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Volumn 7, Issue 1, 2015, Pages

ClinLabGeneticist: A tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CASE REPORT; CHILD; CLINICAL DECISION MAKING; CLINICAL GENETICS; CLINICAL LABORATORY; COMPUTER PROGRAM; CONGENITAL ERYTHROPOIETIC PORPHYRIA; DATA BASE; DIAGNOSIS; EXOME; GENE SEQUENCE; GENETIC SCREENING; GENETIC VARIABILITY; HUMAN; INFANT; INFORMATION PROCESSING; MALE; PRIORITY JOURNAL; SCHOOL CHILD; WORKFLOW; BIOLOGY; CLINICAL LABORATORY SERVICE; DEVELOPMENTAL DISORDER; DNA SEQUENCE; GENETIC VARIATION; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; SOFTWARE;

EID: 84940843853     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0207-6     Document Type: Article
Times cited : (6)

References (44)
  • 1
    • 84877999280 scopus 로고    scopus 로고
    • Molecular genetic testing and the future of clinical genomics
    • Katsanis SH, Katsanis N. Molecular genetic testing and the future of clinical genomics. Nat Rev Genet. 2013;14:415-26.
    • (2013) Nat Rev Genet. , vol.14 , pp. 415-426
    • Katsanis, S.H.1    Katsanis, N.2
  • 2
    • 84863106341 scopus 로고    scopus 로고
    • The wide variation of definitions of genetic testing in international recommendations, guidelines and reports
    • Sequeiros J, Paneque M, Guimaraes B, Rantanen E, Javaher P, Nippert I, et al. The wide variation of definitions of genetic testing in international recommendations, guidelines and reports. J Community Genet. 2012;3:113-24.
    • (2012) J Community Genet. , vol.3 , pp. 113-124
    • Sequeiros, J.1    Paneque, M.2    Guimaraes, B.3    Rantanen, E.4    Javaher, P.5    Nippert, I.6
  • 3
    • 84940849824 scopus 로고    scopus 로고
    • Ingenuity Variant Analysis. Available at: http://www.ingenuity.com/products/variant-analysis .
  • 4
    • 84940875493 scopus 로고    scopus 로고
    • Geneticist Assistant. Available at: http://www.softgenetics.com/GeneticistAssistant.html .
  • 5
    • 84940833475 scopus 로고    scopus 로고
    • VarSeq. Available at: http://www.goldenhelix.com/VarSeq/index.html .
  • 6
    • 84931271931 scopus 로고    scopus 로고
    • VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
    • Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, et al. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics. 2014;31:1469-71.
    • (2014) Bioinformatics. , vol.31 , pp. 1469-1471
    • Mu, J.C.1    Mohiyuddin, M.2    Li, J.3    Bani Asadi, N.4    Gerstein, M.B.5    Abyzov, A.6
  • 7
    • 77956534324 scopus 로고    scopus 로고
    • ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
    • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 8
    • 84940862928 scopus 로고    scopus 로고
    • The Exchange. Available at: https://www.nextcode.com/products-and-services/the-exchange .
  • 11
    • 84940865258 scopus 로고    scopus 로고
    • OMIM. Available at: http://www.omim.org .
  • 12
    • 84891837451 scopus 로고    scopus 로고
    • The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine
    • Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet. 2014;133:1-9.
    • (2014) Hum Genet. , vol.133 , pp. 1-9
    • Stenson, P.D.1    Mort, M.2    Ball, E.V.3    Shaw, K.4    Phillips, A.5    Cooper, D.N.6
  • 14
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-81.
    • (2009) Nat Protoc. , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 16
    • 84946027595 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2015;43:D6-D17.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D6-D17
  • 17
    • 84926430386 scopus 로고    scopus 로고
    • Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies
    • Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015;24:2125-37.
    • (2015) Hum Mol Genet. , vol.24 , pp. 2125-2137
    • Dong, C.1    Wei, P.2    Jian, X.3    Gibbs, R.4    Boerwinkle, E.5    Wang, K.6
  • 18
    • 79955002343 scopus 로고    scopus 로고
    • The GeneInsight Suite: a platform to support laboratory and provider use of DNA-based genetic testing
    • Aronson SJ, Clark EH, Babb LJ, Baxter S, Farwell LM, Funke BH, et al. The GeneInsight Suite: a platform to support laboratory and provider use of DNA-based genetic testing. Hum Mutat. 2011;32:532-6.
    • (2011) Hum Mutat. , vol.32 , pp. 532-536
    • Aronson, S.J.1    Clark, E.H.2    Babb, L.J.3    Baxter, S.4    Farwell, L.M.5    Funke, B.H.6
  • 21
    • 84880535720 scopus 로고    scopus 로고
    • ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing
    • Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013;15:565-74.
    • (2013) Genet Med. , vol.15 , pp. 565-574
    • Green, R.C.1    Berg, J.S.2    Grody, W.W.3    Kalia, S.S.4    Korf, B.R.5    Martin, C.L.6
  • 22
    • 84940853353 scopus 로고    scopus 로고
    • Cartagenia. Available at: http://www.cartagenia.com .
  • 23
    • 84940885430 scopus 로고    scopus 로고
    • Clinical Sequence Analyzer. Available at: https://www.nextcode.com .
  • 24
    • 84856495873 scopus 로고    scopus 로고
    • Reasons for participating and genetic information needs among racially and ethnically diverse biobank participants: a focus group study
