Genome Analysis with Chromoscope and cBioPortal
1. In cBio, query the PCAWG cohort using clinical features or by genes.
2. View cases with variants in a selected gene (BRCA1), acording to their consequence
3. Select a breast cancer sample
4. View prioritized coding variants
5. Find out the dominant mutational signature
6. In Chromoscope, view the overall SV pattern. This genome is full of tandem duplications and chromoscome arm losses - a telltale of HRD!
7. Variant view allows you to inspect variants on individual chromosomes
8. Search for PTEN - a gene often inactivated in breast cancer
9. Evaluate the impact of a tandem duplication on exons of PTEN
Chromoscope can also help you explore your own whole genome data.
dominik_glodzik@hms.harvard.edu
Chief Science Officer & Data Platforms Expert | Driving technology, policy, & collaboration to help advance precision medicine
4 个月Looks really slick, congrats Dominik Glodzik & team! I particularly appreciate how this opens up cancer research to a more diverse user community who thrive in more visually guided analysis rather than writing bespoke code. I believe that collaboration, along with these technological advancements, will really move the needle in developing more personalized treatment options. Excited to see where this leads in terms of new discoveries and improved clinical outcomes.
DeTAnomics Lab(academic research lab) at the MCW;MCWpathology; Innovation, Discovery|Prostate cancer, Precision medicine, Integrative Genomics, Mol Tumor Board, Clinical Trial, DNA repair, Cell free DNA, Comp Bio
4 个月Divin Wilson komal sharma
Director @ Repare Therapeutics | Clinical and Translational Bioinformatics
4 个月A great resource for the community. Thanks Dominik and team.
Instructor of Biomedical Informatics at Harvard Medical School
4 个月