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Volumn 28, Issue 21, 2012, Pages 2711-2718

Statistical challenges associated with detecting copy number variations with next-generation sequencing

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CHROMOSOME MAP; COPY NUMBER VARIATION; DNA BASE COMPOSITION; DNA SEQUENCE; EPIDEMIOLOGY; GENE DELETION; GENE DUPLICATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; REVIEW; STATISTICS;

EID: 84868016827     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts535     Document Type: Review
Times cited : (170)

References (46)
  • 1
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • Abyzov, A. et al. (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res., 21, 974-33.
    • (2011) Genome Res. , vol.21 , pp. 974-1033
    • Abyzov, A.1
  • 2
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan, C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-33.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 363-433
    • Alkan, C.1
  • 3
    • 70349556543 scopus 로고    scopus 로고
    • Personalized copy number and segmental duplication maps using next-generation sequencing
    • Alkan, C. et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-33.
    • (2009) Nat. Genet. , vol.41 , pp. 1061-2043
    • Alkan, C.1
  • 4
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • Aird, D. et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol., 12, R18.
    • (2011) Genome Biol. , vol.12
    • Aird, D.1
  • 5
    • 84861548193 scopus 로고    scopus 로고
    • Summarizing and correction for GC-content bias in high throughput sequencing
    • doi:10.1093/nar/gks001
    • Benjamini, Y. and Speed, T.P. (2012) Summarizing and correction for GC-content bias in high throughput sequencing. Nucleic Acids Res., 40, e72. doi:10.1093/nar/gks001.
    • (2012) Nucleic Acids Res. , vol.40
    • Benjamini, Y.1    Speed, T.P.2
  • 6
    • 84856561659 scopus 로고    scopus 로고
    • Control-FREEC: A tool for assessing copy number and allelic content using next-generation sequencing data
    • Boeva, V. et al. (2012) Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics, 28, 423-33.
    • (2012) Bioinformatics , vol.28 , pp. 423-433
    • Boeva, V.1
  • 7
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: An algorithm for high resolution mapping of genomic structural variation
    • Chen, K. et al. (2009) BreakDancer: an algorithm for high resolution mapping of genomic structural variation. Nat. Methods, 6, 677-33.
    • (2009) Nat. Methods , vol.6 , pp. 677-733
    • Chen, K.1
  • 8
    • 58149218240 scopus 로고    scopus 로고
    • High-resolution mapping of copy-number alterations with massively parallel sequencing
    • Chiang, D.Y. et al. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-33.
    • (2009) Nat. Methods , vol.6 , pp. 99-33
    • Chiang, D.Y.1
  • 9
  • 10
    • 77950461601 scopus 로고    scopus 로고
    • Origins and functional impact of copy number variation in the human genome
    • Conrad, D.F. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-33.
    • (2010) Nature , vol.464 , pp. 704-733
    • Conrad, D.F.1
  • 11
    • 77954402321 scopus 로고    scopus 로고
    • Inversion variants in the human genome: Role in disease and genome architecture
    • Feuk, L. (2010) Inversion variants in the human genome: role in disease and genome architecture. Genome Med., 2, 11.
    • (2010) Genome Med. , vol.2 , pp. 11
    • Feuk, L.1
  • 12
    • 79952194317 scopus 로고    scopus 로고
    • Discovery and genotyping of genome structural polymorphism by sequencing on population scale
    • Handsaker, R.E. et al. (2011) Discovery and genotyping of genome structural polymorphism by sequencing on population scale. Nat. Genet., 43, 269-33.
    • (2011) Nat. Genet. , vol.43 , pp. 269-333
    • Handsaker, R.E.1
  • 13
    • 65449144325 scopus 로고    scopus 로고
    • Evaluation of next generation sequencing platforms for population targeted sequencing studies
    • doi: 10.1186/gb-2009-10-3-r32
    • Harismendy, O. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32. doi: 10.1186/gb-2009-10-3-r32.
    • (2009) Genome Biol. , vol.10
    • Harismendy, O.1
  • 14
    • 79957842730 scopus 로고    scopus 로고
    • Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions
    • He, D. et al. (2011) Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions. Bioinformatics, 27, 1513-33.
    • (2011) Bioinformatics , vol.27 , pp. 1513-1533
    • He, D.1
  • 15
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • Hormozdiari, F. et al. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-33.
