Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder

American Journal of Human Genetics

Volumn 93, Issue 4, 2013, Pages 607-619

  Poultney, Christopher S ^a   Goldberg, Arthur P ^a   Drapeau, Elodie ^a   Kou, Yan ^a   Harony Nicolas, Hala ^a   Kajiwara, Yuji ^a   De Rubeis, Silvia ^a   Durand, Simon ^a   Stevens, Christine ^b   Rehnström, Karola ^c,d   Palotie, Aarno ^b,c   Daly, Mark J ^b,e   Ma'Ayan, Avi ^a   Fromer, Menachem ^a   Buxbaum, Joseph D ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c UNIVERSITY OF HELSINKI   (Finland)

^d WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^e MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTISM; AUTOPHAGY; CONTROLLED STUDY; COPY NUMBER VARIATION; CYTOSKELETON; DNA BASE COMPOSITION; EXOME; EXON; GENE CONTROL; GENE DELETION; GENE DISRUPTION; GENE FREQUENCY; GENE SEQUENCE; GENETIC IDENTIFICATION; GENOME ANALYSIS; GENOTYPE; HIDDEN MARKOV MODEL; HUMAN; INDEL MUTATION; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REAL TIME POLYMERASE CHAIN REACTION;

EID: 84885222459     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2013.09.001     Document Type: Article

References (47)

