Next generation sequencing for neurological diseases: New hope or new hype?

Clinical Neurology and Neurosurgery

Volumn 115, Issue 7, 2013, Pages 948-953

  Keogh, M J ^a   Chinnery, P F ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Exome; Mendelian; Mutation; Next generation; Sequencing

Indexed keywords

DNA; DNA POLYMERASE;

ALZHEIMER DISEASE; AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; DATA ANALYSIS; DATA PROCESSING; DISEASE ASSOCIATION; DNA SEQUENCE; EPILEPSY; EXOME; EXON; GENETIC DISORDER; HEREDITARY MOTOR SENSORY NEUROPATHY; HUMAN; KABUKI MAKEUP SYNDROME; MULTIPLE SCLEROSIS; NEUROLOGIC DISEASE; NEUROSCIENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

DATA INTERPRETATION, STATISTICAL; EXOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NERVOUS SYSTEM DISEASES; SEQUENCE ANALYSIS, DNA;

EID: 84878825120     PISSN: 03038467     EISSN: 18726968     Source Type: Journal    
DOI: 10.1016/j.clineuro.2012.09.030     Document Type: Article

References (52)

1. D.A. Hafler, A. Compston, S. Sawcer, E.S. Lander, M.J. Daly, and P.L. De Jager Risk alleles for multiple sclerosis identified by a genomewide study New England Journal of Medicine 357 9 2007 851 862
2. Genome-wide association study of severity in multiple sclerosis. Genes and Immunity 2011;12(8):615-25.
3. X. Liu, R. Cheng, M. Verbitsky, S. Kisselev, A. Browne, and H. Mejia-Sanatana Genome-wide association study identifies candidate genes for Parkinson's disease in an Ashkenazi Jewish population BMC Medical Genetics 12 2011 104
4. M.H. Polymeropoulos, C. Lavedan, E. Leroy, S.E. Ide, A. Dehejia, and A. Dutra Mutation in the alpha-synuclein gene identified in families with Parkinson's disease Science 276 5321 1997 2045 2047
5. T. Kitada, S. Asakawa, N. Hattori, H. Matsumine, Y. Yamamura, and S. Minoshima Mutations in the parkin gene cause autosomal recessive Juvenile Parkinsonism Nature 392 6676 1998 605 608
6. D. Kasperaviciute, C.B. Catarino, E.L. Heinzen, C. Depondt, G.L. Cavalleri, and L.O. Caboclo Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study Brain 133 Pt 7 2010 2136 2147
7. B. Maher Personal genomes: the case of the missing heritability Nature 456 7218 2008 18 21
8. E.T. Cirulli, and D.B. Goldstein Uncovering the roles of rare variants in common disease through whole-genome sequencing Nature Reviews Genetics 11 6 2010 415 425
9. J. Kaiser Human genetics. Affordable 'exomes' fill gaps in a catalog of rare diseases Science 330 6006 2010 p903
10. W.A. Gahl, T.C. Markello, C. Toro, K.F. Fajardo, M. Sincan, and F. Gill The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases Genetics in Medicine 14 1 2012 51 59
11. J. Majewski, J. Schwartzentruber, E. Lalonde, A. Montpetit, and N. Jabado What can exome sequencing do for you? Journal of Medical Genetics 48 9 2011 580 589
12. M.L. Metzker Sequencing technologies-the next generation Nature Reviews Genetics 11 1 2010 31 46
13. R. Sachidanandam, D. Weissman, S.C. Schmidt, J.M. Kakol, L.D. Stein, and G. Marth A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms Nature 409 6822 2001 928 933
14. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, and J. Baldwin Initial sequencing and analysis of the human genome Nature 409 6822 2001 860 921
15. J.D. McPherson, M. Marra, L. Hillier, R.H. Waterston, A. Chinwalla, and J. Wallis A physical map of the human genome Nature 409 6822 2001 934 941
16. D.N. Cooper, M. Krawczak, and S.E. Antonorakis The nature and mechanisms of human gene mutation C. Scriver, A.L. Beaudet, W.S. Sly, D. Valle, The metabolic and molecular bases of inherited disease 7th ed. 1995 McGraw-Hill New York, NY 259 291
17. P.D. Stenson, E.V. Ball, K. Howells, A.D. Phillips, M. Mort, and D.N. Cooper The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics Human Genetics 4 2 2009 69 72
18. F. Sanger, and A.R. Coulson A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase Journal of Molecular Biology 94 3 1975 441 448
19. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain-terminating inhibitors Proceedings of the National Academy of Sciences of the United States of America 74 12 1977 5463 5467
20. M.J. Bamshad, S.B. Ng, A.W. Bigham, H.K. Tabor, M.J. Emond, and D.A. Nickerson Exome sequencing as a tool for Mendelian disease gene discovery Nature Reviews Genetics 12 11 2011 745 755
21. Information, T.N.C.f.B. sbSNP Short genetic variations. Available from: http://www.ncbi.nlm.nih.gov/projects/SNP/; 2012 [18 February 2012].
22. M. Via, C. Gignoux, and E.G. Burchard The 1000 Genomes Project: new opportunities for research and social challenges Genome Medicine 2 1 2010 3
23. A.B. Singleton Exome sequencing: a transformative technology Lancet Neurology 10 10 2011 942 946
