A large genome scan for rare CNVs in amyotrophic lateral sclerosis

Human Molecular Genetics

Volumn 19, Issue 20, 2010, Pages 4091-4099

  Blauw, Hylke M ^a   Al Chalabi, Ammar ^c   Andersen, Peter M ^d,e   van Vught, Paul W J ^a   Diekstra, Frank P ^a   van Es, Michael A ^a   Saris, Christiaan G J ^a   Groen, Ewout J N ^a   van Rheenen, Wouter ^a   Koppers, Max ^a   Slot, Ruben van't ^b   Strengman, Eric ^b   Estrada, Karol ^f   Rivadeneira, Fernando ^f   Hofman, Albert ^f   Uitterlinden, Andre G ^f   Kiemeney, Lambertus A ^g   Vermeulen, Sita H M ^g   Birve, Anna ^d   Waibel, Stefan ^e   Meyer, Thomas ^h   Cronin, Simon ⁱ   McLaughlin, Russell L ⁱ   Hardiman, Orla ^i,j   Sapp, Peter C ^k,l,m,n   Tobin, Martin D ^o   Wain, Louise V ^o   Tomik, Barbara ^p   Slowik, Agnieszka ^p   Lemmens, Robin ^q,r   Rujescu, Dan ^s   Schulte, Claudia ^t   Gasser, Thomas ^t   Brown Jr , Robert H ^k,l   Landers, John E ^k,l   Robberecht, Wim ^q,r   Ludolph, Albert C ^e   Ophoff, Roel A ^a,u   Veldink, Jan H ^a   van den Berg, Leonard H ^a   more..

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b Department of Medical Genetics ^*  (Netherlands)

^c KING'S COLLEGE LONDON   (United Kingdom)

^d UMEÅ UNIVERSITY   (Sweden)

^e UNIVERSITY OF ULM   (Germany)

^f ERASMUS MEDICAL CENTER   (Netherlands)

^g RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^h CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

ⁱ BEAUMONT HOSPITAL   (Ireland)

^j TRINITY COLLEGE DUBLIN   (Ireland)

^k MASSACHUSETTS GENERAL HOSPITAL   (United States)

^l UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^m HOWARD HUGHES MEDICAL INSTITUTE   (United States)

ⁿ MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^o UNIVERSITY OF LEICESTER   (United Kingdom)

^p JAGIELLONIAN UNIVERSITY   (Poland)

^q UNIVERSITY HOSPITALS LEUVEN   (Belgium)

^r DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^s LUDWIG MAXIMILIANS UNIVERSITY   (Germany)

^t GERMAN CENTER FOR NEURODEGENERATIVE DISEASES DZNE   (Germany)

^u UNIVERSITY OF CALIFORNIA   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DISEASE PREDISPOSITION; FOLLOW UP; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENE REPLICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE; HEREDITARY MOTOR SENSORY NEUROPATHY; HUMAN; LINKAGE ANALYSIS; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION;

AMYOTROPHIC LATERAL SCLEROSIS; CASE-CONTROL STUDIES; DIPEPTIDYL-PEPTIDASES AND TRIPEPTIDYL-PEPTIDASES; DNA COPY NUMBER VARIATIONS; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MEMBRANE PROTEINS; MOTOR NEURONS; NERVE TISSUE PROTEINS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; POTASSIUM CHANNELS; RISK FACTORS; SPASTIC PARAPLEGIA, HEREDITARY;

EID: 77957739219     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddq323     Document Type: Article

References (52)

