publication . Article . 2016

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

Talevich, Eric; Shain, A. Hunter; Botton, Thomas; Bastian, Boris C.;
Open Access
  • Published: 01 Apr 2016 Journal: volume 12, issue 4issn: 1553-734X, eissn: 1553-7358, Copyright policy
  • Publisher: eScholarship, University of California
Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecific...
Subjects
free text keywords: Computational Biology, Molecular Biology, Information and Computing Sciences, Research Article, Array CGH, Software, High-Throughput Nucleotide Sequencing, DNA construction, Genomic Libraries, Repeated Sequences, Genetics, Morphogenesis, Fluorescence, Genome Analysis, Molecular Biology Techniques, DNA, Genomics, Sequence Analysis, Human, DNA sequencing, Sequencing Techniques, Biology and Life Sciences, Developmental Biology, Research and Analysis Methods, Mathematical Sciences, DNA library construction, Comparative Genomic Hybridization, Biological Sciences, QH301-705.5, Genome, Genomic Library Construction, DNA Copy Number Variations, Genome-Wide Association Study, Bioinformatics, Morphogenic Segmentation, Genome Sequencing, Humans, Biology (General), In Situ Hybridization
Funded by
NIH| Biomarker Discovery for the Classification of Melanoma
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA131524-02
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Expression pathways in melanoma progression for diagnosis and prognosis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P01CA025874-23S2
  • Funding stream: NATIONAL CANCER INSTITUTE
45 references, page 1 of 3

1 Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, et al High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics. 1998 10;20(2):207–11. doi: 10.1038/2524 9771718 [PubMed]

2 Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nature Genetics. 2005 6;37 Suppl(5):S11–7. doi: 10.1038/ng1569 15920524 [PubMed]

3 Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Research. 2009 9;19(9):1586–92. doi: 10.1101/gr.092981.109 19657104 [OpenAIRE] [PubMed]

4 Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics. 2013 1;14 Suppl 1(Suppl 11):S1 doi: 10.1186/1471-2105-14-S11-S1

5 Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, Nilsson M, et al Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proceedings of the National Academy of Sciences of the United States of America. 2007 5;104(22):9387–92. doi: 10.1073/pnas.0702165104 17517648 [OpenAIRE] [PubMed]

6 Med vedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Research. 2010 11;20(11):1613–22. doi: 10.1101/gr.106344.110 20805290 [OpenAIRE] [PubMed]

7 Sathirapongsasuti JF, Lee H, Horst BAJ, Brunner G, Cochran AJ, Binder S, et al Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics. 2011 10;27(19):2648–54. doi: 10.1093/bioinformatics/btr462 21828086 [OpenAIRE] [PubMed]

8 Love MI, MyšičkováA, Sun R, Kalscheuer V, Vingron M, Haas Sa. Modeling read counts for CNV detection in exome sequencing data. Statistical Applications in Genetics and Molecular Biology. 2011 1;10(1). doi: 10.2202/1544-6115.1732 23089826 [OpenAIRE] [PubMed]

9 Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle Ma, Ryland GL, et al CONTRA: copy number analysis for targeted resequencing. Bioinformatics. 2012 5;28(10):1307–13. doi: 10.1093/bioinformatics/bts146 22474122 [OpenAIRE] [PubMed]

10 Krumm N, Sudmant PH, Ko A, O’Roak BJ, Malig M, Coe BP, et al Copy number variation detection and genotyping from exome sequence data. Genome Research. 2012 8;22(8):1525–32. doi: 10.1101/gr.138115.112 22585873 [OpenAIRE] [PubMed]

11 Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S, et al A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012;28(21):2747–2754. doi: 10.1093/bioinformatics/bts526 22942019 [OpenAIRE] [PubMed]

12 Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research. 2012 3;22(3):568–76. doi: 10.1101/gr.129684.111 22300766 [OpenAIRE] [PubMed]

13 Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, et al Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. American Journal of Human Genetics. 2012 10;91(4):597–607. doi: 10.1016/j.ajhg.2012.08.005 23040492 [OpenAIRE] [PubMed]

14 Gartner JJ, Davis S, Wei X, Lin JC, Trivedi NS, Teer JK, et al Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics. 2012 1;13(1):505 doi: 10.1186/1471-2164-13-505 23006843 [OpenAIRE] [PubMed]

15 Magi A, Tattini L, Cifola I, D’Aurizio R, Benelli M, Mangano E, et al EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biology. 2013 1;14(10):R120 doi: 10.1186/gb-2013-14-10-r120 24172663 [OpenAIRE] [PubMed]

