메뉴 건너뛰기




Volumn 8, Issue 1, 2015, Pages

Performance of case-control rare copy number variation annotation in classification of autism

Author keywords

Autism Spectrum Disorders (ASD); Copy number variation (CNV); machine learning classification; Random Forest (RF); rare genetic variants

Indexed keywords

ARTICLE; AUTISM; CASE CONTROL STUDY; CONDITIONAL INFERENCE FOREST; CONTROLLED STUDY; COPY NUMBER VARIATION; DISEASE CLASSIFICATION; FEMALE; HUMAN; INTERMETHOD COMPARISON; MACHINE LEARNING; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; RANDOM FOREST; BIOLOGY; CLASSIFICATION; GENE ONTOLOGY; GENETICS; MOLECULAR GENETICS; PROCEDURES;

EID: 84964502119     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-8-S1-S7     Document Type: Article
Times cited : (17)

References (60)
  • 1
    • 84896715530 scopus 로고    scopus 로고
    • Autism
    • 24074734
    • Lai MC, Lombardo MV, Baron-Cohen S: Autism. Lancet. 2014, 383 (9920): 896-910. 10.1016/S0140-6736(13)61539-1.
    • (2014) Lancet , vol.383 , Issue.9920 , pp. 896-910
    • Lai, M.C.1    Lombardo, M.V.2    Baron-Cohen, S.3
  • 3
    • 84873060273 scopus 로고    scopus 로고
    • Autism recurrence in half siblings: Strong support for genetic mechanisms of transmission in ASD
    • 1:STN:280:DC%2BC38vksFansQ%3D%3D 22371046
    • Constantino JN, Todorov A, Hilton C, Law P, Zhang Y, Molloy E, Fitzgerald R, Geschwind D: Autism recurrence in half siblings: strong support for genetic mechanisms of transmission in ASD. Molecular psychiatry. 2013, 18 (2): 137-138. 10.1038/mp.2012.9.
    • (2013) Molecular Psychiatry , vol.18 , Issue.2 , pp. 137-138
    • Constantino, J.N.1    Todorov, A.2    Hilton, C.3    Law, P.4    Zhang, Y.5    Molloy, E.6    Fitzgerald, R.7    Geschwind, D.8
  • 4
    • 79958032110 scopus 로고    scopus 로고
    • Rare de novo and transmitted copy-number variation in autistic spectrum disorders
    • 1:CAS:528:DC%2BC3MXnsVyrt7c%3D 21658582
    • Levy D, Ronemus M, Yamrom B, Lee YH, Leotta A, Kendall J, Marks S, Lakshmi B, Pai D, Ye K, et al: Rare de novo and transmitted copy-number variation in autistic spectrum disorders. Neuron. 2011, 70 (5): 886-897. 10.1016/j.neuron.2011.05.015.
    • (2011) Neuron , vol.70 , Issue.5 , pp. 886-897
    • Levy, D.1    Ronemus, M.2    Yamrom, B.3    Lee, Y.H.4    Leotta, A.5    Kendall, J.6    Marks, S.7    Lakshmi, B.8    Pai, D.9    Ye, K.10
  • 6
    • 79958074870 scopus 로고    scopus 로고
    • Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism
    • 3939065 1:CAS:528:DC%2BC3MXnsVyrt7Y%3D 21658581
    • Sanders SJ, Ercan-Sencicek AG, Hus V, Luo R, Murtha MT, Moreno-De-Luca D, Chu SH, Moreau MP, Gupta AR, Thomson SA, et al: Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron. 2011, 70 (5): 863-885. 10.1016/j.neuron.2011.05.002.
    • (2011) Neuron , vol.70 , Issue.5 , pp. 863-885
    • Sanders, S.J.1    Ercan-Sencicek, A.G.2    Hus, V.3    Luo, R.4    Murtha, M.T.5    Moreno-De-Luca, D.6    Chu, S.H.7    Moreau, M.P.8    Gupta, A.R.9    Thomson, S.A.10
  • 10
    • 84860712363 scopus 로고    scopus 로고
    • Patterns and rates of exonic de novo mutations in autism spectrum disorders
    • 3613847 1:CAS:528:DC%2BC38XmtVerurs%3D 22495311
    • Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, et al: Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012, 485 (7397): 242-245. 10.1038/nature11011.
    • (2012) Nature , vol.485 , Issue.7397 , pp. 242-245
    • Neale, B.M.1    Kou, Y.2    Liu, L.3    Ma'ayan, A.4    Samocha, K.E.5    Sabo, A.6    Lin, C.F.7    Stevens, C.8    Wang, L.S.9    Makarov, V.10
  • 12
    • 84860741138 scopus 로고    scopus 로고
    • Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
    • 3350576 22495309
    • O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, et al: Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 2012, 485 (7397): 246-250. 10.1038/nature10989.
    • (2012) Nature , vol.485 , Issue.7397 , pp. 246-250
    • O'Roak, B.J.1    Vives, L.2    Girirajan, S.3    Karakoc, E.4    Krumm, N.5    Coe, B.P.6    Levy, R.7    Ko, A.8    Lee, C.9    Smith, J.D.10
