Improved inherited peripheral neuropathy genetic diagnosis by whole-exome sequencing

Molecular Genetics and Genomic Medicine

Volumn 3, Issue 2, 2015, Pages 143-154

  Drew, Alexander P ^a   Zhu, Danqing ^b   Kidambi, Aditi ^a   Ly, Carolyn ^a   Tey, Shelisa ^d   Brewer, Megan H ^a,c   Ahmad Annuar, Azlina ^d   Nicholson, Garth A ^a,b,c   Kennerson, Marina L ^a,b,c  

^a ANZAC RESEARCH INSTITUTE   (Australia)

^b ANZAC Research Institute   (Australia)

^c UNIVERSITY OF SYDNEY   (Australia)

^d UNIVERSITY OF MALAYA   (Malaysia)

Author keywords

Charcot Marie Tooth disease; Genetic diagnosis; Inherited peripheral neuropathy; Whole exome sequencing

Indexed keywords

EID: 84949673333     PISSN: None     EISSN: 23249269     Source Type: Journal    
DOI: 10.1002/mgg3.126     Document Type: Article

References (56)

1. Adzhubei, I. A., S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova, P. Bork, et al. 2010. A method and server for predicting damaging missense mutations. Nat. Methods 7:248–249.
2. Angiari, C., T. Cavallaro, M. Ferrarini, F. Taioli, I. Cabrini, S. Ferrari, et al. 2006. Phenotypical and genotypical heterogeneity of Charcot-Marie-Tooth disease type 2A associated with the mitofusin 2 gene (MFN2). J. Peripheral Nervous Syst. 11:179.
3. Auer-Grumbach, M., B. Schlotter-Weigel, H. Lochmuller, G. Strobl-Wildemann, P. Auer-Grumbach, R. Fischer, et al. 2005. Phenotypes of the N88S Berardinelli-Seip congenital lipodystrophy 2 mutation. Ann. Neurol. 57:415–424.
4. Auer-Grumbach, M., A. Olschewski, L. Papic, H. Kremer, M. E. McEntagart, S. Uhrig, et al. 2010. Alterations in the ankyrin domain of TRPV4 cause congenital distal SMA, scapuloperoneal SMA and HMSN2C. Nat. Genet. 42:160–164.
5. Bone, L. J., S. M. Deschenes, R. J. Balice-Gordon, K. H. Fischbeck, and S. S. Scherer. 1997. Connexin32 and X-linked Charcot-Marie-Tooth disease. Neurobiol. Dis. 4:221–230.
6. Chen, Y. Z., C. L. Bennett, H. M. Huynh, I. P. Blair, I. Puls, J. Irobi, et al. 2004. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am. J. Hum. Genet. 74:1128–1135.
7. Choi, B. O., M. S. Lee, S. H. Shin, J. H. Hwang, K. G. Choi, W. K. Kim, et al. 2004. Mutational analysis of PMP22, MPZ, GJB1, EGR2 and NEFL in Korean Charcot-Marie-Tooth neuropathy patients. Hum. Mutat. 24:185–186.
8. Choi, M., U. I. Scholl, W. Ji, T. Liu, I. R. Tikhonova, P. Zumbo, et al. 2009. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl. Acad. Sci. USA 106:19096–19101.
9. Choi, B. O., S. K. Koo, M. H. Park, H. Rhee, S. J. Yang, K. G. Choi, et al. 2012. Exome sequencing is an efficient tool for genetic screening of Charcot-Marie-Tooth disease. Hum. Mutat. 33:1610–1615.
10. Chung, K. W., S. B. Kim, K. D. Park, K. G. Choi, J. H. Lee, H. W. Eun, et al. 2006. Early onset severe and late-onset mild Charcot-Marie-Tooth disease with mitofusin 2 (MFN2) mutations. Brain 129:2103–2118.
11. Cooper, G. M., D. L. Goode, S. B. Ng, A. Sidow, M. J. Bamshad, J. Shendure, et al. 2010. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat. Methods 7:250–251.
12. Deng, H. X., C. J. Klein, J. Yan, Y. Shi, Y. Wu, F. Fecto, et al. 2010. Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4. Nat. Genet. 42:165–169.
13. Dierick, I., J. Baets, J. Irobi, A. Jacobs, E. de Vriendt, T. Deconinck, et al. 2008. Relative contribution of mutations in genes for autosomal dominant distal hereditary motor neuropathies: a genotype-phenotype correlation study. Brain 131:1217–1227.
14. Fabrizi, G. M., T. Cavallaro, C. Angiari, I. Cabrini, F. Taioli, G. Malerba, et al. 2007. Charcot-Marie-Tooth disease type 2E, a disorder of the cytoskeleton. Brain 130:394–403.
15. Hahn, A. F., C. F. Bolton, C. M. White, W. F. Brown, S. E. Tuuha, C. C. Tan, et al. 1999. Genotype/phenotype correlations in X-linked dominant Charcot-Marie-Tooth disease. Ann. N. Y. Acad. Sci. 883:366–382.
