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Volumn 13, Issue 1, 2012, Pages

Exome-assistant: A rapid and easy detection of disease-related genes and genetic variations from exome sequencing

Author keywords

Insertions and deletions; Mendelian disease; Minor allele frequency; Next generation sequencing; Single nucleotide polymorphisms; Variation filtering

Indexed keywords

ARTICLE; DATA ANALYSIS SOFTWARE; EXOME; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; INDEL MUTATION; INFORMATION PROCESSING; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84870680379     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-692     Document Type: Article
Times cited : (10)

References (32)
  • 1
    • 50849102293 scopus 로고    scopus 로고
    • A catalog of neutral and deleterious polymorphism in yeast
    • 10.1371/journal.pgen.1000183, 2515631, 18769710
    • Doniger SW, Kim HS, Swain D, Corcuera D, Williams M, Yang SP, Fay JC. A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet 2008, 4(8):e1000183. 10.1371/journal.pgen.1000183, 2515631, 18769710.
    • (2008) PLoS Genet , vol.4 , Issue.8
    • Doniger, S.W.1    Kim, H.S.2    Swain, D.3    Corcuera, D.4    Williams, M.5    Yang, S.P.6    Fay, J.C.7
  • 6
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    • 10.1101/gr.107524.110, 2928508, 20644199
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5    Kernytsky, A.6    Garimella, K.7    Altshuler, D.8    Gabriel, S.9    Daly, M.10
  • 7
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • 10.1093/bioinformatics/btp352, 2723002, 19505943, Genome Project Data Processing S
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, Genome Project Data Processing S.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 8
    • 66449114324 scopus 로고    scopus 로고
    • SNP detection for massively parallel whole-genome resequencing
    • 10.1101/gr.088013.108, 2694485, 19420381
    • Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K. SNP detection for massively parallel whole-genome resequencing. Genome Res 2009, 19(6):1124-1132. 10.1101/gr.088013.108, 2694485, 19420381.
    • (2009) Genome Res , vol.19 , Issue.6 , pp. 1124-1132
    • Li, R.1    Li, Y.2    Fang, X.3    Yang, H.4    Wang, J.5    Kristiansen, K.6
  • 9
    • 69949122158 scopus 로고    scopus 로고
    • VarScan: variant detection in massively parallel sequencing of individual and pooled samples
    • 10.1093/bioinformatics/btp373, 2734323, 19542151
    • Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009, 25(17):2283-2285. 10.1093/bioinformatics/btp373, 2734323, 19542151.
    • (2009) Bioinformatics , vol.25 , Issue.17 , pp. 2283-2285
    • Koboldt, D.C.1    Chen, K.2    Wylie, T.3    Larson, D.E.4    McLellan, M.D.5    Mardis, E.R.6    Weinstock, G.M.7    Wilson, R.K.8    Ding, L.9
  • 10
    • 80455129691 scopus 로고    scopus 로고
    • SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data
    • 10.1093/nar/gkr599, 3201884, 21813454
    • Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H. SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res 2011, 39(19):e132. 10.1093/nar/gkr599, 3201884, 21813454.
    • (2011) Nucleic Acids Res , vol.39 , Issue.19
    • Wei, Z.1    Wang, W.2    Hu, P.3    Lyon, G.J.4    Hakonarson, H.5
  • 11
    • 80051547469 scopus 로고    scopus 로고
    • A probabilistic disease-gene finder for personal genomes
    • 10.1101/gr.123158.111, 3166837, 21700766
    • Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG. A probabilistic disease-gene finder for personal genomes. Genome Res 2011, 21(9):1529-1542. 10.1101/gr.123158.111, 3166837, 21700766.
    • (2011) Genome Res , vol.21 , Issue.9 , pp. 1529-1542