1. A.J. Iafrate, L. Feuk, M.N. Rivera, M.L. Listewnik, P.K. Donahoe, Y. Qi, S.W. Scherer, and C. Lee Detection of large-scale variation in the human genome Nat. Genet. 36 2004 949 951
2. S.J. Sanders, A.G. Ercan-Sencicek, V. Hus, R. Luo, M.T. Murtha, D. Moreno-De-Luca, S.H. Chu, M.P. Moreau, A.R. Gupta, and S.A. Thomson Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism Neuron 70 2011 863 885
3. J. Sebat, B. Lakshmi, J. Troge, J. Alexander, J. Young, P. Lundin, S. Månér, H. Massa, M. Walker, and M. Chi Large-scale copy number polymorphism in the human genome Science 305 2004 525 528
4. G.M. Cooper, B.P. Coe, S. Girirajan, J.A. Rosenfeld, T.H. Vu, C. Baker, C. Williams, H. Stalker, R. Hamid, and V. Hannig A copy number variation morbidity map of developmental delay Nat. Genet. 43 2011 838 846
5. M. Jakobsson, S.W. Scholz, P. Scheet, J.R. Gibbs, J.M. VanLiere, H.-C. Fung, Z.A. Szpiech, J.H. Degnan, K. Wang, and R. Guerreiro Genotype, haplotype and copy-number variation in worldwide human populations Nature 451 2008 998 1003
6. E.H. Cook Jr., and S.W. Scherer Copy-number variations associated with neuropsychiatric conditions Nature 455 2008 919 923
7. D. Pinto, A.T. Pagnamenta, L. Klei, R. Anney, D. Merico, R. Regan, J. Conroy, T.R. Magalhaes, C. Correia, and B.S. Abrahams Functional impact of global rare copy number variation in autism spectrum disorders Nature 466 2010 368 372
8. The 1000 Genomes Project Consortium G.R. Abecasis, D. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, and G.A. McVean A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
9. C.M. Durand, C. Betancur, T.M. Boeckers, J. Bockmann, P. Chaste, F. Fauchereau, G. Nygren, M. Rastam, I.C. Gillberg, and H. Anckarsäter Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are associated with autism spectrum disorders Nat. Genet. 39 2007 25 27
10. M. Elsabbagh, G. Divan, Y.-J. Koh, Y.S. Kim, S. Kauchali, C. Marcín, C. Montiel-Nava, V. Patel, C.S. Paula, and C. Wang Global prevalence of autism and other pervasive developmental disorders Autism Res. 5 2012 160 179
11. J. Liu, D.R. Nyholt, P. Magnussen, E. Parano, P. Pavone, D. Geschwind, C. Lord, P. Iversen, J. Hoh, J. Ott, T.C. Gilliam Autism Genetic Resource Exchange Consortium A genomewide screen for autism susceptibility loci Am. J. Hum. Genet. 69 2001 327 340
12. I. Iossifov, M. Ronemus, D. Levy, Z. Wang, I. Hakker, J. Rosenbaum, B. Yamrom, Y.H. Lee, G. Narzisi, and A. Leotta De novo gene disruptions in children on the autistic spectrum Neuron 74 2012 285 299
13. B.M. Neale, Y. Kou, L. Liu, A. Ma'ayan, K.E. Samocha, A. Sabo, C.F. Lin, C. Stevens, L.S. Wang, and V. Makarov Patterns and rates of exonic de novo mutations in autism spectrum disorders Nature 485 2012 242 245
14. S.J. Sanders, M.T. Murtha, A.R. Gupta, J.D. Murdoch, M.J. Raubeson, A.J. Willsey, A.G. Ercan-Sencicek, N.M. DiLullo, N.N. Parikshak, and J.L. Stein De novo mutations revealed by whole-exome sequencing are strongly associated with autism Nature 485 2012 237 241
15. B.J. O'Roak, L. Vives, S. Girirajan, E. Karakoc, N. Krumm, B.P. Coe, R. Levy, A. Ko, C. Lee, and J.D. Smith Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations Nature 485 2012 246 250
16. C. Betancur Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting Brain Res. 1380 2011 42 77
17. J. Sebat, B. Lakshmi, D. Malhotra, J. Troge, C. Lese-Martin, T. Walsh, B. Yamrom, S. Yoon, A. Krasnitz, and J. Kendall Strong association of de novo copy number mutations with autism Science 316 2007 445 449
18. J.T. Glessner, K. Wang, G. Cai, O. Korvatska, C.E. Kim, S. Wood, H. Zhang, A. Estes, C.W. Brune, and J.P. Bradfield Autism genome-wide copy number variation reveals ubiquitin and neuronal genes Nature 459 2009 569 573
19. M. Fromer, J.L. Moran, K. Chambert, E. Banks, S.E. Bergen, D.M. Ruderfer, R.E. Handsaker, S.A. McCarroll, M.C. O'Donovan, and M.J. Owen Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth Am. J. Hum. Genet. 91 2012 597 607
20. E.T. Lim, S. Raychaudhuri, S.J. Sanders, C. Stevens, A. Sabo, D.G. MacArthur, B.M. Neale, A. Kirby, D.M. Ruderfer, M. Fromer NHLBI Exome Sequencing Project Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders Neuron 77 2013 235 242
21. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
22. D. Karolchik, A.S. Hinrichs, T.S. Furey, K.M. Roskin, C.W. Sugnet, D. Haussler, and W.J. Kent The UCSC Table Browser data retrieval tool Nucleic Acids Res. 32 Database issue 2004 D493 D496
23. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A. Ferreira, D. Bender, J. Maller, P. Sklar, P.I. de Bakker, M.J. Daly, and P.C. Sham PLINK: a tool set for whole-genome association and population-based linkage analyses Am. J. Hum. Genet. 81 2007 559 575
24. E.J. Rossin, K. Lage, S. Raychaudhuri, R.J. Xavier, D. Tatar, Y. Benita, C. Cotsapas, M.J. Daly International Inflammatory Bowel Disease Genetics Constortium Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology PLoS Genet. 7 2011 e1001273