1. Chiò, A., Logroscino, G., Hardiman, O., Swingler, R., Mitchell, D., Beghi, E., Traynor, B.G. and Consortium, O.B.O.T.E. (2009) Prognostic factors in ALS: a critical review. Amyotroph. Lateral Scler., 10, 310-323.
2. Dion, P.A., Daoud, H. and Rouleau, G.A. (2009) Genetics of motor neuron disorders: new insights into pathogenic mechanisms. Nat. Rev. Genet., 10, 769-782.
3. Graham, A.J., Macdonald, A.M. and Hawkes, C.H. (1997) British motor neuron disease twin study. J. Neurol. Neurosurg. Psychiatry, 62, 562-569.
4. van Es, M.A., Veldink, J.H., Saris, C.G.J., Blauw, H.M., Van Vught, P.W.J., Birve, A., Lemmens, R., Schelhaas, H.J., Groen, E.J.N., Huisman, M.H.B. et al. (2009) Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis. Nat. Genet., 41, 1083-1087.
5. 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.
6. Marshall, C.R., Noor, A., Vincent, J.B., Lionel, A.C., Feuk, L., Skaug, J., Shago, M., Moessner, R., Pinto, D., Ren, Y. et al. (2008) Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet., 82, 477-488.
7. Stefansson, H., Rujescu, D., Cichon, S., Pietiläinen, O.P.H., Ingason, A., Steinberg, S., Fossdal, R., Sigurdsson, E., Sigmundsson, T., Buizer-Voskamp, J.E. et al. (2008) Large recurrent microdeletions associated with schizophrenia. Nature, 455, 232-236.
8. De Kovel, C.G.F., Trucks, H., Helbig, I., Mefford, H.C., Baker, C., Leu, C., Kluck, C., Muhle, H., Von Spiczak, S., Ostertag, P. et al. (2010) Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. Brain, 133, 23-32.
9. Blauw, H.M., Veldink, J.H., van Es, M.A., Van Vught, P.W., Saris, C.G.J., van der Zwaag, B., Franke, L., Burbach, J.P.H., Wokke, J.H., Ophoff, R.A. et al. (2008) Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen. Lancet Neurol., 7, 319-326.
10. Cronin, S., Blauw, H.M., Veldink, J.H., van Es, M.A., Ophoff, R.A., Bradley, D.G., Van Den Berg, L.H. and Hardiman, O. (2008) Analysis of genome-wide copy number variation in Irish and Dutch ALS populations. Hum. Mol. Genet., 17, 3392-3398.
11. Wain, L.V., Pedroso, I., Landers, J.E., Breen, G., Shaw, C.E., Leigh, P.N., Brown, R.H., Tobin, M.D. and Al-Chalabi, A. (2009) The role of copy number variation in susceptibility to amyotrophic lateral sclerosis: genome-wide association study and comparison with published loci. PLoS ONE, 4, e8175.
12. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J. et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
13. Meyer, T., Alber, B., Roemer, K., Martin, T., Kalscheuer, V.M., Göttert, E., Zang, K.D., Ludolph, A.C., Ropers, H.-H. and Prudlo, J. (2003) High rate of constitutional chromosomal rearrangements in apparently sporadic ALS. Neurology, 60, 1348-1350.
14. Locke, D.P., Sharp, A.J., Mccarroll, S.A., McGrath, S.D., Newman, T.L., Cheng, Z., Schwartz, S., Albertson, D.G., Pinkel, D., Altshuler, D.M. et al. (2006) Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet., 79, 275-290.
15. van Es, M.A., Van Vught, P.W., Blauw, H.M., Franke, L., Saris, C.G., Van Den Bosch, L., De Jong, S.W., De Jong, V., Baas, F., Van't Slot, R. et al. (2008) Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. Nat. Genet., 40, 29-31.
16. van Es, M.A., van Vught, P.W., van Kempen, G., Blauw, H.M., Veldink, J.H. and van den Berg, L.H. (2009) Dpp6 is associated with susceptibility to progressive spinal muscular atrophy. Neurology, 72, 1184-1185.
17. Cronin, S., Berger, S., Ding, J., Schymick, J.C., Washecka, N., Hernandez, D.G., Greenway, M.J., Bradley, D.G., Traynor, B.J. and Hardiman, O. (2008) A genome-wide association study of sporadic ALS in a homogenous Irish population. Hum. Mol. Genet., 17, 768-774.
