메뉴 건너뛰기




Volumn 48, Issue 12, 2016, Pages 1581-1586

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

Author keywords

[No Author keywords available]

Indexed keywords

AREA UNDER THE CURVE; ARTICLE; CLASSIFIER; CLINICAL CLASSIFICATION; CONTROLLED STUDY; FALSE POSITIVE RESULT; GENE FREQUENCY; GENETIC CONSERVATION; GENETIC VARIABILITY; HUMAN; LEARNING ALGORITHM; MENDELIAN CLINICALLY APPLICABLE PATHOGENICITY SCORE; MISSENSE MUTATION; PATHOGENICITY; PRIORITY JOURNAL; WHOLE EXOME SEQUENCING; BIOLOGY; DISEASES; DNA MUTATIONAL ANALYSIS; EXOME; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; MUTATION; PREDICTIVE VALUE; PROCEDURES; SOFTWARE;

EID: 84992389439     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3703     Document Type: Article
Times cited : (611)

References (40)
  • 1
    • 84885785987 scopus 로고    scopus 로고
    • Clinical whole-exome sequencing for the diagnosis of mendelian disorders
    • Yang, Y. et al. Clinical whole-exome sequencing for the diagnosis of Mendelian disorders. N. Engl. J. Med. 369, 1502-1511 (2013
    • (2013) N. Engl. J. Med , vol.369 , pp. 1502-1511
    • Yang, Y.1
  • 2
    • 84918793267 scopus 로고    scopus 로고
    • The usefulness of whole-exome sequencing in routine clinical practice
    • Iglesias, A. et al. The usefulness of whole-exome sequencing in routine clinical practice. Genet. Med. 16, 922-931 (2014
    • (2014) Genet. Med , vol.16 , pp. 922-931
    • Iglesias, A.1
  • 3
    • 84918840439 scopus 로고    scopus 로고
    • Clinical exome sequencing for genetic identification of rare mendelian disorders
    • Lee, H. et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. J. Am. Med. Assoc. 312, 1880-1887 (2014
    • (2014) J. Am. Med. Assoc , vol.312 , pp. 1880-1887
    • Lee, H.1
  • 4
    • 84965181241 scopus 로고    scopus 로고
    • An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the clarity challenge
    • Brownstein, C.A. et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 15, R53 (2014
    • (2014) Genome Biol , vol.15 , pp. R53
    • Brownstein, C.A.1
  • 5
    • 84928209346 scopus 로고    scopus 로고
    • Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American college of medical genetics and genomics and the association for molecular pathology
    • Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17, 405-424 (2015
    • (2015) Genet. Med , vol.17 , pp. 405-424
    • Richards, S.1
  • 6
    • 70249111091 scopus 로고    scopus 로고
    • Targeted capture and massively parallel sequencing of 12 human exomes
    • Ng, S.B. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-276 (2009
    • (2009) Nature , vol.461 , pp. 272-276
    • Ng, S.B.1
  • 7
    • 79953197889 scopus 로고    scopus 로고
    • Mutations in notch2 cause hajdu-cheney syndrome, a disorder of severe and progressive bone loss
    • Simpson, M.A. et al. Mutations in NOTCH2 cause Hajdu-Cheney syndrome, a disorder of severe and progressive bone loss. Nat. Genet. 43, 303-305 (2011
    • (2011) Nat. Genet , vol.43 , pp. 303-305
    • Simpson, M.A.1
  • 8
    • 73349110071 scopus 로고    scopus 로고
    • Exome sequencing identifies the cause of a mendelian disorder
    • Ng, S.B. et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42, 30-35 (2010
    • (2010) Nat. Genet , vol.42 , pp. 30-35
    • Ng, S.B.1
  • 9
    • 84933279272 scopus 로고    scopus 로고
    • Factors influencing success of clinical genome sequencing across a broad spectrum of disorders
    • Taylor, J.C. et al. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat. Genet. 47, 717-726 (2015
    • (2015) Nat. Genet , vol.47 , pp. 717-726
    • Taylor, J.C.1
  • 10
    • 84982253941 scopus 로고    scopus 로고
    • Analysis of protein-coding genetic variation in 60,706 humans
    • Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285-291 (2016).
    • (2016) Nature , vol.536 , pp. 285-291
    • Lek, M.1
  • 11
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium
    • 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 (2012
    • (2012) Nature , vol.491 , pp. 56-65
  • 12
    • 84883897500 scopus 로고    scopus 로고
    • Acmg clinical laboratory standards for next-generation sequencing
    • Rehm, H.L. et al. ACMG clinical laboratory standards for next-generation sequencing. Genet. Med. 15, 733-747 (2013
    • (2013) Genet. Med , vol.15 , pp. 733-747
    • Rehm, H.L.1
  • 13
    • 0043122919 scopus 로고    scopus 로고
    • Sift: Predicting amino acid changes that affect protein function
    • Ng, P.C. & Henikoff, S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31, 3812-3814 (2003
    • (2003) Nucleic Acids Res , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 14
    • 77951640946 scopus 로고    scopus 로고
    • A method and server for predicting damaging missense mutations
    • Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249 (2010
    • (2010) Nat. Methods , vol.7 , pp. 248-249
    • Adzhubei, I.A.1
  • 15
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46, 310-315 (2014
    • (2014) Nat. Genet , vol.46 , pp. 310-315
    • Kircher, M.1
  • 16
    • 84926430386 scopus 로고    scopus 로고
    • Comparison and integration of deleteriousness prediction methods for nonsynonymous snvs in whole exome sequencing studies
    • Dong, C. et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum. Mol. Genet. 24, 2125-2137 (2015
    • (2015) Hum. Mol. Genet , vol.24 , pp. 2125-2137
    • Dong, C.1
  • 19
    • 84859786369 scopus 로고    scopus 로고
    • A comparison of random forests, boosting and support vector machines for genomic selection
    • Ogutu, J.O., Piepho, H.-P. & Schulz-Streeck, T. A comparison of random forests, boosting and support vector machines for genomic selection. BMC Proc. 5 (Suppl. 3), S11 (2011
    • (2011) BMC Proc , Issue.S11 , pp. 5
    • Ogutu, J.O.1    Piepho, H.-P.2    Schulz-Streeck, T.3
  • 20
    • 84897456458 scopus 로고    scopus 로고
    • Mutationtaster2: Mutation prediction for the deep-sequencing age
    • Schwarz, J.M., Cooper, D.N., Schuelke, M. & Seelow, D. MutationTaster2: mutation prediction for the deep-sequencing age. Nat. Methods 11, 361-362 (2014
    • (2014) Nat. Methods , vol.11 , pp. 361-362
    • Schwarz, J.M.1    Cooper, D.N.2    Schuelke, M.3    Seelow, D.4
  • 21
    • 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. 39, e118 (2011
    • (2011) Nucleic Acids Res , vol.39 , pp. e118
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 22
    • 84871578629 scopus 로고    scopus 로고
    • Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden markov models
    • Shihab, H.A. et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum. Mutat. 34, 57-65 (2013
    • (2013) Hum. Mutat , vol.34 , pp. 57-65
    • Shihab, H.A.1
  • 23
    • 69749122314 scopus 로고    scopus 로고
    • Identification of deleterious mutations within three human genomes
    • Chun, S. & Fay, J.C. Identification of deleterious mutations within three human genomes. Genome Res. 19, 1553-1561 (2009
    • (2009) Genome Res , vol.19 , pp. 1553-1561
    • Chun, S.1    Fay, J.C.2
  • 24
    • 84884592445 scopus 로고    scopus 로고
    • Genic intolerance to functional variation and the interpretation of personal genomes
    • Petrovski, S., Wang, Q., Heinzen, E.L., Allen, A.S. & Goldstein, D.B. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 9, e1003709 (2013
    • (2013) PLoS Genet , vol.9 , pp. e1003709
    • Petrovski, S.1    Wang, Q.2    Heinzen, E.L.3    Allen, A.S.4    Goldstein, D.B.5
  • 25