45 references, page 1 of 3
Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecific...
Subjects
free text keywords: Computational Biology, Molecular Biology, Information and Computing Sciences, Research Article, Array CGH, Software, High-Throughput Nucleotide Sequencing, DNA construction, Genomic Libraries, Repeated Sequences, Genetics, Morphogenesis, Fluorescence, Genome Analysis, Molecular Biology Techniques, DNA, Genomics, Sequence Analysis, Human, DNA sequencing, Sequencing Techniques, Biology and Life Sciences, Developmental Biology, Research and Analysis Methods, Mathematical Sciences, DNA library construction, Comparative Genomic Hybridization, Biological Sciences, QH301-705.5, Genome, Genomic Library Construction, DNA Copy Number Variations, Genome-Wide Association Study, Bioinformatics, Morphogenic Segmentation, Genome Sequencing, Humans, Biology (General), In Situ Hybridization
Funded by
NIH| Biomarker Discovery for the Classification of Melanoma
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA131524-02
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Expression pathways in melanoma progression for diagnosis and prognosis
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P01CA025874-23S2
  • Funding stream: NATIONAL CANCER INSTITUTE
45 references, page 1 of 3

1 Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, et al High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nature Genetics. 1998 10;20(2):207–11. doi: 10.1038/2524 9771718 [PubMed]

2 Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nature Genetics. 2005 6;37 Suppl(5):S11–7. doi: 10.1038/ng1569 15920524 [PubMed]

3 Yoon S, Xuan Z, Makarov V, Ye K, Sebat J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Research. 2009 9;19(9):1586–92. doi: 10.1101/gr.092981.109 19657104 [OpenAIRE] [PubMed]

4 Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics. 2013 1;14 Suppl 1(Suppl 11):S1 doi: 10.1186/1471-2105-14-S11-S1

5 Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, Nilsson M, et al Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proceedings of the National Academy of Sciences of the United States of America. 2007 5;104(22):9387–92. doi: 10.1073/pnas.0702165104 17517648 [OpenAIRE] [PubMed]

6 Med vedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Research. 2010 11;20(11):1613–22. doi: 10.1101/gr.106344.110 20805290 [OpenAIRE] [PubMed]

7 Sathirapongsasuti JF, Lee H, Horst BAJ, Brunner G, Cochran AJ, Binder S, et al Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics. 2011 10;27(19):2648–54. doi: 10.1093/bioinformatics/btr462 21828086 [OpenAIRE] [PubMed]

8 Love MI, MyšičkováA, Sun R, Kalscheuer V, Vingron M, Haas Sa. Modeling read counts for CNV detection in exome sequencing data. Statistical Applications in Genetics and Molecular Biology. 2011 1;10(1). doi: 10.2202/1544-6115.1732 23089826 [OpenAIRE] [PubMed]

9 Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle Ma, Ryland GL, et al CONTRA: copy number analysis for targeted resequencing. Bioinformatics. 2012 5;28(10):1307–13. doi: 10.1093/bioinformatics/bts146 22474122 [OpenAIRE] [PubMed]

10 Krumm N, Sudmant PH, Ko A, O’Roak BJ, Malig M, Coe BP, et al Copy number variation detection and genotyping from exome sequence data. Genome Research. 2012 8;22(8):1525–32. doi: 10.1101/gr.138115.112 22585873 [OpenAIRE] [PubMed]

11 Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S, et al A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012;28(21):2747–2754. doi: 10.1093/bioinformatics/bts526 22942019 [OpenAIRE] [PubMed]

12 Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research. 2012 3;22(3):568–76. doi: 10.1101/gr.129684.111 22300766 [OpenAIRE] [PubMed]

13 Fromer M, Moran JL, Chambert K, Banks E, Bergen SE, Ruderfer DM, et al Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. American Journal of Human Genetics. 2012 10;91(4):597–607. doi: 10.1016/j.ajhg.2012.08.005 23040492 [OpenAIRE] [PubMed]

14 Gartner JJ, Davis S, Wei X, Lin JC, Trivedi NS, Teer JK, et al Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics. 2012 1;13(1):505 doi: 10.1186/1471-2164-13-505 23006843 [OpenAIRE] [PubMed]

15 Magi A, Tattini L, Cifola I, D’Aurizio R, Benelli M, Mangano E, et al EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biology. 2013 1;14(10):R120 doi: 10.1186/gb-2013-14-10-r120 24172663 [OpenAIRE] [PubMed]

45 references, page 1 of 3
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publication . Article . 2016

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.

Talevich, Eric; Shain, A. Hunter; Botton, Thomas; Bastian, Boris C.;