  • 14
    • 84881664021 scopus 로고    scopus 로고
    • Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing
    • 3738824 1:CAS:528:DC%2BC3sXhtV2rt7vE 23849776
    • Jiang YH, Yuen RK, Jin X, Wang M, Chen N, Wu X, Ju J, Mei J, Shi Y, He M: Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. American journal of human genetics. 2013, 93 (2): 249-63. 10.1016/j.ajhg.2013.06.012.
    • (2013) American Journal of Human Genetics , vol.93 , Issue.2 , pp. 249-263
    • Jiang, Y.H.1    Yuen, R.K.2    Jin, X.3    Wang, M.4    Chen, N.5    Wu, X.6    Ju, J.7    Mei, J.8    Shi, Y.9    He, M.10
  • 15
    • 84862493260 scopus 로고    scopus 로고
    • Genetic architecture in autism spectrum disorder
    • 1:CAS:528:DC%2BC38XltVaktbY%3D
    • Devlin B, Scherer SW: Genetic architecture in autism spectrum disorder. Current opinion in genetics & development. 2012, 22 (3): 229-237. 10.1016/j.gde.2012.03.002.
    • (2012) Current Opinion in Genetics & Development , vol.22 , Issue.3 , pp. 229-237
    • Devlin, B.1    Scherer, S.W.2
  • 16
    • 79952313620 scopus 로고    scopus 로고
    • Etiological heterogeneity in autism spectrum disorders: More than 100 genetic and genomic disorders and still counting
    • 1:CAS:528:DC%2BC3MXisFGnu7c%3D 21129364
    • Betancur C: Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain research. 2011, 1380: 42-77.
    • (2011) Brain Research , vol.1380 , pp. 42-77
    • Betancur, C.1
  • 17
    • 84871371945 scopus 로고    scopus 로고
    • The autism sequencing consortium: Large-scale, high-throughput sequencing in autism spectrum disorders
    • Buxbaum JD, Daly MJ, Devlin B, Lehner T, Roeder K, State MW, Autism Sequencing Consortium: The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders. Neuron. 2013, 76: 1052-1056.
    • (2013) Neuron , vol.76 , pp. 1052-1056
    • Buxbaum, J.D.1    Daly, M.J.2    Devlin, B.3    Lehner, T.4    Roeder, K.5    State, M.W.6
  • 18
    • 79960812993 scopus 로고    scopus 로고
    • American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants
    • Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST, Working Group of the American College of Medical Genetics Laboratory Quality Assurance C: American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genetics in Medicine: official journal of the American College of Medical Genetics. 2011, 13 (7): 680-685. 10.1097/GIM.0b013e3182217a3a.
    • (2011) Genetics in Medicine: Official Journal of the American College of Medical Genetics , vol.13 , Issue.7 , pp. 680-685
    • Kearney, H.M.1    Thorland, E.C.2    Brown, K.K.3    Quintero-Rivera, F.4    South, S.T.5
  • 20
    • 0035478854 scopus 로고    scopus 로고
    • Random Forest
    • Breiman L: Random Forest. Machine Learning Journal. 2001, 45: 5-32. 10.1023/A:1010933404324.
    • (2001) Machine Learning Journal , vol.45 , pp. 5-32
    • Breiman, L.1
  • 22
    • 33847096395 scopus 로고    scopus 로고
    • Bias in random forest variable importance measures: Illustrations, sources and a solution
    • 1796903 17254353
    • Strobl C, Boulesteix AL, Zeileis A, Hothorn T: Bias in random forest variable importance measures: illustrations, sources and a solution. BMC bioinformatics. 2007, 8: 25-10.1186/1471-2105-8-25.
    • (2007) BMC Bioinformatics , vol.8 , pp. 25
    • Strobl, C.1    Boulesteix, A.L.2    Zeileis, A.3    Hothorn, T.4
  • 24
    • 27144489164 scopus 로고    scopus 로고
    • A Tutorial on Support vector Machines for Pattern Recognition
    • Burges CJ: A Tutorial on Support vector Machines for Pattern Recognition. Data Mining and Knowledge Discovery. 1998, 2 (2): 121-167. 10.1023/A:1009715923555.
    • (1998) Data Mining and Knowledge Discovery , vol.2 , Issue.2 , pp. 121-167
    • Burges, C.J.1
  • 27
    • 0027997172 scopus 로고
    • Autism Diagnostic Interview-Revised: A revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders
    • 1:STN:280:DyaK2M7htlOlsg%3D%3D 7814313
