Advertisement

Chromothripsis pp 279-289 | Cite as

ChromothripsisDB: A Curated Database for the Documentation, Visualization, and Mining of Chromothripsis Data

  • Haoyang Cai
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1769)

Abstract

ChromothripsisDB (http://cgma.scu.edu.cn/ChromothripsisDB) is a manually curated database containing a unified description of published chromothripsis cases and relevant genomic aberrations. Available data includes copy number alterations, chromosome structural variations, and gene annotations. The criteria used for detecting chromothripsis in each study are also provided. At present, the molecular mechanisms involved in chromothripsis phenomenon are not fully understood. Thus, further studies with large number of identified chromothripsis samples are needed. The current release of ChromothripsisDB contains more than 400 patient samples, representing over 100 research articles. It represents an extraordinary resource for mining the existing knowledge of chromothripsis.

Keywords

Database Copy number alteration Chromosome structural variation Genomic aberration Cancer genome Data mining 

Notes

Acknowledgments

This work was funded by the National Natural Science Foundation of China [grant numbers 31571314 and U1603120].

References

  1. 1.
    Yang J, Deng G, Cai H (2016) ChromothripsisDB: a curated database of chromothripsis. Bioinformatics 32:1433–1435CrossRefPubMedGoogle Scholar
  2. 2.
    Stephens PJ, Greenman CD, Fu B et al (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:27–40CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Forment JV, Kaidi A, Jackson SP (2012) Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer 12:663–670CrossRefPubMedGoogle Scholar
  4. 4.
    Meyerson M, Pellman D (2011) Cancer genomes evolve by pulverizing single chromosomes. Cell 144:9–10CrossRefPubMedGoogle Scholar
  5. 5.
    Rausch T, Jones DT, Zapatka M et al (2012) Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148:59–71CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Kloosterman WP, Hoogstraat M, Paling O et al (2011) Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol 12:R103CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Molenaar JJ, Koster J, Zwijnenburg DA et al (2012) Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483:589–593CrossRefPubMedGoogle Scholar
  8. 8.
    Nones K, Waddell N, Wayte N et al (2014) Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nat Commun 5:5224CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Kloosterman WP, Guryev V, van Roosmalen M et al (2011) Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet 20:1916–1924CrossRefPubMedGoogle Scholar
  10. 10.
    Northcott PA, Shih DJ, Peacock J et al (2012) Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature 488:49–56CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Wu C, Wyatt AW, McPherson A et al (2012) Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosomes Cancer 51:1144–1153CrossRefPubMedGoogle Scholar
  12. 12.
    Hirsch D, Kemmerling R, Davis S et al (2013) Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma. Cancer Res 73:1454–1460CrossRefPubMedGoogle Scholar
  13. 13.
    Bassaganyas L, Beà S, Escaramís G et al (2013) Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis. Leukemia 27:2376–2379CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Cai H, Kumar N, Bagheri HC et al (2014) Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics 15:82CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Zack TI, Schumacher SE, Carter SL et al (2013) Pan-cancer patterns of somatic copy number alteration. Nat Genet 45:1134–1140CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Magrangeas F, Avet-Loiseau H, Munshi NC et al (2011) Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients. Blood 118:675–678CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Kim TM, Xi R, Luquette LJ et al (2013) Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes. Genome Res 23:217–227CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Li Y, Schwab C, Ryan SL et al (2014) Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 508:98–102CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Korbel JO, Campbell PJ (2013) Criteria for inference of chromothripsis in cancer genomes. Cell 152:1226–1236CrossRefPubMedGoogle Scholar
  20. 20.
    Malhotra A, Lindberg M, Faust GG et al (2013) Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms. Genome Res 23:762–776CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Forbes SA, Beare D, Gunasekaran P et al (2015) COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res 43:D805–D811CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-EnvironmentCollege of Life Sciences, Sichuan UniversityChengduChina

Personalised recommendations