Genetics of neurodegenerative diseases: Insights from high-throughput resequencing

Human Molecular Genetics

Volumn 19, Issue R1, 2010, Pages

  Tsuji, Shoji ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA SYNUCLEIN; GLUCOSYLCERAMIDASE; LEUCINE RICH REPEAT KINASE 2; PARKIN;

ALZHEIMER DISEASE; AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; DEGENERATIVE DISEASE; GAUCHER DISEASE; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN GENOME; LINKAGE ANALYSIS; MUTATIONAL ANALYSIS; PARKINSON DISEASE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEURODEGENERATIVE DISEASES; SEQUENCE ANALYSIS, DNA;

EID: 77953886431     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddq162     Document Type: Article

References (49)

1. The Huntington's Disease Collaborative Research Group. (1993) A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. Cell, 72, 971-983.
2. Koenig, M., Hoffman, E.P., Bertelson, C.J., Monaco, A.P., Feener, C. and Kunkel, L.M. (1987) Complete cloning of the Duchenne muscular dystrophy (DMD) cDNA and preliminary genomic organization of the DMD gene in normal and affected individuals. Cell, 50, 509-517.
3. Monaco, A.P., Neve, R.L., Colletti-Feener, C., Bertelson, C.J., Kurnit, D.M. and Kunkel, L.M. (1986) Isolation of candidate cDNAs for portions of the Duchenne muscular dystrophy gene. Nature, 323, 646-650.
4. Collins, F.S. (1992) Positional cloning: let's not call it reverse anymore. Nat. Genet., 1,3-6.
5. Fukuda, Y., Nakahara, Y., Date, H., Takahashi, Y., Goto, J., Miyashita, A., Kuwano, R., Adachi, H., Nakamura, E. and Tsuji, S. (2009) SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data. BMC Bioinformat., 10, 121.
6. Krueger, K.A., Tsuji, S., Fukuda, Y., Takahashi, Y., Goto, J., Mitsui, J., Ishiura, H., Dalton, J.C., Miller, M.B., Day, J.W. et al. (2009) SNP haplotype mapping in a small ALS family. PLoS ONE, 4, e5687.
7. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature, 431, 931-945.
8. Takahashi, Y., Seki, N., Ishiura, H., Mitsui, J., Matsukawa, T., Kishino, A., Onodera, O., Aoki, M., Shimozawa, N., Murayama, S. et al. (2008) Development of a high-throughput microarray-based resequencing system for neurological disorders and its application to molecular genetics of amyotrophic lateral sclerosis. Arch. Neurol., 65, 1326-1332.
9. Vance, C., Rogelj, B., Hortobagyi, T., De Vos, K.J., Nishimura, A.L., Sreedharan, J., Hu, X., Smith, B., Ruddy, D., Wright, P. et al. (2009) Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science, 323, 1208-1211.
10. Wijesekera, L.C. and Leigh, P.N. (2009) Amyotrophic lateral sclerosis. Orphanet. J. Rare Dis., 4,3.
11. Reich, D.E. and Lander, E.S. (2001) On the allelic spectrum of human disease. Trends Genet., 17, 502-510.
12. Collins, F.S., Guyer, M.S. and Charkravarti, A. (1997) Variations on a theme: cataloging human DNA sequence variation. Science, 278, 1580-1581.
13. Pritchard, J.K. (2001) Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet., 69, 124-137.
14. Hindorff, L.A., Sethupathy, P., Junkins, H.A., Ramos, E.M., Mehta, J.P., Collins, F.S. and Manolio, T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
15. Visscher, P.M. (2008) Sizing up human height variation. Nat. Genet., 40, 489-490.
16. Manolio, T.A., Collins, F.S., Cox, N.J., Goldstein, D.B., Hindorff, L.A., Hunter, D.J., McCarthy, M.I., Ramos, E.M., Cardon, L.R., Chakravarti, A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
17. Sidransky, E., Nalls, M.A., Aasly, J.O., Aharon-Peretz, J., Annesi, G., Barbosa, E.R., Bar-Shira, A., Berg, D., Bras, J., Brice, A. et al. (2009) Multicenter analysis of glucocerebrosidase mutations in Parkinson's disease. N. Engl. J. Med., 361, 1651-1661.
18. Mitsui, J., Mizuta, I., Toyoda, A., Ashida, R., Takahashi, Y., Goto, J., Fukuda, Y., Date, H., Iwata, A., Yamamoto, M. et al. (2009) Mutations for Gaucher disease confer high susceptibility to Parkinson disease. Arch. Neurol., 66, 571-576.
19. Goker-Alpan, O., Schiffmann, R., LaMarca, M.E., Nussbaum, R.L., McInerney-Leo, A. and Sidransky, E. (2004) Parkinsonism among Gaucher disease carriers. J. Med. Genet., 41, 937-940.
20. Neudorfer, O., Giladi, N., Elstein, D., Abrahamov, A., Turezkite, T., Aghai, E., Reches, A., Bembi, B. and Zimran, A. (1996) Occurrence of Parkinson's syndrome in type I Gaucher disease. QJM, 89, 691-694.
21. Satake, W., Nakabayashi, Y., Mizuta, I., Hirota, Y., Ito, C., Kubo, M., Kawaguchi, T., Tsunoda, T., Watanabe, M., Takeda, A. et al. (2009) Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. Nat. Genet., 41, 1303-1307.
22. Metzker, M.L. (2010) Sequencing technologies-the next generation. Nat. Rev. Genet., 11, 31-46.