    • Lord C, Rutter M, Le Couteur A: Autism Diagnostic Interview-Revised: a revised version of a diagnostic interview for caregivers of individuals with possible pervasive developmental disorders. Journal of autism and developmental disorders. 1994, 24 (5): 659-685. 10.1007/BF02172145.
    • (1994) Journal of Autism and Developmental Disorders , vol.24 , Issue.5 , pp. 659-685
    • Lord, C.1    Rutter, M.2    Le Couteur, A.3
  • 31
    • 84863684047 scopus 로고    scopus 로고
    • Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women
    • 3349734 1:CAS:528:DC%2BC38XnslOlt70%3D 22589738
    • Fox CS, Liu Y, White CC, Feitosa M, Smith AV, Heard-Costa N, Lohman K, Consortium G, Consortium M, Consortium G, et al: Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. PLoS genetics. 2012, 8 (5): e1002695-10.1371/journal.pgen.1002695.
    • (2012) PLoS Genetics , vol.8 , Issue.5
    • Fox, C.S.1    Liu, Y.2    White, C.C.3    Feitosa, M.4    Smith, A.V.5    Heard-Costa, N.6    Lohman, K.7    Consortium, G.8    Consortium, M.9    Consortium, G.10
  • 34
    • 78449263023 scopus 로고    scopus 로고
    • Characterising and predicting haploinsufficiency in the human genome
    • 2954820 20976243
    • Huang N, Lee I, Marcotte EM, Hurles ME: Characterising and predicting haploinsufficiency in the human genome. PLoS genetics. 2010, 6 (10): e1001154-10.1371/journal.pgen.1001154.
    • (2010) PLoS Genetics , vol.6 , Issue.10
    • Huang, N.1    Lee, I.2    Marcotte, E.M.3    Hurles, M.E.4
  • 38
    • 79960779323 scopus 로고    scopus 로고
    • FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism
    • 3232425 1:CAS:528:DC%2BC3MXptleksbo%3D 21784246
    • Darnell JC, Van Driesche SJ, Zhang C, Hung KY, Mele A, Fraser CE, Stone EF, Chen C, Fak JJ, Chi SW, et al: FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell. 2011, 146 (2): 247-261. 10.1016/j.cell.2011.06.013.
    • (2011) Cell , vol.146 , Issue.2 , pp. 247-261
    • Darnell, J.C.1    Van Driesche, S.J.2    Zhang, C.3    Hung, K.Y.4    Mele, A.5    Fraser, C.E.6    Stone, E.F.7    Chen, C.8    Fak, J.J.9    Chi, S.W.10
  • 41
    • 84891788593 scopus 로고    scopus 로고
    • The Mouse Genome Database: Integration of and access to knowledge about the laboratory mouse
    • Database issue, 3964950 1:CAS:528:DC%2BC2cXosF2n 24285300
    • Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE, Mouse Genome Database G: The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. Nucleic acids research. 2014, 42 (Database issue): D810-817.
    • (2014) Nucleic Acids Research , vol.42 , pp. D810-D817
    • Mouse Genome Database G1    Blake, J.A.2    Bult, C.J.3    Eppig, J.T.4    Kadin, J.A.5    Richardson, J.E.6
  • 44
    • 0345040873 scopus 로고    scopus 로고
    • Classification and Regression by randomForest
    • Liaw A, Wiener M: Classification and Regression by randomForest. R News. 2002, 2 (3): 18-22.
    • (2002) R News , vol.2 , Issue.3 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 45
    • 84905989703 scopus 로고    scopus 로고
    • Party: A Laboratory for Recursive Partytioning
    • Hothorn T, Hornik K, Zeileis A: party: A Laboratory for Recursive Partytioning. CRAN. 2013
    • (2013) CRAN
    • Hothorn, T.1    Hornik, K.2    Zeileis, A.3
  • 47
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: Criteria of max-dependency, max-relevance, and min-redundancy
    • 16119262
    • Peng H, Long F, Ding C: Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE transactions on pattern analysis and machine intelligence. 2005, 27 (8): 1226-1238.
    • (2005) IEEE Transactions on Pattern Analysis and Machine Intelligence , vol.27 , Issue.8 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 49
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • 102409 1:CAS:528:DC%2BD3cXhvVGqu74%3D 10592173
    • Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research. 2000, 28 (1): 27-30. 10.1093/nar/28.1.27.
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 50
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: Back to metabolism in KEGG
    • Database issue, 3965122 1:CAS:528:DC%2BC2cXoslej 24214961
    • Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M: Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic acids research. 2014, 42 (Database issue): D199-205.
    • (2014) Nucleic Acids Research , vol.42 , pp. D199-D205
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Kawashima, M.4    Furumichi, M.5    Tanabe, M.6
  • 51
    • 84871602426 scopus 로고    scopus 로고
    • Annotating cancer variants and anti-cancer therapeutics in reactome
    • 3712731 1:CAS:528:DC%2BC38XhvVahu7vK 24213504
    • Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, D'Eustachio P, Stein L: Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers. 2012, 4 (4): 1180-1211. 10.3390/cancers4041180.
    • (2012) Cancers , vol.4 , Issue.4 , pp. 1180-1211
    • Milacic, M.1    Haw, R.2    Rothfels, K.3    Wu, G.4    Croft, D.5    Hermjakob, H.6    D'Eustachio, P.7    Stein, L.8
  • 54
    • 67651229479 scopus 로고    scopus 로고
    • Forging links between human mental retardation-associated CNVs and mouse gene knockout models
    • 2694283 19557186
    • Webber C, Hehir-Kwa JY, Nguyen DQ, de Vries BB, Veltman JA, Ponting CP: Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PLoS genetics. 2009, 5 (6): e1000531-10.1371/journal.pgen.1000531.
    • (2009) PLoS Genetics , vol.5 , Issue.6
    • Webber, C.1    Hehir-Kwa, J.Y.2    Nguyen, D.Q.3    De Vries, B.B.4    Veltman, J.A.5    Ponting, C.P.6
  • 55
    • 79551613921 scopus 로고    scopus 로고
    • Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes
    • 3033180 1:CAS:528:DC%2BC3MXhsFyls7w%3D 21147756
    • Shaikh TH, Haldeman-Englert C, Geiger EA, Ponting CP, Webber C: Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes. Human molecular genetics. 2011, 20 (5): 880-93. 10.1093/hmg/ddq527.
    • (2011) Human Molecular Genetics , vol.20 , Issue.5 , pp. 880-893
    • Shaikh, T.H.1    Haldeman-Englert, C.2    Geiger, E.A.3    Ponting, C.P.4    Webber, C.5
  • 56
    • 84856225986 scopus 로고    scopus 로고
    • De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia
    • 3603134 1:CAS:528:DC%2BC38XhsVWhsLo%3D 22083728
    • Kirov G, Pocklington AJ, Holmans P, Ivanov D, Ikeda M, Ruderfer D, Moran J, Chambert K, Toncheva D, Georgieva L, et al: De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia. Molecular psychiatry. 2012, 17 (2): 142-53. 10.1038/mp.2011.154.
    • (2012) Molecular Psychiatry , vol.17 , Issue.2 , pp. 142-153
    • Kirov, G.1    Pocklington, A.J.2    Holmans, P.3    Ivanov, D.4    Ikeda, M.5    Ruderfer, D.6    Moran, J.7    Chambert, K.8    Toncheva, D.9    Georgieva, L.10
  • 58
    • 84884592445 scopus 로고    scopus 로고
    • Genic intolerance to functional variation and the interpretation of personal genomes
    • 3749936 1:CAS:528:DC%2BC3sXhsVCku7rJ 23990802
    • Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB: Genic intolerance to functional variation and the interpretation of personal genomes. PLoS genetics. 2013, 9 (8): e1003709-10.1371/journal.pgen.1003709.
    • (2013) PLoS Genetics , vol.9 , Issue.8
    • Petrovski, S.1    Wang, Q.2    Heinzen, E.L.3    Allen, A.S.4    Goldstein, D.B.5
  • 59
    • 33747035889 scopus 로고    scopus 로고
    • Predicting disease genes using protein-protein interactions
    • 2564594 1:CAS:528:DC%2BD28XpsFGgsro%3D 16611749
    • Oti M, Snel B, Huynen MA, Brunner HG: Predicting disease genes using protein-protein interactions. Journal of medical genetics. 2006, 43 (8): 691-698. 10.1136/jmg.2006.041376.
    • (2006) Journal of Medical Genetics , vol.43 , Issue.8 , pp. 691-698
    • Oti, M.1    Snel, B.2    Huynen, M.A.3    Brunner, H.G.4
  • 60
    • 84880367143 scopus 로고    scopus 로고
    • Identification of candidate intergenic risk loci in autism spectrum disorder
    • 3734099 1:CAS:528:DC%2BC3sXhsVKrt7rI 23879678
    • Walker S, Scherer SW: Identification of candidate intergenic risk loci in autism spectrum disorder. BMC genomics. 2013, 14: 499-10.1186/1471-2164-14-499.
    • (2013) BMC Genomics , vol.14 , pp. 499
    • Walker, S.1    Scherer, S.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.