publication . Article . Preprint . Other literature type . 2018

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

Soroush Samadian; Jeff P. Bruce; Trevor J. Pugh;
Open Access English
  • Published: 28 Mar 2018 Journal: PLoS Computational Biology, volume 14, issue 3 (issn: 1553-734X, eissn: 1553-7358, Copyright policy)
  • Publisher: Public Library of Science
Abstract
Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary ...
Subjects
free text keywords: Research Article, Biology and Life Sciences, Genetics, Heredity, Genetic Mapping, Haplotypes, Research and Analysis Methods, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Sequence Alignment, Computational Biology, Genome Analysis, Genomics, Genetic Loci, Alleles, Molecular Genetics, Molecular Biology, Genome Complexity, Copy Number Variation, Molecular biology techniques, Sequencing techniques, DNA sequencing, DNA sequence analysis, Biology (General), QH301-705.5, Ecology, Modelling and Simulation, Computational Theory and Mathematics, Ecology, Evolution, Behavior and Systematics, Cellular and Molecular Neuroscience
27 references, page 1 of 2

1 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;btr462. [OpenAIRE]

2 Chiang DY, Getz G, Jaffe DB, O’Kelly MJT, Zhao X, Carter SL, et al High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 2009;6:99–103. doi: 10.1038/nmeth.1276 19043412 [OpenAIRE] [PubMed]

3 Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013;29:1076–7. doi: 10.1093/bioinformatics/btt074 23413434 [OpenAIRE] [PubMed]

4 Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med. 2010;61:437–55. doi: 10.1146/annurev-med-100708-204735 20059347 [OpenAIRE] [PubMed]

5 Tan R, Wang Y, Kleinstein SE, Liu Y, Zhu X, Guo H, et al An evaluation of copy number variation detection tools from whole-exome sequencing data. Hum Mutat. 2014;35:899–907. doi: 10.1002/humu.22537 24599517 [PubMed]

6 Escalona M, Rocha S, Posada D. A comparison of tools for the simulation of genomic next-generation sequencing data. Nat Rev Genet [Internet]. 2016 [cited 2016 Jul 9];advance online publication. Available from: http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg.2016.57.html

7 Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28:593–4. doi: 10.1093/bioinformatics/btr708 22199392 [OpenAIRE] [PubMed]

8 DWGSim [Internet]. Available from: https://github.com/nh13/DWGSIM

9 Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, et al Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Meth. 2015;12:623–30. [OpenAIRE]

10 Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007;81:1084–97. doi: 10.1086/521987 17924348 [OpenAIRE] [PubMed]

11 Picard [Internet]. Picard. Available from: http://broadinstitute.github.io/picard

12 mpileup [Internet]. Available from: http://samtools.sourceforge.net/mpileup.shtml

13 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 Res. 2012;22:568–76. doi: 10.1101/gr.129684.111 22300766 [OpenAIRE] [PubMed]

14 Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, et al Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol. 2015;26:64–70. doi: 10.1093/annonc/mdu479 25319062 [OpenAIRE] [PubMed]

15 Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biology. 2011;12:R41 doi: 10.1186/gb-2011-12-4-r41 21527027 [OpenAIRE] [PubMed]

27 references, page 1 of 2
Abstract
Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary ...
Subjects
free text keywords: Research Article, Biology and Life Sciences, Genetics, Heredity, Genetic Mapping, Haplotypes, Research and Analysis Methods, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Sequence Alignment, Computational Biology, Genome Analysis, Genomics, Genetic Loci, Alleles, Molecular Genetics, Molecular Biology, Genome Complexity, Copy Number Variation, Molecular biology techniques, Sequencing techniques, DNA sequencing, DNA sequence analysis, Biology (General), QH301-705.5, Ecology, Modelling and Simulation, Computational Theory and Mathematics, Ecology, Evolution, Behavior and Systematics, Cellular and Molecular Neuroscience
27 references, page 1 of 2

1 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;btr462. [OpenAIRE]

2 Chiang DY, Getz G, Jaffe DB, O’Kelly MJT, Zhao X, Carter SL, et al High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods. 2009;6:99–103. doi: 10.1038/nmeth.1276 19043412 [OpenAIRE] [PubMed]

3 Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013;29:1076–7. doi: 10.1093/bioinformatics/btt074 23413434 [OpenAIRE] [PubMed]

4 Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med. 2010;61:437–55. doi: 10.1146/annurev-med-100708-204735 20059347 [OpenAIRE] [PubMed]

5 Tan R, Wang Y, Kleinstein SE, Liu Y, Zhu X, Guo H, et al An evaluation of copy number variation detection tools from whole-exome sequencing data. Hum Mutat. 2014;35:899–907. doi: 10.1002/humu.22537 24599517 [PubMed]

6 Escalona M, Rocha S, Posada D. A comparison of tools for the simulation of genomic next-generation sequencing data. Nat Rev Genet [Internet]. 2016 [cited 2016 Jul 9];advance online publication. Available from: http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg.2016.57.html

7 Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics. 2012;28:593–4. doi: 10.1093/bioinformatics/btr708 22199392 [OpenAIRE] [PubMed]

8 DWGSim [Internet]. Available from: https://github.com/nh13/DWGSIM

9 Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, et al Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Meth. 2015;12:623–30. [OpenAIRE]

10 Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007;81:1084–97. doi: 10.1086/521987 17924348 [OpenAIRE] [PubMed]

11 Picard [Internet]. Picard. Available from: http://broadinstitute.github.io/picard

12 mpileup [Internet]. Available from: http://samtools.sourceforge.net/mpileup.shtml

13 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 Res. 2012;22:568–76. doi: 10.1101/gr.129684.111 22300766 [OpenAIRE] [PubMed]

14 Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, et al Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol. 2015;26:64–70. doi: 10.1093/annonc/mdu479 25319062 [OpenAIRE] [PubMed]

15 Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biology. 2011;12:R41 doi: 10.1186/gb-2011-12-4-r41 21527027 [OpenAIRE] [PubMed]

27 references, page 1 of 2
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