ViVar: A comprehensive platform for the analysis and visualization of structural genomic variation

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Sante, Tom ^a   Vergult, Sarah ^a   Volders, Pieter Jan ^a   Kloosterman, Wigard P ^b   Trooskens, Geert ^c   De Preter, Katleen ^a   Dheedene, Annelies ^a   Speleman, Frank ^a   De Meyer, Tim ^c   Menten, Björn ^a  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; COMPUTING PLATFORM; DATA ANALYSIS; DATA PROCESSING; ELECTRONICS; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION PROCESSING; PHENOTYPIC VARIATION; STRUCTURAL GENOMICS; BIOLOGY; GENETIC VARIATION; HUMAN GENOME; INTERNET; KARYOTYPE; PROCEDURES;

COMPUTATIONAL BIOLOGY; GENOME, HUMAN; GENOMIC STRUCTURAL VARIATION; HUMANS; INTERNET; KARYOTYPE;

EID: 84917695118     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113800     Document Type: Article

References (33)

1. Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nature reviews Genetics 7: 85-97.
2. Sharp AJ, Cheng Z, Eichler EE (2006) Structural variation of the human genome. Annual review of genomics and human genetics 7: 407-442.
3. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
4. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
5. Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, et al. (2012) Constitutional Chromothripsis Rearrangements Involve Clustered Double-Stranded DNA Breaks and Nonhomologous Repair Mechanisms. Cell Reports 1: 648-655.
6. Vergult S, Van Binsbergen E, Sante T, Nowak S, Vanakker O, et al. (2013) Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations. Eur J Hum Genet.
7. Talkowski ME, Ernst C, Heilbut A, Chiang C, Hanscom C, et al. (2011) Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research. American journal of human genetics 88: 469-481.
8. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420-426.
9. R Core Team (2013) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
10. Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
11. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 26: 589-595.
12. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 25: 1754-1760.
13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 25: 2078-2079.
14. McKenna AH, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research.
15. Xie C, Tammi MT (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10: 80.
16. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature methods 6: 677-681.
17. Picard Tools. Available: http://picard.sourceforge.net. Accessed 2014 Aug 9.
18. MongoDB. Available: http://www.mongodb.org. Accessed 2014 Aug 9.
19. sqlite Available:https://sqlite.org. Accessed 2014 July 15.
20. Duan J, Zhang JG, Deng HW, Wang YP (2013) Comparative studies of copy number variation detection methods for next-generation sequencing technologies. PLoS One 8: e59128.
21. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology 10: R25.
22. Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome research 21: 936-939.
23. Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome research 11: 1725-1729.
24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal Wand Clustal X version 2.0. Bioinformatics (Oxford, England) 23: 2947-2948.
25. Medvedev P, Stanciu M, Brudno M (2009) Computational methods for discovering structural variation with next-generation sequencing. Nature methods 6: S13-20.
26. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics (Oxford, England) 25: 2865-2871.
27. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic acids research 39: D876-882.
28. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for wholegenome association and population-based linkage analyses. The American Journal of Human Genetics 81: 559-575.
29. MacDonald JR, Ziman R, Yuen RK, Feuk L, Scherer SW (2014) The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res 42: D986-992.
30. Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, Lin ML, et al. (2013) Meander: visually exploring the structural variome using space-filling curves. Nucleic Acids Res 41: e118.
31. Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, et al. (2012) Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP J Bioinform Syst Biol 2012: 15.
32. O'Brien TM, Ritz AM, Raphael BJ, Laidlaw DH (2010) Gremlin: an interactive visualization model for analyzing genomic rearrangements. IEEE Trans Vis Comput Graph 16: 918-926.
33. Volders PJ, Helsens K, Wang X, Menten B, Martens L, et al. (2013) LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res 41: D246-251.