Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing

Orphanet Journal of Rare Diseases

Volumn 11, Issue 1, 2016, Pages

  Lévesque, Sébastien ^a   Auray Blais, Christiane ^a   Gravel, Elaine ^a   Boutin, Michel ^a   Dempsey Nunez, Laura ^a   Jacques, Pierre Etienne ^b   Chenier, Sébastien ^a   Larue, Sandrine ^c   Rioux, Marie France ^a   Al Hertani, Walla ^d   Nadeau, Amelie ^a   Mathieu, Jean ^e   Maranda, Bruno ^a   Désilets, Valérie ^a   Waters, Paula J ^a   Keutzer, Joan ^f   Austin, Stephanie ^g   Kishnani, Priya ^g  

^a CENTRE HOSPITALIER UNIVERSITAIRE DE SHERBROOKE   (Canada)

^b UNIVERSITÉ DE SHERBROOKE   (Canada)

^c NOTRE DAME HOSPITAL   (Canada)

^d UNIVERSITY OF CALGARY   (Canada)

^e Centre de readaptation en deficience physique Jonquiere   (Canada)

^f GENZYME CORPORATION   (United States)

^g DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Lysosomal disorders; Muscle disorders; Next generation sequencing; Pompe disease

Indexed keywords

GLUCAN 1,4 ALPHA GLUCOSIDASE;

ADULT; ARTICLE; CHILD; CLINICAL ARTICLE; COHORT ANALYSIS; CONTROLLED STUDY; DELAYED DIAGNOSIS; ENZYME ACTIVITY; EXON; FEMALE; GAA GENE; GENE; GENETIC VARIABILITY; GENOME SIZE; GLYCOGEN STORAGE DISEASE TYPE 2; HUMAN; INDEL MUTATION; MALE; MIDDLE AGED; MOLECULAR PATHOLOGY; MUSCLE DISEASE; MUSCLE WEAKNESS; NEXT GENERATION SEQUENCING; PHENOTYPE; PRESCHOOL CHILD; RNA SPLICING; SCHOOL CHILD; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM MASS SPECTROMETRY; TREATMENT OUTCOME; YOUNG ADULT; ADOLESCENT; GLYCOGEN STORAGE DISEASE TYPE II; HIGH THROUGHPUT SEQUENCING; INFANT; MUSCULAR DISEASES; ONSET AGE; PROCEDURES;

ADOLESCENT; ADULT; AGE OF ONSET; CHILD; CHILD, PRESCHOOL; FEMALE; GLYCOGEN STORAGE DISEASE TYPE II; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT; MALE; MUSCULAR DISEASES; YOUNG ADULT;

EID: 84955288180     PISSN: None     EISSN: 17501172     Source Type: Journal    
DOI: 10.1186/s13023-016-0390-6     Document Type: Article

References (62)