18. Del Bo, R., Ghezzi, S., Corti, S., Santoro, D., Prelle, A., Mancuso, M., Siciliano, G., Briani, C., Murri, L., Bresolin, N. et al. (2008) DPP6 gene variability confers increased risk of developing sporadic amyotrophic lateral sclerosis in Italian patients. J. Neurol. Neurosurg. Psychiatry, 79, 1085.
19. van Es, M.A., Veldink, J.H., Saris, C.G., Blauw, H.M., van Vught, P.W., Birve, A., Lemmens, R., Schelhaas, H.J., Groen, E.J., Huisman, M.H. et al. (2009) Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis. Nat. Genet., 41, 1083-1087.
20. Daoud, H., Valdmanis, P.N., Dion, P.A. and Rouleau, G.A. (2009) Analysis of DPP6 and FGGY as candidate genes for amyotrophic lateral sclerosis. Amyotroph. Lateral Scler, 11, 389-391.
21. Fogh, I., D'Alfonso, S., Gellera, C., Ratti, A., Cereda, C., Penco, S., Corrado, L., Soraru, G., Castellotti, B., Tiloca, C. et al. (2009) No association of DPP6 with amyotrophic lateral sclerosis in an Italian population. Neurobiol. Aging, in press.
22. Chio, A., Schymick, J.C., Restagno, G., Scholz, S.W., Lombardo, F., Lai, S.L., Mora, G., Fung, H.C., Britton, A., Arepalli, S. et al. (2009) A two-stage genome-wide association study of sporadic amyotrophic lateral sclerosis. Hum. Mol. Genet., 18, 1524-1532.
23. Wong, W., Newell, E.W., Jugloff, D.G., Jones, O.T. and Schlichter, L.C. (2002) Cell surface targeting and clustering interactions between heterologously expressed PSD-95 and the Shal voltage-gated potassium channel, Kv4.2. J. Biol. Chem., 277, 20 423-20 430.
24. Feuk, L., Carson, A.R. and Scherer, S.W. (2006) Structural variation in the human genome. Nat. Rev. Genet., 7, 85-97.
25. Rainier, S., Chai, J.-H., Tokarz, D., Nicholls, R.D. and Fink, J.K. (2003) NIPA1 gene mutations cause autosomal dominant hereditary spastic paraplegia (SPG6). Am. J. Hum. Genet., 73, 967-971.
26. Zhao, J., Matthies, D.S., Botzolakis, E.J., Macdonald, R.L., Blakely, R.D. and Hedera, P. (2008) Hereditary spastic paraplegia-associated mutations in the NIPA1 gene and its Caenorhabditis elegans homolog trigger neural degeneration in vitro and in vivo through a gain-of-function mechanism. J. Neurosci., 28, 13 938-13 951.
27. Orlacchio, A., Babalini, C., Borreca, A., Patrono, C., Massa, R., Basaran, S., Munhoz, R.P., Rogaeva, E.A., St George-Hyslop, P.H., Bernardi, G. et al. (2010) SPATACSIN mutations cause autosomal recessive juvenile amyotrophic lateral sclerosis. Brain, 133, 591-598.
28. Brugman, F., Wokke, J.H.J., Scheffer, H., Versteeg, M.H.A., Sistermans, E.A. and Van Den Berg, L.H. (2005) Spastin mutations in sporadic adult-onset upper motor neuron syndromes. Ann. Neurol., 58, 865-869.
29. Meyer, T., Schwan, A., Dullinger, J.S., Brocke, J., Hoffmann, K.-T., Nolte, C.H., Hopt, A., Kopp, U., Andersen, P., Epplen, J.T. et al. (2005) Early-onset ALS with long-term survival associated with spastin gene mutation. Neurology, 65, 141-143.
30. Tsang, H.T.H., Edwards, T.L., Wang, X., Connell, J.W., Davies, R.J., Durrington, H.J., O'Kane, C.J., Luzio, J.P. and Reid, E. (2009) The hereditary spastic paraplegia proteins NIPA1, spastin and spartin are inhibitors of mammalian BMP signalling. Hum. Mol. Genet., 18, 3805-3821.
31. Williams, A.H., Valdez, G., Moresi, V., Qi, X., Mcanally, J., Elliott, J.L., Bassel-Duby, R., Sanes, J.R. and Olson, E.N. (2009) MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science, 326, 1549-1554.
32. Zollner, S. and Pritchard, J.K. (2007) Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am. J. Hum. Genet., 80, 605-615.
33. van Es, M.A., Van Vught, P.W., Blauw, H.M., Franke, L., Saris, C.G., Andersen, P.M., Van Den Bosch, L., De Jong, S.W., van 't Slot, R., Birve, A. et al. (2007) ITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome-wide association study. Lancet Neurol., 6, 869-877.
34. Schymick, J., Scholz, S., Fung, H., Britton, A., Arepalli, S., Gibbs, J., Lombardo, F., Matarin, M., Kasperaviciute, D. and Hernandez, D. (2007) Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol., 6, 322-328.
