Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology
Abstract
:1. Introduction
2. First Steps of Whole Exome Sequencing
3. Short Nucleotide Variants
4. Integrated Tools
5. Galaxy—An Open Source, Web-Based Platform
6. Copy Number Variations
7. Homologous Recombination Deficiency
8. Response to Immunotherapy
9. Tumor Heterogeneity
10. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Name | Published | Cited in 2018 | Control Needed | InDel detection | Contamination Correction | Trained on Cancer Data | Environment | Ref |
---|---|---|---|---|---|---|---|---|
Varscan2 | 2012 | 2229 | + | + | − | + | Java, Perl, R, Galaxy | [21] |
MuTect2 * | 2013 | 2005 | + | − | + | + | Java, R | [20] |
FreeBayes | 2012 | 1121 | − | + | − | + | C, C++, Galaxy | [24] |
Strelka * | 2012 | 759 | + | + | − | + | C++, Perl | [23] |
Platypus * | 2014 | 462 | − | + | − | + | C, Cython, Python | [36] |
SomaticSniper * | 2012 | 373 | + | − | − | + | C, Galaxy | [22] |
LoFreq * | 2012 | 349 | − | + | + | + | Python | [37] |
VarDict * | 2016 | 171 | − | + | − | + | Perl | [38] |
JointSNVMix * | 2012 | 160 | + | − | − | + | C, C++, Python, Galaxy | [39] |
MutationSeq * | 2012 | 108 | + | − | − | + | C++, Python | [40] |
EBCall * | 2013 | 85 | + | + | − | + | C++, Perl, R, Shell | [41] |
MuSE * | 2016 | 65 | + | − | + | + | C, C++ | [42] |
RADIA | 2014 | 53 | + | − | + | + | Python | [43] |
Virmid | 2013 | 49 | + | − | + | + | Java | [44] |
deepSNV * | 2014 | 47 | + | − | − | + | R | [45] |
Shimmer * | 2013 | 45 | + | − | + | + | C, Perl, R | [46] |
qSNP * | 2013 | 40 | + | − | + | − | Java | [47] |
BAYSIC | 2014 | 39 | + | − | − | + | R | [48] |
SomaticSeq * | 2015 | 38 | + | + | − | + | Python, R | [49] |
CaVEMan * | 2016 | 31 | + | − | + | + | C | [50] |
SNooPer * | 2016 | 26 | − | + | + | + | Perl | [51] |
SNVSniffer * | 2016 | 17 | − | + | − | + | C++ | [52] |
HapMuC | 2014 | 15 | − | + | − | + | C++, Python, Ruby | [53] |
FaSD-somatic | 2014 | 13 | − | − | − | + | C, C++ | [54] |
LocHap * | 2016 | 8 | + | + | + | + | g++ complier, GNU Make | [55] |
LoLoPicker * | 2017 | 6 | + | − | + | + | Python | [56] |
Name | Description | Year | Citation | License | System type | Ref. |
---|---|---|---|---|---|---|
Galaxy | Open-source web-platform with several analysis tools | 2005 | 1977 | free | cloud-based | [77] |
GenePattern | Workflow management system, provides access to multiple genomic analysis tools | 2006 | 1573 | free | cloud-based | [76] |
KNIME | Software enabling creation, analysis, and visualization of data | 2008 | 1476 | free | local installation needed | [73] |
UGENE | Workflow management system installed on a local computer | 2012 | 876 | free | local installation needed | [78] |
Taverna | Open source software tool for designing and executing workflows | 2013 | 643 | free | local installation needed | [72] |
Cancer Genomics Cloud | Provides access to data, tools, and computing resources | 2017 | 32 | commercial | cloud-based | [75] |
SciApps | Platform for building, running, and sharing scientific workflows | 2018 | 5 | free | cloud-based | [79] |
Terra | Bioinformatic workspace, including a repository of public best practices, methods, and public data sets | − | − | commercial | cloud-based | − |
Name | Published | Control Needed | Contamination Correction | GC-Content Correction | Trained on Cancer Data | Cited in 2018 | Environment | Ref. |
---|---|---|---|---|---|---|---|---|
Varscan2 | 2012 | + | − | − | + | 2229 | Java, Perl, R, Galaxy | [21] |
CNVnator | 2011 | + | − | + | − | 767 | C++ | [86] |
CNV-Seq | 2009 | + | − | − | − | 463 | Perl, R | [87] |
CoNIFER | 2012 | − | + | − | − | 378 | Python | [88] |
Control-FREEC * | 2012 | − | + | + | + | 342 | C, C++, R | [89] |
ExomeCNV | 2011 | + | + | − | + | 338 | R | [90] |
XHMM | 2012 | − | + | + | + | 322 | C++ | [91] |
ExomeDepth | 2012 | + | − | + | − | 264 | R | [92] |
cn.MOPS | 2012 | − | + | + | − | 249 | R | [93] |
Cnvkit * | 2016 | + | + | + | + | 219 | Python, Galaxy | [94] |
CONTRA | 2012 | − | − | + | − | 194 | Python, R | [95] |
Sequenza * | 2015 | + | − | + | + | 167 | Python, R | [96] |
EXCAVATOR | 2013 | + | + | + | + | 155 | Perl | [97] |
CODEX | 2015 | − | + | + | + | 72 | R | [98] |
ADTEx | 2014 | + | + | − | + | 57 | Python, R | [99] |
Seqgene | 2011 | + | − | − | + | 43 | R | [100] |
FishingCNV | 2013 | − | − | − | − | 41 | Java, R | [101] |
HMZDelFinder | 2017 | − | − | − | − | 33 | R | [102] |
ExoCNVTest | 2012 | + | − | − | − | 27 | Java, R | [103] |
CLAMMS | 2016 | − | − | + | − | 23 | C | [104] |
falcon | 2015 | + | + | − | + | 22 | C | [105] |
saasCNV * | 2015 | + | + | − | + | 17 | R | [106] |
WISExome | 2017 | − | − | − | − | 1 | C, C++ | [107] |
Tradename | Description | Year | Target | Tumor | Utility |
---|---|---|---|---|---|
Illumina MiSeqDX platform | High throughput DNA sequence analyzer | 2013 | - | - | technology |
FoundationFocus CDxBRCA | NGS oncology panel, somatic or germline variant detection system | 2016 | BRCA | ovarian | diagnosis |
MSK-IMPACT | NGS-based tumor profiling test | 2017 | 468 genes | various | predisposition, diagnosis |
FoundationOne CDx | NGS oncology panel, somatic or germline variant detection system | 2017 | 324 genes | various | predisposition, diagnosis |
Oncomine Dx Target Test | NGS oncology panel, somatic or germline variant detection system | 2017 | 24 genes | lung | diagnosis |
Praxis Extended RAS Panel | NGS oncology panel, somatic or germline variant detection system | 2017 | RAS | colon | diagnosis |
Adaptive Biotechnologies clonoSEQ | DNA-based test for minimal residual disease for hematologic malignancies | 2018 | BCL1, BCL2 | leukemia, myeloma | follow-up |
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Bartha, Á.; Győrffy, B. Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. Cancers 2019, 11, 1725. https://doi.org/10.3390/cancers11111725
Bartha Á, Győrffy B. Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. Cancers. 2019; 11(11):1725. https://doi.org/10.3390/cancers11111725
Chicago/Turabian StyleBartha, Áron, and Balázs Győrffy. 2019. "Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology" Cancers 11, no. 11: 1725. https://doi.org/10.3390/cancers11111725