24. J.M. Schwarz, C. Rodelsperger, M. Schuelke, and D. Seelow MutationTaster evaluates disease-causing potential of sequence alterations Nature Methods 7 8 2010 575 576
25. C. Ferrer-Costa, J.L. Gelpi, L. Zamakola, I. Parraga, X. de la Cruz, and M. Orozco PMUT: a web-based tool for the annotation of pathological mutations on proteins Bioinformatics 21 14 2005 3176 3178
26. I.A. Adzhubei, S. Schmidt, L. Peshkin, V.E. Ramensky, A. Gerasimova, and P. Bork A method and server for predicting damaging missense mutations Nature Methods 7 4 2010 248 249
27. S.B. Ng, E.H. Turner, P.D. Robertson, S.D. Flygare, A.W. Bigham, and C. Lee Targeted capture and massively parallel sequencing of 12 human exomes Nature 461 7261 2009 272 276
28. J.K. Teer, and J.C. Mullikin Exome sequencing: the sweet spot before whole genomes Human Molecular Genetics 19 R2 2010 R145 R151
29. A.E. Renton, E. Majounie, A. Waite, J. Simon-Sanchez, S. Rollinson, and J.R. Gibbs A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD Neuron 72 2 2011 257 268
30. S.M. Mirkin Expandable DNA repeats and human disease Nature 447 7147 2007 932 940
31. C.E. Pearson, K. Nichol Edamura, and J.D. Cleary Repeat instability: mechanisms of dynamic mutations Nature Reviews Genetics 6 10 2005 729 742
32. B. Wold, and R.M. Myers Sequence census methods for functional genomics Nature Methods 5 1 2008 19 21
33. J.L. Wang, X. Yang, K. Xia, Z.M. Hu, L. Weng, and X. Jin TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing Brain 133 Pt 12 2010 3510 3518
34. J.O. Johnson, J. Mandrioli, M. Benatar, Y. Abramzon, V.M. Van Deerlin, and J.Q. Trojanowski Exome sequencing reveals VCP mutations as a cause of familial ALS Neuron 68 5 2010 857 864
35. H. Saitsu, H. Osaka, M. Sasaki, J. Takanashi, K. Hamada, and A. Yamashita Mutations in POLR3A and POLR3B encoding RNA Polymerase III subunits cause an autosomal-recessive hypomyelinating leukoencephalopathy American Journal of Human Genetics 89 5 2011 644 651
36. Y.M. Lim, I. Koh, Y.M. Park, J.J. Kim, D.S. Kim, and H.J. Kim Exome sequencing identifies KIAA1377 and C5orf42 as susceptibility genes for monomelic amyotrophy Neuromuscular Disorders 22 5 2012 394 400
37. A. Hoischen, B.W. van Bon, C. Gilissen, P. Arts, B. van Lier, and M. Steehouwer De novo mutations of SETBP1 cause Schinzel-Giedion syndrome Nature Genetics 42 6 2010 483 485
38. S.B. Ng, A.W. Bigham, K.J. Buckingham, M.C. Hannibal, M.J. McMillin, and H.I. Gildersleeve Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome Nature Genetics 42 9 2010 790 793
39. G. Montenegro, E. Powell, J. Huang, F. Speziani, Y.J. Edwards, and G. Beecham Exome sequencing allows for rapid gene identification in a Charcot-Marie-Tooth family Annals of Neurology 69 3 2011 464 470
40. N.A. Patsopoulos, P.I. de Bakker, F. Esposito, J. Reischl, S. Lehr, and D. Bauer Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci Annals of Neurology 70 6 2011 897 912
41. S. Sanna, M. Pitzalis, M. Zoledziewska, I. Zara, C. Sidore, and R. Murru Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis Nature Genetics 42 6 2010 495 497
42. D. Harold, R. Abraham, P. Hollingworth, R. Sims, A. Gerrish, and M.L. Hamshere Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease Nature Genetics 41 10 2009 1088 1093
43. S. Seshadri, A.L. Fitzpatrick, M.A. Ikram, A.L. DeStefano, V. Gudnason, and M. Boada Genome-wide analysis of genetic loci associated with Alzheimer disease American Journal of Medical Association 303 18 2010 1832 1840
44. Y. Guo, L.W. Baum, P.C. Sham, V. Wong, P.W. Ng, and C.H. Lui Two-stage genome-wide association study identifies variants in CAMSAP1L1 as susceptibility loci for epilepsy in Chinese Human Molecular Genetics 21 5 2012 1184 1189
45. W. Bodmer, and C. Bonilla Common and rare variants in multifactorial susceptibility to common diseases Nature Genetics 40 6 2008 695 701
46. J.K. Pritchard Are rare variants responsible for susceptibility to complex diseases? American Journal of Human Genetics 69 1 2001 124 137
47. B.J. O'Roak, P. Deriziotis, C. Lee, L. Vives, J.J. Schwartz, and S. Girirajan Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations Nature Genetics 43 6 2011 585 589
48. J.M. Bras, and A.B. Singleton Exome sequencing in Parkinson's disease Clinical Genetics 80 2 2011 104 109
49. C. Dias, M. Sincan, P.F. Cherukuri, R. Rupps, Y. Huang, and H. Briemberg An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia Human Mutation 2012
50. A.B. Singleton, M. Farrer, J. Johnson, A. Singleton, S. Hague, and J. Kachergus alpha-Synuclein locus triplication causes Parkinson's disease Science 302 5646 2003 p841
51. S.B. Ng, K.J. Buckingham, C. Lee, A.W. Bigham, H.K. Tabor, and K.M. Dent Exome sequencing identifies the cause of a Mendelian disorder Nature Genetics 42 1 2010 30 35
52. L.G. Biesecker Exome sequencing makes medical genomics a reality Nature Genetics 42 1 2010 13 14