16. Haites, N. E., E. Nelis, and C. van Broeckhoven. 1998. 3rd workshop of the European CMT consortium: 54th ENMC International Workshop on genotype/phenotype correlations in Charcot-Marie-Tooth type 1 and hereditary neuropathy with liability to pressure palsies 28-30 November 1997, Naarden, The Netherlands. Neuromuscul. Disord. 8:591–603.
17. Harding, A. E., and P. K. Thomas. 1984. Peroneal muscular atrophy with pyramidal features. J. Neurol. Neurosurg. Psychiatry 47:168–172.
18. Hedges, D. J., D. Burges, E. Powell, C. Almonte, J. Huang, S. Young, et al. 2009. Exome sequencing of a multigenerational human pedigree. PLoS One 4:e8232.
19. Hirano, M., C. M. Quinzii, H. Mitsumoto, A. P. Hays, J. K. Roberts, P. Richard, et al. 2011. Senataxin mutations and amyotrophic lateral sclerosis. Amyotroph. Lateral. Scler. 12:223–227.
20. Houlden, H., M. Laura, F. Wavrant-De Vrieze, J. Blake, N. Wood, M. M. Reilly. 2008. Mutations in the HSP27 (HSPB1) gene cause dominant, recessive, and sporadic distal HMN/CMT type 2. Neurology 71:1660–1668.
21. Hovig, E., B. Smith-Sorensen, A. Brogger, and A. L. Borrensen. 1991. Constant denaturant gel electrophoresis, a modification of denaturing gradient gel electrophoresis, in mutation detection. Mutat. Res. 263:61.
22. Huang, J., X. Wu, G. Montenegro, J. Price, G. Wang, J. M. Vance, et al. 2010. Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease. J. Neurol. 257: 735–741.
23. Irobi, J., P. van den Bergh, L. Merlini, C. Verellen, L. van Maldergem, I. Dierick, et al. 2004. The phenotype of motor neuropathies associated with BSCL2 mutations is broader than Silver syndrome and distal HMN type V. Brain 127:2124–2130.
24. de Jonghe, P., M. Auer-Grumbach, J. Irobi, K. Wagner, B. Plecko, M. Kennerson, et al. 2002. Autosomal dominant juvenile amyotrophic lateral sclerosis and distal hereditary motor neuronopathy with pyramidal tract signs: synonyms for the same disorder? Brain 125:1320–1325.
25. Karolchik, D., G. P. Barber, J. Casper, H. Clawson, M. S. Cline, M. Diekhans, et al. 2014. The UCSC genome browser database: 2014 update. Nucleic Acids Res. 42:D764–D770.
26. Kennerson, M. L., T. Warburton, E. Nelis, M. Brewer, P. Polly, P. de Jonghe, et al. 2007. Mutation scanning the GJB1 gene with high-resolution melting analysis: implications for mutation scanning of genes for Charcot-Marie-Tooth disease. Clin. Chem. 53:349–352.
27. Kent, W. J., C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, et al. 2002. The human genome browser at UCSC. Genome Res. 12:996–1006.
28. Kumar, P., S. Henikoff, and P. C. Ng. 2009. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4:1073–1081.
29. Li, H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.
30. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079.
31. Macarthur, D. G., T. A. Manolio, D. P. Dimmock, H. L. Rehm, J. Shendure, G. R. Abecasis, et al. 2014. Guidelines for investigating causality of sequence variants in human disease. Nature 508:469–476.
32. McLaughlin, H. M., R. Sakaguchi, W. Giblin, T. E. Wilson, L. Biesecker, J. R. Lupski, et al. 2012. A recurrent loss-of-function alanyl-tRNA synthetase (AARS) mutation in patients with Charcot-Marie-Tooth disease type 2N (CMT2N). Hum. Mutat. 33:244–253.
33. Mersiyanova, I. V., A. V. Perepelov, A. V. Polyakov, V. F. Sitnikov, E. L. Dadali, R. B. Oparin, et al. 2000. A new variant of Charcot-Marie-Tooth disease type 2 is probably the result of a mutation in the neurofilament-light gene. Am. J. Hum. Genet. 67:37–46.
34. Montenegro, G., E. Powell, J. Huang, F. Speziani, Y. J. Edwards, G. Beecham, et al. 2011. Exome sequencing allows for rapid gene identification in a Charcot-Marie-Tooth family. Ann. Neurol. 69:464–470.
35. Nelis, E., S. Simokovic, V. Timmerman, A. Lofgren, H. Backhovens, P. de Jonghe, et al. 1997. Mutation analysis of the connexin 32 (Cx32) gene in Charcot-Marie-Tooth neuropathy type 1: identification of five new mutations. Hum. Mutat. 9:47–52.