    • (2009) Genome Res. , vol.19 , pp. 1270-2243
    • Hormozdiari, F.1
  • 16
    • 84856246802 scopus 로고    scopus 로고
    • De novo assembly and genotyping of variants using colored de Bruijn graphs
    • Iqbal, Z. et al. (2011) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet., 44, 226-33.
    • (2011) Nat. Genet. , vol.44 , pp. 226-233
    • Iqbal, Z.1
  • 17
    • 62549131646 scopus 로고    scopus 로고
    • PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    • Korbel, J. et al. (2009) PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
    • (2009) Genome Biol. , vol.10
    • Korbel, J.1
  • 18
    • 79952088032 scopus 로고    scopus 로고
    • A computer simulator for assessing different challenges and strategies of de novo sequence assembly
    • Knudsen, B. et al. (2010) A computer simulator for assessing different challenges and strategies of de novo sequence assembly. Genes, 1, 263-33.
    • (2010) Genes , vol.1 , pp. 263-333
    • Knudsen, B.1
  • 19
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li, H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-33.
    • (2008) Genome Res. , vol.18 , pp. 1851-2843
    • Li, H.1
  • 20
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R. et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res., 20, 265-33.
    • (2010) Genome Res. , vol.20 , pp. 265-333
    • Li, R.1
  • 21
    • 52949141845 scopus 로고    scopus 로고
    • Integrated detection and population-genetic analysis of SNPs and copy number variation
    • McCarroll, S.A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., 40, 1166-33.
    • (2008) Nat. Genet. , vol.40 , pp. 1166-2143
    • McCarroll, S.A.1
  • 22
    • 69749090013 scopus 로고    scopus 로고
    • Sequence and structural variation in a human genome uncovered by massively parallel ligation sequencing using two-base encoding
    • McKernan, K.J. et al. (2009) Sequence and structural variation in a human genome uncovered by massively parallel ligation sequencing using two-base encoding. Genome Res., 19, 1527-33.
    • (2009) Genome Res. , vol.19 , pp. 1527-1533
    • McKernan, K.J.1
  • 23
    • 70449704529 scopus 로고    scopus 로고
    • Computational methods for discovering structural variation with next-generation sequencing
    • Medvedev, P. et al. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6 (11 Suppl.), S13-S20.
    • (2009) Nat. Methods , vol.6 , Issue.11 SUPPL.
    • Medvedev, P.1
  • 24
    • 78649309503 scopus 로고    scopus 로고
    • Detecting copy number variation with mated short reads
    • Medvedev, P. et al. (2010) Detecting copy number variation with mated short reads. Genome Res., 20, 1613-33.
    • (2010) Genome Res. , vol.20 , pp. 1613-1633
    • Medvedev, P.1
  • 25
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies\the next generation
    • Metzker, M.L. (2010) Sequencing technologies\the next generation. Nat. Rev. Genet., 11, 31-33.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 31-33
    • Metzker, M.L.1
  • 26
    • 84975804424 scopus 로고    scopus 로고
    • Mapping copy number variation by population-scale genome sequencing
    • Mills, R.E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-33.
    • (2011) Nature , vol.470 , pp. 59-33
    • Mills, R.E.1
  • 27
    • 77952296952 scopus 로고    scopus 로고
    • Towards a comprehensive structural variation map of an individual human genome
    • doi: 10.1186/gb-2010-11-5-r52
    • Pang, A.W. et al. (2010) Towards a comprehensive structural variation map of an individual human genome. Genome Biol., 11, R52. doi: 10.1186/gb-2010-11- 5-r52.
    • (2010) Genome Biol. , vol.11
    • Pang, A.W.1
  • 28
    • 0035859921 scopus 로고    scopus 로고
    • An Eulerian path approach to DNA fragment assembly
    • Pevzner, P.A. et al. (2001) An Eulerian path approach to DNA fragment assembly. Proc. Natl Acad. Sci. USA, 98, 9748-33.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 9748-10743
    • Pevzner, P.A.1
  • 29
    • 16644381328 scopus 로고    scopus 로고
    • Comparative genome assembly
    • Pop, M. et al. (2004) Comparative genome assembly. Brief. Bioinformatics, 5, 237-33.
    • (2004) Brief. Bioinformatics , vol.5 , pp. 237-333
    • Pop, M.1
  • 30
    • 77951860138 scopus 로고    scopus 로고
    • Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    • Quinlan, A.R. et al. (2010) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res., 20, 623-33.
    • (2010) Genome Res. , vol.20 , pp. 623-633
    • Quinlan, A.R.1
  • 31
    • 80053446554 scopus 로고    scopus 로고
