OncoGenomics Explorer2

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OncoGenomics Explorer2

  1. 1. 22 March 2012OncoGenomics Explorer Taming Big DataCopyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  2. 2. Page: 2 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  3. 3. Which are the most frequently mutated genes in ovarian serous carcinoma? Samples from ovarian serous carcinomaPage: 3 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  4. 4. TP53, BRCA1 and BRCA2 are the three most frequently mutated genes TP53 is mutated in almost all tumorsPage: 4 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  5. 5. Mutation of the p53 gene is the key event in the development of high-grade tumors. Unlike low-grade serous carcinoma, mutations of KRAS, BRAF, or ERBB2 occur very infrequently in high-grade carcinoma.Page: 5 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  6. 6. Most high-grade tumors are characterized by TP53 mutations and lack mutations of KRAS, BRAF, or ERBB2.Vang R., et al., 2009: Ovarian low-grade and high-grade serouscarcinoma: pathogenesis,clinicopathologic and molecularbiologic features, and diagnosticproblems.Page: 6 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  7. 7. Serous ovarian cancer is also characterized by a low prevalence but statistically recurrent mutations in a number of other genes, including NF1, RB1 and FAT3.Page: 7 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  8. 8. Study for example the proportions of point mutations or AA types in NF1...Page: 8 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  9. 9. ...or study the mutations in NF1 in detail with the Gene viewer - The blue boxes represent the exons - Substitutions are shown as red vertical lines, insertions as light blue triangles, and deletions as pink triangles - The SIFT score predicts whether a mutations will affect protein function Can be zoomed all the way down to sequence levelPage: 9 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  10. 10. Is there a correlation between copy number variations of CCNE1 and overall survival of the patients ? Select the gene/genes of interest, in this case CCNE1Page: 10 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  11. 11. Overall survival tends to be lower for patients with CCNE1 amplificationThe Cancer GenomeAtlas ResearchNetwork, 2011:Integrated genomicanalyses of ovariancarcinomaPage: 11 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  12. 12. RAB25 seems to be epigenetically silenced in a subset of HG-OvCa tumors The Cancer Genome Atlas Research Network, 2011: Integrated genomic analyses of ovarian carcinomaPage: 12 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  13. 13. Genes with correlated CNV and expression include KRAS, POP4 and C19orf2 Wrzeszczynski KO. et al, 2011: Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancerPage: 13 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  14. 14. Are genes in a region of frequent copy number gain differentially expressed between amplified and unamplified groups of samples? Define the two groups to be compared, for example samples with copy number gain vs. samples with normal copy number Select the genes to be included, for example all genes in chromosome region 3q26Page: 14 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  15. 15. A volcano plot presenting the results of expression analyses between amplified and unamplified samples in the 3q26 region The results are shown as a volcano plot that enables the identification of genes that display high differences in expression that also are statistically significantPage: 15 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  16. 16. MYNN is a gene that is located in a region of frequent copy number gain on 3q26.2. It is differently expressed between amplified and unamplified groups MYNN shows a strong correlation between copy number and expression Ramakrishna M. et al., 2010: Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysisPage: 16 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  17. 17. In the volcano plot, an interesting group of genes can be selected Select for example genes with significant p-values and large difference estimatesPage: 17 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  18. 18. A heat map can be drawn of the genes from the defined gene selection and of the samples from the two selected sample groups Select an interesting cluster of samples in the heat map... ...and examine a summary of clinical covariatesPage: 18 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  19. 19. Find out how genetic values correlate with clinical reference data... Study for example how expression values of genes in chromosome region 8p correlate with overall survivalPage: 19 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  20. 20. ...or how genetic values correlate with genetic reference data Study for example Interesting how expression genes can be values of genes in selected for chromosome further analysis region 8p correlate with CNVs of BRCA1Page: 20 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  21. 21. - Find new drug targets - Find new biomarkers - Stratify patient groups - Find clinical correlationsPage: 21 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  22. 22. Contact us for demo •contact@medisapiens.com •tommi.pisto@medisapiens.comPage: 22 | Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
  23. 23. MediSapiens Ltd. Biomedicum Helsinki +358 50 363 1848 Tukholmankatu 8A contact@medisapiens.com FIN-00290 Helsinki medisapiens.comCopyright © 2012 MediSapiens Ltd. All rights reserved. • www.medisapiens.com

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