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. & Siepel, A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20, 110-121 (2010
    • (2010) Genome Res , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 26
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 27
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. & Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 28
    • 66349086264 scopus 로고    scopus 로고
    • Identifying novel constrained elements by exploiting biased substitution patterns
    • Garber, M. et al. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25, i54-i62 (2009
    • (2009) Bioinformatics , vol.25 , pp. i54-i62
    • Garber, M.1
  • 29
    • 78651237647 scopus 로고    scopus 로고
    • Identifying a high fraction of the human genome to be under selective constraint using gerp++
    • Davydov, E.V. et al. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput. Biol. 6, e1001025 (2010
    • (2010) PLoS Comput. Biol , vol.6 , pp. e1001025
    • Davydov, E.V.1
  • 30
    • 84875608234 scopus 로고    scopus 로고
    • The ucsc genome browser and associated tools
    • Kuhn, R.M., Haussler, D. & Kent, W.J. The UCSC genome browser and associated tools. Brief. Bioinform. 14, 144-161 (2013
    • (2013) Brief. Bioinform , vol.14 , pp. 144-161
    • Kuhn, R.M.1    Haussler, D.2    Kent, W.J.3
  • 31
    • 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, P.D. et al. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum. Genet. 133, 1-9 (2014
    • (2014) Hum. Genet , vol.133 , pp. 1-9
    • Stenson, P.D.1
  • 32
    • 84956688641 scopus 로고    scopus 로고
    • A spectral approach integrating functional genomic annotations for coding and noncoding variants
    • Ionita-Laza, I., McCallum, K., Xu, B. & Buxbaum, J.D. A spectral approach integrating functional genomic annotations for coding and noncoding variants. Nat. Genet. 48, 214-220 (2016
    • (2016) Nat. Genet , vol.48 , pp. 214-220
    • Ionita-Laza, I.1    McCallum, K.2    Xu, B.3    Buxbaum, J.D.4
  • 33
    • 84946069451 scopus 로고    scopus 로고
    • Uniprot: A hub for protein information
    • UniProt Consortium
    • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 43, D204-D212 (2015
    • (2015) Nucleic Acids Res , vol.43 , pp. D204-D212
  • 34
    • 84918771753 scopus 로고    scopus 로고
    • Molecular findings among patients referred for clinical whole-exome sequencing
    • Yang, Y. et al. Molecular findings among patients referred for clinical whole-exome sequencing. J. Am. Med. Assoc. 312, 1870-1879 (2014
    • (2014) J. Am. Med. Assoc , vol.312 , pp. 1870-1879
    • Yang, Y.1
  • 35
    • 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, e164 (2010
    • (2010) Nucleic Acids Res , vol.38 , pp. e164
    • Wang, K.1    Li, M.2    Hakonarson, H.3
  • 36
    • 79960763462 scopus 로고    scopus 로고
    • Dbnsfp: A lightweight database of human nonsynonymous snps and their functional predictions
    • Liu, X., Jian, X. & Boerwinkle, E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum. Mutat. 32, 894-899 (2011
    • (2011) Hum. Mutat , vol.32 , pp. 894-899
    • Liu, X.1    Jian, X.2    Boerwinkle, E.3
  • 37
    • 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. 34, E2393-E2402 (2013
    • (2013) Hum. Mutat , vol.34 , pp. E2393-E2402
    • Liu, X.1    Jian, X.2    Boerwinkle, E.3
  • 38
    • 80555140075 scopus 로고    scopus 로고
    • Scikit-learn: Machine learning in python
    • Pedregosa, F. et al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825-2830 (2011
    • (2011) J. Mach. Learn. Res , vol.12 , pp. 2825-2830
    • Pedregosa, F.1
  • 39
    • 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, 589-595 (2010
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 40
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.