    • Yandell, M.1    Huff, C.2    Hu, H.3    Singleton, M.4    Moore, B.5    Xing, J.6    Jorde, L.B.7    Reese, M.G.8
  • 12
    • 79959671356 scopus 로고    scopus 로고
    • SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data
    • Deng X. SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. BMC Bioinforma 2011, 12:267.
    • (2011) BMC Bioinforma , vol.12 , pp. 267
    • Deng, X.1
  • 13
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • 10.1093/bioinformatics/btp394, 2781750, 19561018
    • Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25(21):2865-2871. 10.1093/bioinformatics/btp394, 2781750, 19561018.
    • (2009) Bioinformatics , vol.25 , Issue.21 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 15
    • 41649083448 scopus 로고    scopus 로고
    • WGAViewer: software for genomic annotation of whole genome association studies
    • 10.1101/gr.071571.107, 2279251, 18256235
    • Ge D, Zhang K, Need AC, Martin O, Fellay J, Urban TJ, Telenti A, Goldstein DB. WGAViewer: software for genomic annotation of whole genome association studies. Genome Res 2008, 18(4):640-643. 10.1101/gr.071571.107, 2279251, 18256235.
    • (2008) Genome Res , vol.18 , Issue.4 , pp. 640-643
    • Ge, D.1    Zhang, K.2    Need, A.C.3    Martin, O.4    Fellay, J.5    Urban, T.J.6    Telenti, A.7    Goldstein, D.B.8
  • 16
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • 10.1093/nar/gkq603, 2938201, 20601685
    • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010, 38(16):e164. 10.1093/nar/gkq603, 2938201, 20601685.
    • (2010) Nucleic Acids Res , vol.38 , Issue.16
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 17
    • 77951959817 scopus 로고    scopus 로고
    • CandiSNPer: a web tool for the identification of candidate SNPs for causal variants
    • 10.1093/bioinformatics/btq068, 20172942
    • Schmitt AO, Assmus J, Bortfeldt RH, Brockmann GA. CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. Bioinformatics 2010, 26(7):969-970. 10.1093/bioinformatics/btq068, 20172942.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 969-970
    • Schmitt, A.O.1    Assmus, J.2    Bortfeldt, R.H.3    Brockmann, G.A.4
  • 18
    • 78650580271 scopus 로고    scopus 로고
    • GAMES identifies and annotates mutations in next-generation sequencing projects
    • 10.1093/bioinformatics/btq603, 20971986
    • Sana ME, Iascone M, Marchetti D, Palatini J, Galasso M, Volinia S. GAMES identifies and annotates mutations in next-generation sequencing projects. Bioinformatics 2011, 27(1):9-13. 10.1093/bioinformatics/btq603, 20971986.
    • (2011) Bioinformatics , vol.27 , Issue.1 , pp. 9-13
    • Sana, M.E.1    Iascone, M.2    Marchetti, D.3    Palatini, J.4    Galasso, M.5    Volinia, S.6
  • 19
    • 61449107734 scopus 로고    scopus 로고
    • SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms
    • 10.1093/bioinformatics/btn653, 2647830, 19098027
    • Chelala C, Khan A, Lemoine NR. SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 2009, 25(5):655-661. 10.1093/bioinformatics/btn653, 2647830, 19098027.
    • (2009) Bioinformatics , vol.25 , Issue.5 , pp. 655-661
    • Chelala, C.1    Khan, A.2    Lemoine, N.R.3
  • 21
    • 84862929636 scopus 로고    scopus 로고
    • TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data
    • 10.1093/bioinformatics/btr612, 3259432, 22088845
    • Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, et al. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics 2012, 28(2):277-278. 10.1093/bioinformatics/btr612, 3259432, 22088845.
    • (2012) Bioinformatics , vol.28 , Issue.2 , pp. 277-278
    • Asmann, Y.W.1    Middha, S.2    Hossain, A.3    Baheti, S.4    Li, Y.5    Chai, H.S.6    Sun, Z.7    Duffy, P.H.8    Hadad, A.A.9    Nair, A.10
  • 22
    • 79961182320 scopus 로고    scopus 로고
