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Volumn 13, Issue 6, 2013, Pages 529-540

Clinical analysis of genome next-generation sequencing data using the Omicia platform

Author keywords

analysis and selection tool; genome analysis; next generation sequencing; variant annotation; variant workflows; whole genome sequencing

Indexed keywords

ARTICLE; CLINICAL LABORATORY; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC DISORDER; HUMAN; RECEIVER OPERATING CHARACTERISTIC;

EID: 84881104150     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.2013.811907     Document Type: Article
Times cited : (27)

References (30)
  • 2
    • 73149123343 scopus 로고    scopus 로고
    • Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
    • Choi M, Scholl UI, Ji W et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl Acad. Sci. USA 106(45), 19096-19101 (2009
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , Issue.45 , pp. 19096-19101
    • Choi, M.1    Scholl, U.I.2    Ji, W.3
  • 3
    • 77950475726 scopus 로고    scopus 로고
    • Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy
    • Lupski JR, Reid JG, Gonzaga-Jauregui C et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362(13), 1181-1191 (2010
    • (2010) N. Engl. J. Med , vol.362 , Issue.13 , pp. 1181-1191
    • Lupski, J.R.1    Reid, J.G.2    Gonzaga-Jauregui, C.3
  • 4
    • 73349110071 scopus 로고    scopus 로고
    • Exome sequencing identifies the cause of a mendelian disorder
    • Ng SB, Buckingham KJ, Lee C et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42(1), 30-35 (2010
    • (2010) Nat. Genet , vol.42 , Issue.1 , pp. 30-35
    • Ng, S.B.1    Buckingham, K.J.2    Lee, C.3
  • 5
    • 77954158128 scopus 로고    scopus 로고
    • Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene
    • Sobreira NL, Cirulli ET, Avramopoulos D et al. Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet. 6(6), e1000991 (2010
    • (2010) PLoS Genet , vol.6 , Issue.6
    • Sobreira, N.L.1    Cirulli, E.T.2    Avramopoulos, D.3
  • 6
    • 79251645624 scopus 로고    scopus 로고
    • Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease
    • Worthey EA, Mayer AN, Syverson GD et al. Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 13(3), 255-262 (2011
    • (2011) Genet. Med , vol.13 , Issue.3 , pp. 255-262
    • Worthey, E.A.1    Mayer, A.N.2    Syverson, G.D.3
  • 7
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754-1760 (2009
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 8
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5), 589-595 (2010
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 9
    • 68549104404 scopus 로고    scopus 로고
    • 1000 Genome project data processing subgroup the sequence alignment/map format and samtools
    • Li H, Handsaker B, Wysoker A et al.; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16), 2078-2079 (2009
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 10
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo MA, Banks E, Poplin R et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43(5), 491-498 (2011
    • (2011) Nat. Genet , vol.43 , Issue.5 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3
  • 11
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20(9), 1297-1303 (2010
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3
  • 12
    • 84874687425 scopus 로고    scopus 로고
    • Developing genome and exome sequencing for candidate gene identification in inherited disorders: An integrated technical and bioinformatics approach
    • Coonrod EM, Durtschi JD, Margraf RL, Voelkerding KV. Developing genome and exome sequencing for candidate gene identification in inherited disorders: An integrated technical and bioinformatics approach. Arch. Pathol. Lab. Med. 137(3), 415-433 (2013
    • (2013) Arch. Pathol. Lab. Med , vol.137 , Issue.3 , pp. 415-433
    • Coonrod, E.M.1    Durtschi, J.D.2    Margraf, R.L.3    Voelkerding, K.V.4
  • 13
    • 84896448861 scopus 로고    scopus 로고
    • A survey of tools for variant analysis of next-generation genome sequencing data
    • doi:10.1093/bib/bbs086 Epub ahead of print
    • Pabinger S, Dander A, Fischer M et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. doi:10.1093/bib/bbs086 (2013) (Epub ahead of print
    • (2013) Brief Bioinform
    • Pabinger, S.1    Dander, A.2    Fischer, M.3
  • 14
    • 80051547469 scopus 로고    scopus 로고
    • A probabilistic disease-gene finder for personal genomes
