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Cancers with CCNE1 Amplifications

The CCNE1 gene is commonly amplified in different cancer types, and results in oncogenic stress.1 Cancers with CCNE1 amplifications often display a characteristic signature of structural variants and are dominated by somatic tandem duplications.2

In order to explore the patterns of structural variants in CCNE1-amplified cancers, we created a Chromoscope configuration with 58 cancer genomes from the PCAWG study with CCNE1 amplifications. The visualizations highlight the common tandem duplicator, and to a lesser extent, a deletion pattern that makes chromosomal instability in this tumor group. The tandem duplications are often seen in highly transcribed regions. Additionally, we can observe 'synthetic duplications' (gains delineated by translocations, example) and more complex structural variants (example).

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The Chromoscope configuration with 58 cancer genomes with CCNE1 amplifications is available at:

https://chromoscope.bio/app/?showSamples=true&external=https://somatic-browser-test.s3.amazonaws.com/ccne1_amp/configs/ccne1_amp.all.config.json

  1. Gallo, David et al. “CCNE1 amplification is synthetic lethal with PKMYT1 kinase inhibition.” Nature vol. 604,7907 (2022): 749-756. ↩
  2. Menghi, Francesca et al. “The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations.” Cancer cell vol. 34,2 (2018): 197-210.e5. doi:10.1016/j.ccell.2018.06.008↩