    • In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
    • 10.1093/bioinformatics/btr372, 3150039, 21697123
    • Grant JR, Arantes AS, Liao X, Stothard P. In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 2011, 27(16):2300-2301. 10.1093/bioinformatics/btr372, 3150039, 21697123.
    • (2011) Bioinformatics , vol.27 , Issue.16 , pp. 2300-2301
    • Grant, J.R.1    Arantes, A.S.2    Liao, X.3    Stothard, P.4
  • 23
    • 38549158538 scopus 로고    scopus 로고
    • F-SNP: computationally predicted functional SNPs for disease association studies
    • 2238878, 17986460, Database issue
    • Lee PH, Shatkay H, Database issue F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res 2008, 36:D820-D824. 2238878, 17986460, Database issue.
    • (2008) Nucleic Acids Res , vol.36
    • Lee, P.H.1    Shatkay, H.2
  • 24
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: predict effect of non-synonymous polymorphisms on function
    • 10.1093/nar/gkm238, 1920242, 17526529
    • Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 2007, 35(11):3823-3835. 10.1093/nar/gkm238, 1920242, 17526529.
    • (2007) Nucleic Acids Res , vol.35 , Issue.11 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 25
    • 84872184094 scopus 로고    scopus 로고
    • Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools
    • In press
    • San Lucas FA, Wang G, Scheet P, Peng B. Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. Bioinformatics 2011, In press.
    • (2011) Bioinformatics
    • San Lucas, F.A.1    Wang, G.2    Scheet, P.3    Peng, B.4
  • 26
    • 84858278790 scopus 로고    scopus 로고
    • VAR-MD: a tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance
    • 10.1002/humu.22034, 22290570
    • Sincan M, Simeonov DR, Adams D, Markello TC, Pierson TM, Toro C, Gahl WA, Boerkoel CF. VAR-MD: a tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance. Hum Mutat 2012, 33(4):593-598. 10.1002/humu.22034, 22290570.
    • (2012) Hum Mutat , vol.33 , Issue.4 , pp. 593-598
    • Sincan, M.1    Simeonov, D.R.2    Adams, D.3    Markello, T.C.4    Pierson, T.M.5    Toro, C.6    Gahl, W.A.7    Boerkoel, C.F.8
  • 27
    • 67650064594 scopus 로고    scopus 로고
    • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    • 10.1101/gr.080531.108, 2704439, 19498102
    • Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009, 19(7):1316-1323. 10.1101/gr.080531.108, 2704439, 19498102.
    • (2009) Genome Res , vol.19 , Issue.7 , pp. 1316-1323
    • Pruitt, K.D.1    Harrow, J.2    Harte, R.A.3    Wallin, C.4    Diekhans, M.5    Maglott, D.R.6    Searle, S.7    Farrell, C.M.8    Loveland, J.E.9    Ruef, B.J.10
  • 29
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 30
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • 10.1093/nar/gkg509, 168916, 12824425
    • Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003, 31(13):3812-3814. 10.1093/nar/gkg509, 168916, 12824425.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 31
    • 84866084933 scopus 로고    scopus 로고
    • Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing
    • Wu J, Shen E, Shi D, Sun Z, Cai T. Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing. Genet Med 2012,
    • (2012) Genet Med
    • Wu, J.1    Shen, E.2    Shi, D.3    Sun, Z.4    Cai, T.5
  • 32
    • 81455128285 scopus 로고    scopus 로고
    • Familial amyotrophic lateral sclerosis, a historical perspective
    • 3235825, 22106714
    • Siddique T, Ajroud-Driss S. Familial amyotrophic lateral sclerosis, a historical perspective. Acta Myol 2011, 30(2):117-120. 3235825, 22106714.
    • (2011) Acta Myol , vol.30 , Issue.2 , pp. 117-120
    • Siddique, T.1    Ajroud-Driss, S.2


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