    • Exome sequencing-based copy number variation and loss of heterozygosity detection: ExomeCNV
    • Sathirapongsasuti, J.F. et al. (2011) Exome sequencing-based copy number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics, 27, 2648-33.
    • (2011) Bioinformatics , vol.27 , pp. 2648-3643
    • Sathirapongsasuti, J.F.1
  • 32
    • 78650868150 scopus 로고    scopus 로고
    • A window into third-generation sequencing
    • Schadt, E.E. et al. (2010) A window into third-generation sequencing. Hum. Mol. Genet., 19, R227-R240.
    • (2010) Hum. Mol. Genet. , vol.19
    • Schadt, E.E.1
  • 33
    • 77956279237 scopus 로고    scopus 로고
    • Assembly of large genomes using second generation sequencing
    • Schatz, M.C. et al. (2010) Assembly of large genomes using second generation sequencing. Genome Res., 20, 1165-33.
    • (2010) Genome Res. , vol.20 , pp. 1165-2143
    • Schatz, M.C.1
  • 34
    • 84866240316 scopus 로고    scopus 로고
    • Change-point model on nonhomogeneous poisson processes with application in copy number profiling by next-generation DNA sequencing
    • Shen, J.J. and Zhang, N. (2012) Change-point model on nonhomogeneous poisson processes with application in copy number profiling by next-generation DNA sequencing. Ann. Appl. Stat., 6, 476-33.
    • (2012) Ann. Appl. Stat. , vol.6 , pp. 476-533
    • Shen, J.J.1    Zhang, N.2
  • 35
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: A parallel assembler for short read sequence data
    • Simpson, J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-33.
    • (2009) Genome Res. , vol.19 , pp. 1117-1133
    • Simpson, J.T.1
  • 36
    • 78049412267 scopus 로고    scopus 로고
    • Diversity of human copy number variation and multicopy genes
    • Sudmant, P.H. et al. (2010) Diversity of human copy number variation and multicopy genes. Science, 330, 641-33.
    • (2010) Science , vol.330 , pp. 641-733
    • Sudmant, P.H.1
  • 37
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • The 1000 Genomes Project Consortium.
    • The 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-33.
    • (2010) Nature , vol.467 , pp. 1061-2043
  • 38
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: Computational challenges and solutions
    • Treangen, T.J. and Salzberg, S.L. (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet., 13, 36-33.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 36-33
    • Treangen, T.J.1    Salzberg, S.L.2
  • 39
    • 35948984173 scopus 로고    scopus 로고
    • PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP geno-typing data
    • Wang, K. et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP geno-typing data. Genome Res., 17, 1665-33.
    • (2007) Genome Res. , vol.17 , pp. 1665-2643
    • Wang, K.1
  • 40
    • 55549097849 scopus 로고    scopus 로고
    • The diploid genome sequence of an Asian individual
    • Wang, J. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-33.
    • (2008) Nature , vol.456 , pp. 60-33
    • Wang, J.1
  • 41
    • 79955004110 scopus 로고    scopus 로고
    • Detecting structural variations in the human genome using next generation sequencing
    • Xi, R. et al. (2011) Detecting structural variations in the human genome using next generation sequencing. Brief. Funct. Genomics, 9, 405-33.
    • (2011) Brief. Funct. Genomics , vol.9 , pp. 405-433
    • Xi, R.1
  • 42
    • 64849083125 scopus 로고    scopus 로고
    • CNV-seq, a new method to detect copy number variation using high-throughput sequencing
    • Xie, C. and Tammi, M.T. (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10, 80.
    • (2009) BMC Bioinformatics , vol.10 , pp. 80
    • Xie, C.1    Tammi, M.T.2
  • 43
    • 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
    • Ye, K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865-33.
    • (2009) Bioinformatics , vol.25 , pp. 2865-3843
    • Ye, K.1
  • 44
    • 69749122557 scopus 로고    scopus 로고
    • Sensitive and accurate detection of copy number variants using read depth of coverage
    • Yoon, S. et al. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-33.
    • (2009) Genome Res. , vol.19 , pp. 1586-2543
    • Yoon, S.1
  • 45
    • 77955044283 scopus 로고    scopus 로고
    • SVDetect: A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
    • Zeitouni, B. et al. (2010) SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinformatics, 26, 1895-33.
    • (2010) Bioinformatics , vol.26 , pp. 1895-2843
    • Zeitouni, B.1
  • 46
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


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