23. Okou, D.T., Steinberg, K.M., Middle, C., Cutler, D.J., Albert, T.J. and Zwick, M.E. (2007) Microarray-based genomic selection for high-throughput resequencing. Nat. Methods, 4, 907-909.
24. Albert, T.J., Molla, M.N., Muzny, D.M., Nazareth, L., Wheeler, D., Song, X., Richmond, T.A., Middle, C.M., Rodesch, M.J., Packard, C.J. et al. (2007) Direct selection of human genomic loci by microarray hybridization. Nat. Methods, 4, 903-905.
25. Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M.N., Smith, S.W., Middle, C.M., Rodesch, M.J., Albert, T.J., Hannon, G.J. et al. (2007) Genome-wide in situ exon capture for selective resequencing. Nat. Genet., 39, 1522-1527.
26. Volpi, L., Roversi, G., Colombo, E.A., Leijsten, N., Concolino, D., Calabria, A., Mencarelli, M.A., Fimiani, M., Macciardi, F., Pfundt, R. et al. (2010) Targeted next-generation sequencing appoints c16orf57 as clericuzio-type poikiloderma with neutropenia gene. Am. J. Hum. Genet., 86, 72-76.
27. Hedges, D.J., Burges, D., Powell, E., Almonte, C., Huang, J., Young, S., Boese, B., Schmidt, M., Pericak-Vance, M.A., Martin, E. et al. (2009) Exome sequencing of a multigenerational human pedigree. PLoS ONE, 4, e8232.
28. Zaghloul, N.A. and Katsanis, N. (2010) Functional modules, mutational load and human genetic disease. Trends Genet., 26, 168-176.
29. Biesecker, L.G. (2010) Exome sequencing makes medical genomics a reality. Nat. Genet., 42, 13-14.
30. Ng, S.B., Buckingham, K.J., Lee, C., Bigham, A.W., Tabor, H.K., Dent, K.M., Huff, C.D., Shannon, P.T., Jabs, E.W., Nickerson, D.A. et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet., 42, 30-35.
31. Choi, M., Scholl, U.I., Ji, W., Liu, T., Tikhonova, I.R., Zumbo, P., Nayir, A., Bakkaloglu, A., Ozen, S., Sanjad, S. et al. (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl Acad. Sci. USA, 106, 19096-19101.
32. Ng, S.B., Turner, E.H., Robertson, P.D., Flygare, S.D., Bigham, A.W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E.E. et al. (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272-276.
33. Maher, B. (2009) Exome sequencing takes centre stage in cancer profiling. Nature, 459, 146-147.
34. Ng, P.C., Levy, S., Huang, J., Stockwell, T.B., Walenz, B.P., Li, K., Axelrod, N., Busam, D.A., Strausberg, R.L. and Venter, J.C. (2008) Genetic variation in an individual human exome. PLoS Genet., 4, e1000160.
35. Schuster, S.C., Miller, W., Ratan, A., Tomsho, L.P., Giardine, B., Kasson, L.R., Harris, R.S., Petersen, D.C., Zhao, F., Qi, J. et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature, 463, 943-947.
36. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
37. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Guo, Y. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
38. Ahn, S.M., Kim, T.H., Lee, S., Kim, D., Ghang, H., Kim, D.S., Kim, B.C., Kim, S.Y., Kim, W.Y., Kim, C. et al. (2009) The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res., 19, 1622-1629.
39. Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.J., Makhijani, V., Roth, G.T. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
40. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
41. Li, R., Li, Y., Kristiansen, K. and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
42. Wang, J. and Mu, Q. (2003) Soap-HT-BLAST: high throughput BLAST based on Web services. Bioinformatics, 19, 1863-1864.
43. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
44. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
45. Mitsui, J., Fukuda, Y., Azuma, K., Tozaki, H., Ishiura, H., Takahashi, Y., Goto, J. andTsuji,S.(2009) Multiplexed resequencinganalysistoidentify rare variants in pooled DNA with barcode indexing employing next-generation sequencer. J. Hum. Genet.
46. Druley, T.E., Vallania, F.L., Wegner, D.J., Varley, K.E., Knowles, O.L., Bonds, J.A., Robison, S.W., Doniger, S.W., Hamvas, A., Cole, F.S. et al. (2009) Quantification of rare allelic variants from pooled genomic DNA. Nat. Methods, 6, 263-265.
47. Lupski, J.R., Reid, J.G., Gonzaga-Jauregui, C., Rio Deiros, D., Chen, D.C., Nazareth, L., Bainbridge, M., Dinh, H., Jing, C., Wheeler, D.A. et al. (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med., 362, 1181-1191.
48. Sveinbjornsdottir, S., Hicks, A.A., Jonsson, T., Petursson, H., Gugmundsson, G., Frigge, M.L., Kong, A., Gulcher, J.R. and Stefansson, K. (2000) Familial aggregation of Parkinson's disease in Iceland. N. Engl. J. Med., 343, 1765-1770.
49. Fang, F., Kamel, F., Lichtenstein, P., Bellocco, R., Sparen, P., Sandler, D.P. and Ye, W. (2009) Familial aggregation of amyotrophic lateral sclerosis. Ann. Neurol., 66, 94-99.