1. Hoefsloot LH, Hoogeveen-Westerveld M, Kroos MA, van Beeumen J, Reuser AJ, Oostra BA. Primary structure and processing of lysosomal alpha-glucosidase; homology with the intestinal sucrase-isomaltase complex. EMBO J. 1988;7:1697-704.
2. Hobson-Webb L, Proia AD, Thurberg BL, Banugaria S, Prater SN, Kishnani PS. Autopsy findings in late-onset Pompe disease: a case report and systematic review of the literature. Mol Genet Metab. 2012;106:462-9.
3. Kishnani PS, Beckemeyer AA, Mendelsohn NJ. The new era of Pompe disease: advances in the detection, understanding of the phenotypic spectrum, pathophysiology, and management. Am J Med Genet C: Semin Med Genet. 2012;160:1-7.
4. Kishnani PS, Steiner RD, Bali D, Berger K, Byrne BJ, Case LE, et al. Pompe disease diagnosis and management guideline. Genet Med. 2006;8:267-88.
5. Kishnani PS, Hwu WL, Mandel H, Nicolino M, Yong F, Corzo D, et al. A retrospective, multinational, multicenter study on the natural history of infantile-onset Pompe disease. J Pediatr. 2006;148:671-6.
6. van den Hout HM, Hop W, van Diggelen OP, Smeitink JA, Smit GP, Poll-The B, et al. The natural course of infantile Pompe's disease: 20 original cases compared with 133 cases from the literature. Pediatrics. 2003;112:332-40.
7. Schuller A, Wenninger S, Strigl-Pill N, Schoser B. Toward deconstructing the phenotype of late-onset Pompe disease. Am J Med Genet C: Semin Med Genet. 2012;160:80-8.
8. Gutiérrez-Rivas E, Bautista J, Vílchez JJ, Muelas N, Díaz-Manera J, Illa I, et al. Targeted screening for the detection of Pompe disease in patients with unclassified limb-girdle muscular dystrophy or asymptomatic hyperCKemia using dried blood: A Spanish cohort. Neuromuscul Disord. 2015;25:548-53.
9. Martiniuk F, Chen A, Mack A, Arvanitopoulos E, Chen Y, Rom WN, et al. Carrier frequency for glycogen storage disease type II in New York and estimates of affected individuals born with the disease. Am J Med Genet. 1998;79:69-72.
10. Ausems MG, Verbiest J, Hermans MP, Kroos MA, Beemer FA, Wokke JH, et al. Frequency of glycogen storage disease type II in The Netherlands: implications for diagnosis and genetic counselling. Eur J Hum Genet. 1999;7:713-6.
11. Hopkins PV, Campbell C, Klug T, Rogers S, Raburn-Miller J, Kiesling J. Lysosomal storage disorder screening implementation: findings from the first six months of full population pilot testing in Missouri. J Pediatr. 2015;166:172-7.
12. Liao H-C, Chiang C-C, Niu D-M, Wang C-H, Kao S-M, Tsai F-J, et al. Detecting multiple lysosomal storage diseases by tandem mass spectrometry - a national newborn screening program in Taiwan. Clin Chim Acta. 2014;431:80-6.
13. Mechtler TP, Stary S, Metz TF, De Jesus VR, Greber-Platzer S, Pollak A, et al. Neonatal screening for lysosomal storage disorders: feasibility and incidence from a nationwide study in Austria. Lancet (London, England). 2012;379:335-41.
14. Kemper AR, Hwu WL, Lloyd-Puryear M, Kishnani PS. Newborn screening for Pompe disease: synthesis of the evidence and development of screening recommendations. Pediatrics. 2007;120:e1327-34.
15. Regnery C, Kornblum C, Hanisch F, Vielhaber S, Strigl-Pill N, Grunert B, et al. 36 months observational clinical study of 38 adult Pompe disease patients under alglucosidase alfa enzyme replacement therapy. J Inherit Metab Dis. 2012;35:837-45.
16. Yang C-F, Liu H-C, Hsu T-R, Tsai F-C, Chiang S-F, Chiang C-C, et al. A large-scale nationwide newborn screening program for Pompe disease in Taiwan: towards effective diagnosis and treatment. Am J Med Genet A. 2014;164A:54-61.
17. Chien YH, Lee NC, Thurberg BL, Chiang SC, Zhang XK, Keutzer J, et al. Pompe disease in infants: improving the prognosis by newborn screening and early treatment. Pediatrics. 2009;124:e1116-25.
18. Burton BK. Newborn screening for Pompe disease: an update, 2011. Am J Med Genet C: Semin Med Genet. 2012;160:8-12.
19. Gelb MH, Turecek F, Scott CR, Chamoles NA. PMC2488386; Direct multiplex assay of enzymes in dried blood spots by tandem mass spectrometry for the newborn screening of lysosomal storage disorders. J Inherit Metab Dis. 2006;29:397-404.
20. Scott CR, Elliott S, Buroker N, Thomas LI, Keutzer J, Glass M, et al. Identification of infants at risk for developing Fabry, Pompe, or mucopolysaccharidosis-I from newborn blood spots by tandem mass spectrometry. J Pediatr. 2013;163:498-503.
21. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11:31-46.
22. Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 2011;12:R94.
23. Samorodnitsky E, Datta J, Jewell BM, Hagopian R, Miya J, Wing MR, et al. Comparison of custom capture for targeted next-generation DNA sequencing. J Mol Diagn. 2015;17:64-75.
24. Howell RR, Byrne B, Darras BT, Kishnani P, Nicolino M, van der Ploeg A. Diagnostic challenges for Pompe disease: an under-recognized cause of floppy baby syndrome. Genet Med. 2006;8:289-96.
25. Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014;32:246-51.
26. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114-20.
27. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
28. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-303.
29. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;11:11.10.1-11.10.33.
30. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6:80-92.
31. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980-5.
32. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;24-26.
33. Retterer K, Scuffins J, Schmidt D, Lewis R, Pineda-Alvarez D, Stafford A, et al. Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. Genet Med. 2014;17:623-9.
34. Samarakoon PS, Sorte HS, Kristiansen BE, Skodje T, Sheng Y, Tjonnfjord GE, et al. Identification of copy number variants from exome sequence data. BMC Genomics. 2014;15:661.
35. Tan R, Wang Y, Kleinstein SE, Liu Y, Zhu X, Guo H, et al. An evaluation of copy number variation detection tools from whole-exome sequencing data. Hum Mutat. 2014;35:899-907.
36. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
37. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.
38. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010;Chapter 19:Unit 19.10.1-21.
39. Dajnoki A, Mühl A, Fekete G, Keutzer J, Orsini J, Dejesus V, et al. Newborn screening for Pompe disease by measuring acid alpha-glucosidase activity using tandem mass spectrometry. Clin Chem. 2008;54:1624-9.
40. Jack RM, Gordon C, Scott CR, Kishnani PS, Bali D. The use of acarbose inhibition in the measurement of acid alpha-glucosidase activity in blood lymphocytes for the diagnosis of Pompe disease. Genet Med. 2006;8:307-12.
41. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405-24.
42. Wicklund MP, Kissel JT. The limb-girdle muscular dystrophies. Neurol Clin. 2014;32:729-49. ix.
43. Bartoli M, Desvignes J-P, Nicolas L, Martin K. Exome sequencing as a second-tier diagnostic approach for clinically suspected dysferlinopathy patients. Muscle Nerve. 2014;50:1007-10.
44. Seong M-W, Cho A, Park HW, Seo SH, Lim BC, Seol D, et al. Clinical applications of next-generation sequencing-based gene panel in patients with muscular dystrophy: Korean experience. Clin Genet. 2015.
45. Dai Y, Wei X, Zhao Y, Ren H, Lan Z, Yang Y, et al. A comprehensive genetic diagnosis of Chinese muscular dystrophy and congenital myopathy patients by targeted next-generation sequencing. Neuromuscul Disord. 2015;25:617-24.
46. Scoto M, Cullup T, Cirak S, Yau S, Manzur AY, Feng L, et al. Nebulin (NEB) mutations in a childhood onset distal myopathy with rods and cores uncovered by next generation sequencing. Eur J Hum Genet. 2013;21:1249-52.
47. Romero NB, Lehtokari V-L, Quijano-Roy S, Monnier N, Claeys KG, Carlier RY, et al. Core-rod myopathy caused by mutations in the nebulin gene. Neurology. 2009;73:1159-61.
48. Wallgren-Pettersson C, Lehtokari V-L, Kalimo H, Paetau A, Nuutinen E, Hackman P, et al. Distal myopathy caused by homozygous missense mutations in the nebulin gene. Brain. 2007;130(Pt 6):1465-76.
49. Piteau SJ, Rossiter JP, Smith RG, MacKenzie JJ. Congenital myopathy with cap-like structures and nemaline rods: case report and literature review. Pediatr Neurol. 2014;51:192-7.
50. Hoogerwaard EM, van der Wouw PA, Wilde AA, Bakker E, Ippel PF, Oosterwijk JC, et al. Cardiac involvement in carriers of Duchenne and Becker muscular dystrophy. Neuromuscul Disord. 1999;9:347-51.
51. Sumita DR, Vainzof M, Campiotto S, Cerqueira AM, Canovas M, Otto PA, et al. Absence of correlation between skewed X inactivation in blood and serum creatine-kinase levels in Duchenne/Becker female carriers. Am J Med Genet. 1998;80:356-61.
52. Papa R, Madia F, Bartolomeo D, Trucco F, Pedemonte M, Traverso M, et al. Genetic and Early Clinical Manifestations of Females Heterozygous for Duchenne/Becker Muscular Dystrophy. Pediatr Neurol. 2015.
53. Mercier S, Toutain A, Toussaint A, Raynaud M, de Barace C, Marcorelles P, et al. Genetic and clinical specificity of 26 symptomatic carriers for dystrophinopathies at pediatric age. Eur J Hum Genet. 2013;21:855-63.
54. Kroos M, Hoogeveen-Westerveld M, van der Ploeg A, Reuser AJJ. The genotype-phenotype correlation in Pompe disease. Am J Med Genet C: Semin Med Genet. 2012;160C:59-68.
55. Hermans MMP, van Leenen D, Kroos MA, Beesley CE, Van Der Ploeg AT, Sakuraba H, et al. Twenty-two novel mutations in the lysosomal alpha-glucosidase gene (GAA) underscore the genotype-phenotype correlation in glycogen storage disease type II. Hum Mutat. 2004;23:47-56.
56. Montalvo AL, Bembi B, Donnarumma M, Filocamo M, Parenti G, Rossi M, et al. Mutation profile of the GAA gene in 40 Italian patients with late onset glycogen storage disease type II. Hum Mutat. 2006;27:999-1006.
57. Oba-Shinjo SM, da Silva R, Andrade FG, Palmer RE, Pomponio RJ, Ciociola KM, et al. Pompe disease in a Brazilian series: clinical and molecular analyses with identification of nine new mutations. J Neurol. 2009;256:1881-90.
58. Liu X, Wang Z, Jin W, Lv H, Zhang W, Que C, et al. Clinical and GAA gene mutation analysis in mainland Chinese patients with late-onset Pompe disease: identifying c.2238G > C as the most common mutation. BMC Med Genet. 2014;15:141.
59. Consugar MB, Navarro-Gomez D, Place EM, Bujakowska KM, Sousa ME, Fonseca-Kelly ZD, et al. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet Med. 2015;17:253-61.
60. Ankala A, da Silva C, Gualandi F, Ferlini A, Bean LJH, Collins C, et al. A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield. Ann Neurol. 2015;77:206-14.
61. Sun Y, Ruivenkamp CAL, Hoffer MJV, Vrijenhoek T, Kriek M, van Asperen CJ, et al. Next-generation diagnostics: gene panel, exome, or whole genome? Hum Mutat. 2015;36:648-55.
62. Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA. 2014;312:1880-7.