/The-origins-and-vulnerabilities-of-two-transmissible-cancers-in-Tasmanian-devils

Analyses for "The origins and vulnerabilities of two transmissible cancers in Tasmanian devils". Cancer Cell 33(4), 607-619 (2018).

Primary LanguageR

The origins and vulnerabilities of two transmissible cancers in Tasmanian devils (soon available).

R scripts utilised for the analysis of Tasmanian devil genomic analyses used in our study "The origins and vulnerabilities of two transmissible cancers in Tasmanian devils". Cancer Cell 33(4), 607-619 (2018).

Data

  1. Genomic data (BAM files) can be accessed via the European Nucleotide Archive: https://www.ebi.ac.uk/ena/data/view/PRJEB21902
  2. Additional tables, FISH, genome assembly, IHC and mutation data is available via Mendeley data: http://dx.doi.org/10.17632/znfphvhmbv.1

Figure 1:

  • integrate and process SNP data from 398 Tasmanian devils by Brüniche-Olsen et al., 2016
  • integrate genotype calls of our samples
    • 86T, 88T (DFT1)
    • 202T2, 203T3 (DFT2)
    • 91H, 202H1, 203H (Normals)
  • draw hierarchical clustering map

Figure 2:

  • integrate somatic DFT1 and DFT2 single-nucleotide variants (SNVs)
  • draw somatic mutational spectrum of DFT1 (86T-unique & 88T-unique)
  • draw somatic mutational spectrum of DFT2 (202T2-unique & 203T3-unique)
  • normalise 30 COSMIC signatures to Tasmanian devil 7.1 reference genome base-triplet frequency
  • fit DFT1 and DFT2 mutational spectrum to different combinations of COSMIC signatures

Figure 3

  • integrate DFT1 and DFT2 structural variant (SV) calls
  • draw circos plots by sample
  • draw barplots of SV repair classes by sample

Figure 4

  • integrate copy-number calls
  • integrate gene dosage alteration calls
  • draw Venn diagrams
  • draw PDGFRA, PDGFRB and B2M Campbellgrams

Figure 5 (shortly also as a shiny app)

  • integrate drug screening IC50 data from DFT1, DFT2 and human cancer cell lines (https://www.cancerrxgene.org/, Yang et al., 2014)
  • process samples
  • draw hierarchical clustering map
  • draw cross-sample IC50 boxplots with sample-wise 'beeswarming', for drugs Afatinib, Axitinib, Sorafenib, Dasatinib, Talazoparib and AZD7762