25. K. Lage, E.O. Karlberg, Z.M. Størling, P.I. Olason, A.G. Pedersen, O. Rigina, A.M. Hinsby, Z. Tümer, F. Pociot, and N. Tommerup A human phenome-interactome network of protein complexes implicated in genetic disorders Nat. Biotechnol. 25 2007 309 316
26. T.S. Keshava Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, and A. Venugopal Human Protein Reference Database - 2009 update Nucleic Acids Res. 37 Database issue 2009 D767 D772
27. A. Ceol, A. Chatr Aryamontri, L. Licata, D. Peluso, L. Briganti, L. Perfetto, L. Castagnoli, and G. Cesareni MINT, the molecular interaction database: 2009 update Nucleic Acids Res. 38 Database issue 2010 D532 D539
28. C. Stark, B.J. Breitkreutz, A. Chatr-Aryamontri, L. Boucher, R. Oughtred, M.S. Livstone, J. Nixon, K. Van Auken, X. Wang, and X. Shi The BioGRID Interaction Database: 2011 update Nucleic Acids Res. 39 Database issue 2011 D698 D704
29. B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A.T. Ghanbarian, S. Kerrien, and J. Khadake The IntAct molecular interaction database in 2010 Nucleic Acids Res. 38 Database issue 2010 D525 D531
30. K.F. Aoki, and M. Kanehisa Using the KEGG database resource Current protocols in bioinformatics / editoral board, Andreas D Baxevanis [et al] Chapter 1 2005 Unit 1 12
31. B.J. O'Roak, L. Vives, W. Fu, J.D. Egertson, I.B. Stanaway, I.G. Phelps, G. Carvill, A. Kumar, C. Lee, and K. Ankenman Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders Science 338 2012 1619 1622
32. E.Y. Chen, C.M. Tan, Y. Kou, Q. Duan, Z. Wang, G.V. Meirelles, N.R. Clark, and A. Ma'ayan Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool BMC Bioinformatics 14 2013 128
33. S.I. Berger, J.M. Posner, and A. Ma'ayan Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases BMC Bioinformatics 8 2007 372
34. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig The Gene Ontology Consortium Gene ontology: tool for the unification of biology Nat. Genet. 25 2000 25 29
35. M.A. DePristo, E. Banks, R. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A. Rivas, and M. Hanna A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat. Genet. 43 2011 491 498
36. J.M. Korn, F.G. Kuruvilla, S.A. McCarroll, A. Wysoker, J. Nemesh, S. Cawley, E. Hubbell, J. Veitch, P.J. Collins, and K. Darvishi Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs Nat. Genet. 40 2008 1253 1260
37. J.E. Melom, and J.T. Littleton Synapse development in health and disease Curr. Opin. Genet. Dev. 21 2011 256 261
38. C. Betancur, and J.D. Buxbaum SHANK3 haploinsufficiency: a "common" but underdiagnosed highly penetrant monogenic cause of autism spectrum disorders Molecular Autism 4 2013 17
39. I. Voineagu, X. Wang, P. Johnston, J.K. Lowe, Y. Tian, S. Horvath, J. Mill, R.M. Cantor, B.J. Blencowe, and D.H. Geschwind Transcriptomic analysis of autistic brain reveals convergent molecular pathology Nature 474 2011 380 384
40. G.R. Handrigan, D. Chitayat, A.C. Lionel, M. Pinsk, A.K. Vaags, C.R. Marshall, S. Dyack, L.F. Escobar, B.A. Fernandez, and J.C. Stegman Deletions in 16q24.2 are associated with autism spectrum disorder, intellectual disability and congenital renal malformation J. Med. Genet. 50 2013 163 173
41. A.J. Griswold, D. Ma, H.N. Cukier, L.D. Nations, M.A. Schmidt, R.H. Chung, J.M. Jaworski, D. Salyakina, I. Konidari, and P.L. Whitehead Evaluation of copy number variations reveals novel candidate genes in autism spectrum disorder-associated pathways Hum. Mol. Genet. 21 2012 3513 3523
42. Y. Komoike, K. Shimojima, J.S. Liang, H. Fujii, Y. Maegaki, M. Osawa, S. Fujii, T. Higashinakagawa, and T. Yamamoto A functional analysis of GABARAP on 17p13.1 by knockdown zebrafish J. Hum. Genet. 55 2010 155 162
43. A.C. Krepischi-Santos, D. Rajan, I.K. Temple, V. Shrubb, J.A. Crolla, S. Huang, S. Beal, P.A. Otto, N.P. Carter, A.M. Vianna-Morgante, and C. Rosenberg Constitutional haploinsufficiency of tumor suppressor genes in mentally retarded patients with microdeletions in 17p13.1 Cytogenet. Genome Res. 125 2009 1 7
44. J.J. Fernández, R. Martínez, E. Andújar, M. Pérez-Alegre, A. Costa, V. Bonilla-Henao, F. Sobrino, C.O. Pintado, and E. Pintado Gene expression profiles in the cerebellum of transgenic mice over expressing the human FMR1 gene with CGG repeats in the normal range Genet. Mol. Res. 11 2012 467 483
45. A.M. Choi, S.W. Ryter, and B. Levine Autophagy in human health and disease N. Engl. J. Med. 368 2013 1845 1846
46. W. Shen, and B. Ganetzky Nibbling away at synaptic development Autophagy 6 2010 168 169
47. J.N. Le Grand, K. Bon, A. Fraichard, J. Zhang, M. Jouvenot, P.Y. Risold, M. Boyer-Guittaut, and R. Delage-Mourroux Specific distribution of the autophagic protein GABARAPL1/GEC1 in the developing and adult mouse brain and identification of neuronal populations expressing GABARAPL1/GEC1 PLoS ONE 8 2013 e63133