Abstract
Collections of genomic intervals are a common data type across many areas of computational biology. In cancer genomics, in particular, the intervals often represent regions with altered DNA copy number, and their collections exhibit recurrent features, characteristic of a given cancer type. Cores of Recurrent Events (CORE) is a versatile computational tool for identification of such recurrent features. Here we provide practical guidance for the use of CORE, implemented as an eponymous R package.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899–905. https://doi.org/10.1038/Nature08822
Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M (2011) Tumour evolution inferred by single-cell sequencing. Nature 472(7341):90–94. https://doi.org/10.1038/Nature09807
Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Borresen-Dale AL, Naume B, Schlicting E, Norton L, Hagerstrom T, Skoog L, Auer G, Maner S, Lundin P, Zetterberg A (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16(12):1465–1479. https://doi.org/10.1101/Gr.5460106
Krishnamurti U, Silverman JF (2014) HER2 in breast cancer: a review and update. Adv Anat Pathol 21(2):100–107. https://doi.org/10.1097/PAP.0000000000000015
Xue W, Kitzing T, Roessler S, Zuber J, Krasnitz A, Schultz N, Revill K, Weissmueller S, Rappaport AR, Simon J, Zhang J, Luo W, Hicks J, Zender L, Wang XW, Powers S, Wigler M, Lowe SW (2012) A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc Natl Acad Sci U S A 109(21):8212–8217. https://doi.org/10.1073/pnas.1206062109
Krasnitz A, Sun G, Andrews P, Wigler M (2013) Target inference from collections of genomic intervals. Proc Natl Acad Sci U S A 110(25):E2271–E2278. https://doi.org/10.1073/pnas.1306909110
Sun G, Krasnitz A (2014) CORE: cores of recurrent events. https://cran.r-project.org/package=CORE
Kendall J, Krasnitz A (2014) Computational methods for DNA copy-number analysis of tumors. Methods Mol Biol 1176:243–259. https://doi.org/10.1007/978-1-4939-0992-6_20
Bajjani BA, Theisen AP, Ballif BC, Shaffer LG (2005) Array-based comparative genomic hybridization in clinical diagnosis. Expert Rev Mol Diagn 5(3):421–429
Mei R, Galipeau PC, Prass C, Berno A, Ghandour G, Patil N, Wolff RK, Chee MS, Reid BJ, Lockhart DJ (2000) Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res 10(8):1126–1137. https://doi.org/10.1101/gr.10.8.1126
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Sun, G., Krasnitz, A. (2019). CORE: A Software Tool for Delineating Regions of Recurrent DNA Copy Number Alteration in Cancer. In: Krasnitz, A. (eds) Cancer Bioinformatics. Methods in Molecular Biology, vol 1878. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8868-6_4
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8868-6_4
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8866-2
Online ISBN: 978-1-4939-8868-6
eBook Packages: Springer Protocols