    • Streicher SA, Sanderson SC, Jabs EW, Diefenbach M, Smirnoff M, Peter I, et al. Reasons for participating and genetic information needs among racially and ethnically diverse biobank participants: a focus group study. J Community Genet. 2011;2:153-63.
    • (2011) J Community Genet. , vol.2 , pp. 153-163
    • Streicher, S.A.1    Sanderson, S.C.2    Jabs, E.W.3    Diefenbach, M.4    Smirnoff, M.5    Peter, I.6
  • 26
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
    • Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6:80-92.
    • (2012) Fly. , vol.6 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    Wang, L.3    Coon, M.4    Nguyen, T.5    Wang, L.6
  • 27
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: application to cancer genomics
    • Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39:e118.
    • (2011) Nucleic Acids Res. , vol.39 , pp. e118
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 28
    • 84940839426 scopus 로고    scopus 로고
    • ClinLabGeneticist Installation Guideline. Available at: http://rongchenlab.org/wp-content/uploads/2014/11/Guidline-of-ClinLabGeneticist1.pptx .
  • 29
    • 84940879389 scopus 로고    scopus 로고
    • OMIM Congenital Erythropoietic Porphyria. Available at: http://www.omim.org/entry/263700 .
  • 30
    • 77953027360 scopus 로고    scopus 로고
    • The PtdIns(3,4)P(2) phosphatase INPP4A is a suppressor of excitotoxic neuronal death
    • Sasaki J, Kofuji S, Itoh R, Momiyama T, Takayama K, Murakami H, et al. The PtdIns(3,4)P(2) phosphatase INPP4A is a suppressor of excitotoxic neuronal death. Nature. 2010;465:497-501.
    • (2010) Nature. , vol.465 , pp. 497-501
    • Sasaki, J.1    Kofuji, S.2    Itoh, R.3    Momiyama, T.4    Takayama, K.5    Murakami, H.6
  • 31
    • 77956176969 scopus 로고    scopus 로고
    • PRMT3 is essential for dendritic spine maturation in rat hippocampal neurons
    • Miyata S, Mori Y, Tohyama M. PRMT3 is essential for dendritic spine maturation in rat hippocampal neurons. Brain Res. 2010;1352:11-20.
    • (2010) Brain Res. , vol.1352 , pp. 11-20
    • Miyata, S.1    Mori, Y.2    Tohyama, M.3
  • 33
    • 84899558396 scopus 로고    scopus 로고
    • When a "disease-causing mutation" is not a pathogenic variant
    • Wang J, Shen Y. When a "disease-causing mutation" is not a pathogenic variant. Clin Chem. 2014;60:711-3.
    • (2014) Clin Chem. , vol.60 , pp. 711-713
    • Wang, J.1    Shen, Y.2
  • 34
    • 84881618216 scopus 로고    scopus 로고
    • XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing
    • Piton A, Redin C, Mandel JL. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. Am J Hum Genet. 2013;93:368-83.
    • (2013) Am J Hum Genet. , vol.93 , pp. 368-383
    • Piton, A.1    Redin, C.2    Mandel, J.L.3
  • 36
    • 84872143942 scopus 로고    scopus 로고
    • Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants
    • Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013;493:216-20.
    • (2013) Nature. , vol.493 , pp. 216-220
    • Fu, W.1    O'Connor, T.D.2    Jun, G.3    Kang, H.M.4    Abecasis, G.5    Leal, S.M.6
  • 37
    • 84887674768 scopus 로고    scopus 로고
    • Implementing a successful data-management framework: the UK10K managed access model
    • Muddyman D, Smee C, Griffin H, Kaye J. Implementing a successful data-management framework: the UK10K managed access model. Genome Med. 2013;5:100.
    • (2013) Genome Med. , vol.5 , pp. 100
    • Muddyman, D.1    Smee, C.2    Griffin, H.3    Kaye, J.4
  • 38
    • 84940922955 scopus 로고    scopus 로고
    • SG-ADVISER CNV: copy-number variant annotation and interpretation
    • Erikson GA, Deshpande N, Kesavan BG, Torkamani A. SG-ADVISER CNV: copy-number variant annotation and interpretation. Genet Med. 2014. doi: 10.1038/gim.2014.180 .
    • (2014) Genet Med
  • 39
    • 84940832926 scopus 로고    scopus 로고
    • ExAC. Available at: http://exac.broadinstitute.org .
  • 40
    • 84881613239 scopus 로고    scopus 로고
    • dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations
    • Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013;34:E2393-402.
    • (2013) Hum Mutat , vol.34 , pp. E2393-E2402
    • Liu, X.1    Jian, X.2    Boerwinkle, E.3
  • 43
    • 79960700796 scopus 로고    scopus 로고
    • Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array
    • Hoffmann TJ, Kvale MN, Hesselson SE, Zhan Y, Aquino C, Cao Y, et al. Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array. Genomics. 2011;98:79-89.
    • (2011) Genomics. , vol.98 , pp. 79-89
    • Hoffmann, T.J.1    Kvale, M.N.2    Hesselson, S.E.3    Zhan, Y.4    Aquino, C.5    Cao, Y.6
  • 44
    • 81955167912 scopus 로고    scopus 로고
    • Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm
    • Hoffmann TJ, Zhan Y, Kvale MN, Hesselson SE, Gollub J, Iribarren C, et al. Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm. Genomics. 2011;98:422-30.
    • (2011) Genomics. , vol.98 , pp. 422-430
    • Hoffmann, T.J.1    Zhan, Y.2    Kvale, M.N.3    Hesselson, S.E.4    Gollub, J.5    Iribarren, C.6


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