36. Neveling, K., L. A. Martinez-Carrera, I. Holker, A. Heister, A. Verrips, S. M. Hosseini-Barkooie, et al. 2013. Mutations in BICD2, which encodes a golgin and important motor adaptor, cause congenital autosomal-dominant spinal muscular atrophy. Am. J. Hum. Genet. 92:946–954.
37. Nishimura, G., J. Dai, E. Lausch, S. Unger, A. Megarbane, H. Kitoh, et al. 2010. Spondylo-epiphyseal dysplasia, Maroteaux type (pseudo-Morquio syndrome type 2), and parastremmatic dysplasia are caused by TRPV4 mutations. Am. J. Med. Genet. A 152A:1443–1449.
38. Numakura, C., C. Lin, T. Ikegami, P. Guldberg, and K. Hayasaka. 2002. Molecular analysis in Japanese patients with Charcot-Marie-Tooth disease: DGGE analysis for PMP22, MPZ, and Cx32/GJB1 mutations. Hum. Mutat. 20:392–398.
39. Oh, S., Y. Ri, M. V. Bennett, E. B. Trexler, V. K. Verselis, and T. A. Bargiello. 1997. Changes in permeability caused by connexin 32 mutations underlie X-linked Charcot-Marie-Tooth disease. Neuron 19:927–938.
40. Ohnishi, A., T. Yoshimura, A. Takazawa, T. Hashimoto, T. Yamamoto, and Y. Fukushima. 1995. A family of X-linked motor and sensory neuropathy with a new type of connexin32 mutation. Rinsho. Shinkeigaku. (Clin. Neurol.) 35:843–849.
41. Pitceathly, R. D., S. M. Murphy, E. Cottenie, A. Chalasani, M. G. Sweeney, C. Woodward, et al. 2012. Genetic dysfunction of MT-ATP6 causes axonal Charcot-Marie-Tooth disease. Neurology 79:1145–1154.
42. Pollard, K. S., M. J. Hubisz, K. R. Rosenbloom, and A. Siepel. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20:110–121.
43. R Core Team. 2010. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
44. Rossor, A. M., J. M. Polke, H. Houlden, and M. M. Reilly. 2013. Clinical implications of genetic advances in Charcot-Marie-Tooth disease. Nat. Rev. Neurol. 9:562–571.
45. Saito, M., Y. Hayashi, T. Suzuki, H. Tanaka, I. Hozumi, and S. Tsuji. 1997. Linkage mapping of the gene for Charcot-Marie-Tooth disease type 2 to chromosome 1p (CMT2A) and the clinical features of CMT2A. Neurology 49:1630–1635.
46. Saporta, M. A., and M. E. Shy. 2013. Inherited peripheral neuropathies. Neurol. Clin. 31:597–619.
47. Saporta, A. S., S. L. Sottile, L. J. Miller, S. M. Feely, C. E. Siskind, and M. E. Shy. 2011. Charcot-Marie-Tooth disease subtypes and genetic testing strategies. Ann. Neurol. 69:22–33.
48. Silander, K., P. Meretoja, H. Pihko, V. Juvonen, J. Issakainen, P. Aula, et al. 1997. Screening for connexin 32 mutations in Charcot-Marie-Tooth disease families with possible X-linked inheritance. Hum. Genet. 100:391–397.
49. Siskind, C. E., S. Panchal, C. O. Smith, S. M. Feely, J. C. Dalton, A. B. Schindler, et al. 2013. A review of genetic counseling for Charcot Marie Tooth disease (CMT). J. Genet. Couns. 22:422–436.
50. Timmerman, V., A. V. Strickland, and S. Zuchner. 2014. Genetics of Charcot-Marie-Tooth (CMT) Disease within the Frame of the human genome project success. Genes (Basel) 5:13–32.
51. Wang, K., M. Li, and H. Hakonarson. 2010. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38:e164.
52. Wildeman, M., E. van Ophuizen, J. T. den Dunnen, and P. E. Taschner. 2008. Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker. Hum. Mutat. 29:6–13.
53. Windpassinger, C., M. Auer-Grumbach, J. Irobi, H. Patel, E. Petek, G. Horl, et al. 2004. Heterozygous missense mutations in BSCL2 are associated with distal hereditary motor neuropathy and Silver syndrome. Nat. Genet. 36:271– 276.
54. Yoshimura, T., A. Ohnishi, T. Yamamoto, Y. Fukushima, M. Kitani, and T. Kobayashi. 1996. Two novel mutations (C53S, S26L) in the connexin32 of Charcot-Marie-Tooth disease type X families. Hum. Mutat. 8:270–272.
55. Zhao, C., J. Takita, Y. Tanaka, M. Setou, T. Nakagawa, S. Takeda, et al. 2001. Charcot-Marie-Tooth disease type 2A caused by mutation in a microtubule motor KIF1Bbeta. Cell 105:587–597.
56. Zuchner, S., P. de Jonghe, A. Jordanova, K. G. Claeys, V. Guergueltcheva, S. Cherninkova, et al. 2006. Axonal neuropathy with optic atrophy is caused by mutations in mitofusin 2. Ann. Neurol. 59:276–281.