35. Chiò, A., Schymick, J.C., Restagno, G., Scholz, S.W., Lombardo, F., Lai, S.-L., Mora, G., Fung, H.-C., Britton, A., Arepalli, S. et al. (2009) A two-stage genome-wide association study of sporadic amyotrophic lateral sclerosis. Hum. Mol. Genet., 18, 1524-1532.
36. Dunckley, T., Huentelman, M.J., Craig, D.W., Pearson, J.V., Szelinger, S., Joshipura, K., Halperin, R.F., Stamper, C., Jensen, K.R., Letizia, D. et al. (2007) Whole-genome analysis of sporadic amyotrophic lateral sclerosis. N. Engl. J. Med., 357, 775-788.
37. Brooks, B.R. (1994) El Escorial World Federation of Neurology criteria for the diagnosis of amyotrophic lateral sclerosis. Subcommittee on Motor Neuron Diseases/Amyotrophic Lateral Sclerosis of the World Federation of Neurology Research Group on Neuromuscular Diseases and the El Escorial 'Clinical limits of amyotrophic lateral sclerosis' workshop contributors. J. Neurol. Sci., 124 (suppl.), 96-107.
38. Hofman, A., Breteler, M.M., van Duijn, C.M., Krestin, G.P., Pols, H.A., Stricker, B.H., Tiemeier, H., Uitterlinden, A.G., Vingerling, J.R. and Witteman, J.C. (2007) The Rotterdam Study: objectives and design update. Eur. J. Epidemiol., 22, 819-829.
39. Kiemeney, L.A., Thorlacius, S., Sulem, P., Geller, F., Aben, K.K.H., Stacey, S.N., Gudmundsson, J., Jakobsdottir, M., Bergthorsson, J.T., Sigurdsson, A. et al. (2008) Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat. Genet., 40, 1307-1312.
40. Stefansson, H., Ophoff, R.A., Steinberg, S., Andreassen, O.A., Cichon, S., Rujescu, D., Werge, T., Pietiläinen, O.P.H., Mors, O., Mortensen, P.B. et al. (2009) Common variants conferring risk of schizophrenia. Nature, 460, 744-747.
41. Simón-Sánchez, J., Schulte, C., Bras, J.M., Sharma, M., Gibbs, J.R., Berg, D., Paisan-Ruiz, C., Lichtner, P., Scholz, S.W., Hernandez, D.G. et al. (2009) Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nat. Genet., 41, 1308-1312.
42. Landers, J.E., Melki, J., Meininger, V., Glass, J.D., van den Berg, L.H., van Es, M.A., Sapp, P.C., Van Vught, P.W.J., McKenna-Yasek, D.M., Blauw, H.M. et al. (2009) Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis. Proc. Natl. Acad. Sci. USA, 106, 9004-9009.
43. Marioni, J.C., Thorne, N.P., Valsesia, A., Fitzgerald, T., Redon, R., Fiegler, H., Andrews, T.D., Stranger, B.E., Lynch, A.G., Dermitzakis, E.T. et al. (2007) Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol., 8, R228.
44. Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F.A., Hakonarson, H. and Bucan, M. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res., 17, 1665-1674.
45. Itsara, A., Cooper, G., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R., Myers, R., Ridker, P. and Chasman, D. (2009) Population analysis of large copy number variants and hotspots of human genetic disease. Am. J. Hum. Genet., 84, 148-161.
46. Qin, J., Jones, R.C. and Ramakrishnan, R. (2008) Studying copy number variations using a nanofluidic platform. Nucleic Acids Res., 36, e116-e116.
47. Hellemans, J., Mortier, G., De Paepe, A., Speleman, F. and Vandesompele, J. (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol., 8, R19.
48. Gonzalez, E. (2005) The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science, 307, 1434-1440.
49. Scrucca, L. (2009) qcc R package. R NEWS, 4/1, 11-17.
50. Mccarroll, S.A. and Altshuler, D.M. (2007) Copy-number variation and association studies of human disease. Nat. Genet., 39, S37-S42.
51. Barrett, J.C., Fry, B., Maller, J. and Daly, M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.
52. Faul, F., Erdfelder, E., Lang, A.G. and Buchner, A. (2007) G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behav. Res. Methods, 39, 175-191.