The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models
1 Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
2 Memorial Sloan Kettering Cancer Center and Weill-Cornell Medical College, New York, NY 10065, USA
3 Department of Human Genetics, VIB and University of Leuven, B-3000, Leuven, Belgium
4 Delft Bioinformatics Lab, Delft University of Technology, Delft 2628CD, the Netherlands
5 MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research Centre, Edinburgh EH4 2XU, UK
6 Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
7 Department of Electrical Engineering, University of Leuven, B-3001, Leuven, Belgium
8 Dana Farber Cancer Institute and Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
9 Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298-0033, USA
10 Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
Genome Biology 2013, 14:R113 doi:10.1186/gb-2013-14-10-r113Published: 23 October 2013
Additional file 1: Tables S1 to S10:
Table S1: zebrafish tumors used in the exome study. Table S2: sequencing coverage and metrics. Table S3: somatic mutations identified in the 53 zebrafish melanomas. Table S4: copy number changes identified in the 53 zebrafish melanomas. Table S5: P-values of genes occurring in amplifications. Table S6: P-values of genes occurring in homozygous deletions. Table S7: insertion and deletions identified in the 53 zebrafish melanomas. Table S8: statistical analysis of mutation burden correlation. Table S9: significance of genes with respect to frequency and modality. Table S10 Mutated pathways and their significance from enrichment analysis.
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Additional file 2: Figures S1 to S8:
Figure S1: effect of SNP density on germline and somatic substitution calling performance using CaVEMan. Figure S2: comparison of substitution calling algorithms on zebrafish melanoma data. Figure S3: experimental outline. Figure S4: evidence of two additional cluster of mutations in ZD8a on chromosome 10. Figure S5: comparison of copy number aberration profiles between ASCAT and aCGH. Figure S6: unsupervised clustering analysis of copy number aberrations. Figure S7: pathway analysis of all mutations. Figure S8: distribution of co-occurring copy number alterations and/or somatic mutations in TP53, MITF, and CDKN2A across 120 BRAF mutant melanomas identified in the SKCM TCGA dataset.
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Additional file 3:
Supplementary text describing the mutation calling simulations and comparison of mutation callers.
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