga-Jauregui C et al (2010) Wholegenome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 362:1181-1191
15. Messina S, Hartley L, MainMet al (2004) Pilot trial of salbutamol in central core and multi-minicore diseases. Neuropediatrics 35:262-266 (Pubitemid 39536640)
16. Montenegro G, Powell E, Huang J et al (2011) Exome sequencing allows for rapid gene identification in a Charcot-Marie-Tooth family. Ann Neurol 69:464-470
17. Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812-3814 (Pubitemid 37442253)
18. Ng SB, Buckingham KJ, Lee C et al (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42:30-35
19. Ng SB, Nickerson DA, Bamshad MJ, Shendure J (2010) Massively parallel sequencing and rare disease. Hum Mol Genet 19:R119-R124
20. Ng SB, Turner EH, Robertson PD et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272-276
21. North K (2008) What's new in congenital myopathies? Neuromuscul Disord 18:433-442
22. Pareyson D, Marchesi C (2009) Diagnosis, natural history, and management of Charcot-Marie-Tooth disease. Lancet Neurol 8:654-667
23. Ramensky V, Bork P, Sunyaev S (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30:3894-3900 (Pubitemid 35012462)
24. Reese MG, Eeckman FH, Kulp D, Haussler D (1997) Improved splice site detection in Genie. J Comput Biol 4:311-323 (Pubitemid 27355870)
25. Robinson JT, Thorvaldsdottir H, Winckler W et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24-26
26. Romero NB, Monnier N, Viollet L et al (2003) Dominant and recessive central core disease associated with RYR1 mutations and fetal akinesia. Brain 126:2341-2349 (Pubitemid 37314426)
27. Saillour Y, Cossee M, Leturcq F et al (2008) Detection of exonic copy-number changes using a highly efficient oligonucleotidebased comparative genomic hybridization-array method. Hum Mutat 29:1083-1090
28. Sauna ZE, Kimchi-Sarfaty C (2011) Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet 12:683-691
29. Treves S, Jungbluth H, Muntoni F, Zorzato F (2008) Congenital muscle disorders with cores: the ryanodine receptor calcium channel paradigm. Curr Opin Pharmacol 8:319-326
30. Walsh T, Lee MK, Casadei S et al (2010) Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 107:12629-12633
31. Wheeler DA, Srinivasan M, Egholm M et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872-876 (Pubitemid 351550870)
32. Yeo G, Burge CB (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11:377-394 (Pubitemid 38901668)