    • Yandell M, Huff C, Hu H et al. A probabilistic disease-gene finder for personal genomes. Genome Res. 21(9), 1529-1542 (2011
    • (2011) Genome Res , vol.21 , Issue.9 , pp. 1529-1542
    • Yandell, M.1    Huff, C.2    Hu, H.3
  • 15
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred II Error probabilities
    • Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8(3), 186-194 (1998
    • (1998) Genome Res , vol.8 , Issue.3 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 16
    • 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, 38(16), e164 (2010
    • (2010) Nucleic Acids Res , vol.38 , Issue.16
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 18
    • 84859436530 scopus 로고    scopus 로고
    • CBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • Database issue
    • Pruitt KD, Tatusova T, Brown GR, Maglott DR. NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res. 40(Database issue), D130-D135 (2012
    • (2012) Nucleic Acids Res , vol.40
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 19
    • 0033987736 scopus 로고    scopus 로고
    • Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion
    • den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum. Mutat. 15(1), 7-12 (2000
    • (2000) Hum. Mutat , vol.15 , Issue.1 , pp. 7-12
    • Den Dunnen, J.T.1    Antonarakis, S.E.2
  • 21
    • 34248336122 scopus 로고    scopus 로고
    • PhenCode: Connecting ENCODE data with mutations and phenotype
    • Giardine B, Riemer C, Hefferon T et al. PhenCode: Connecting ENCODE data with mutations and phenotype. Hum. Mutat. 28(6), 554-562 (2007
    • (2007) Hum. Mutat , vol.28 , Issue.6 , pp. 554-562
    • Giardine, B.1    Riemer, C.2    Hefferon, T.3
  • 22
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20(1), 110-121 (2010
    • (2010) Genome Res , vol.20 , Issue.1 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 23
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Machine Learning 45(1), 5-23 (2001
    • (2001) Machine Learning , vol.45 , Issue.1 , pp. 5-23
    • Breiman, L.1
  • 24
    • 79960405019 scopus 로고    scopus 로고
    • The variant call format and VCFtools
    • Danecek P, Auton A, Abecasis G et al. The variant call format and VCFtools. Bioinformatics 27(15), 2156-2158 (2011
    • (2011) Bioinformatics , vol.27 , Issue.15 , pp. 2156-2158
    • Danecek, P.1    Auton, A.2    Abecasis, G.3
  • 25
    • 0031907132 scopus 로고    scopus 로고
    • A gene encoding a P-Type ATPase mutated in two forms of hereditary cholestasis
    • Bull LN, van Eijk MJ, Pawlikowska L et al. A gene encoding a P-Type ATPase mutated in two forms of hereditary cholestasis. Nat. Genet. 18(3), 219-224 (1998
    • (1998) Nat. Genet , vol.18 , Issue.3 , pp. 219-224
    • Bull, L.N.1    Van Eijk, M.J.2    Pawlikowska, L.3
  • 26
    • 0033652101 scopus 로고    scopus 로고
    • A missense mutation in FIC1 is associated with greenland familial cholestasis
    • Klomp LW, Bull LN, Knisely AS et al. A missense mutation in FIC1 is associated with greenland familial cholestasis. Hepatology 32(6), 1337-1341 (2000
    • (2000) Hepatology , vol.32 , Issue.6 , pp. 1337-1341
    • Klomp, L.W.1    Bull, L.N.2    Knisely, A.S.3
  • 27
    • 0034307655 scopus 로고    scopus 로고
    • Mutations in the gene encoding neutrophil elastase in congenital and cyclic neutropenia
    • Dale DC, Person RE, Bolyard AA et al. Mutations in the gene encoding neutrophil elastase in congenital and cyclic neutropenia. Blood 96(7), 2317-2322 (2000
    • (2000) Blood , vol.96 , Issue.7 , pp. 2317-2322
    • Dale, D.C.1    Person, R.E.2    Bolyard, A.A.3
  • 28
    • 80051550297 scopus 로고    scopus 로고
    • Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-Terminal acetyltransferase deficiency
    • Rope AF, Wang K, Evjenth R et al. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-Terminal acetyltransferase deficiency. Am. J. Hum. Genet. 89(1), 28-43 (2011
    • (2011) Am. J. Hum. Genet , vol.89 , Issue.1 , pp. 28-43
    • Rope, A.F.1    Wang, K.2    Evjenth, R.3
  • 29
    • 77955977450 scopus 로고    scopus 로고
    • A standard variation file format for human genome sequences
    • Reese MG, Moore B, Batchelor C et al. A standard variation file format for human genome sequences. Genome Biol. 11(8), R88 (2010
    • (2010) Genome Biol , vol.11 , Issue.8
    • Reese, M.G.1    Moore, B.2    Batchelor, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.