cnvCurator: an interactive visualization and editing tool for somatic copy number variations

Lingnan Ma1, Maochun Qin1, Biao Liu1, Qiang Hu1, Lei Wei1, Jianmin Wang1, Song Liu1
1Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet. 2009;10(8):551–64.

Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7(2):85–97.

Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363–76.

Shlien A, Malkin D. Copy number variations and cancer. Genome Med. 2009;1(6):62.

Santarius T, Shipley J, Brewer D, Stratton MR, Cooper CS. EPIGENETICS AND GENETICS A census of amplified and overexpressed human cancer genes. Nat Rev Cancer. 2010;10(1):59–64.

Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010;11(10):685–96.

Liu B, Morrison CD, Johnson CS, Trump DL, Qin M, Conroy JC, et al. Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. Oncotarget. 2013;4(11):1868–81.

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;14 Suppl 11:S1.

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(7):899–907.

Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, et al. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotech. 2011;29(6):512–20.

Duan J, Zhang JG, Deng HW, Wang YP. Comparative studies of copy number variation detection methods for next-generation sequencing technologies. PLoS One. 2013;8(3):e59128.

Alkodsi A, Louhimo R, Hautaniemi S. Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Brief Bioinform. 2015;16(2):242–54.

Gordon DJ, Resio B, Pellman D. Causes and consequences of aneuploidy in cancer. Nat Rev Genet. 2012;13(3):189–203.

Marusyk A, Almendro V, Polyak K. Intra-tumour heterogeneity: a looking glass for cancer? Nat Rev Cancer. 2012;12(5):323–34.

Shackleton M, Quintana E, Fearon ER, Morrison SJ. Heterogeneity in cancer: cancer stem cells versus clonal evolution. Cell. 2009;138(5):822–9.

Andersson AK, Ma J, Wang J, Chen X, Gedman AL, Dang J, et al. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat Genet. 2015;47(4):330–7.

Chen X, Bahrami A, Pappo A, Easton J, Dalton J, Hedlund E, et al. Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Reports. 2014;7(1):104–12.

Holmfeldt L, Wei L, Diaz-Flores E, Walsh M, Zhang J, Ding L, et al. The genomic landscape of hypodiploid acute lymphoblastic leukemia. Nat Genet. 2013;45(3):242–52.

Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29(1):24–6.

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17(11):1665–74.

Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, et al. Diverse mechanisms of somatic structural variations in human cancer genomes. Cell. 2013;153(4):919–29.

Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, et al. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011;8(8):652–4.

Liu B, Conroy JM, Morrison CD, Odunsi AO, Qin M, Wei L, et al. Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives. Oncotarget. 2015;6(8):5477–89.

Qin M, Liu B, Conroy JM, Morrison CD, Hu Q, Cheng Y, et al. SCNVSim: somatic copy number variation and structure variation simulator. BMC Bioinformatics. 2015;16:66.

Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5(4):557–72.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.

Chen X, Gupta P, Wang J, Nakitandwe J, Roberts K, Dalton JD, et al. CONSERTING: integrating copy-number analysis with structural-variation detection. Nat Methods. 2015;12(6):527–30.