IGV Hands-on Exercise: UI basics and data integration

Transcription

1 IGV Hands-on Exercise: UI basics and data integration Verhaak, R.G. et al. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH, EGFR, and NF. Cancer Cell 7, 98 (00). Step Action Load expression and sample data from server 7 Select genome assembly hg8 Open The Cancer Genome Atlas (hg8) Open GBM Subtypes (Verhaak et. al.) Select Sample Information and Expression View whole genome Click on icon in tool bar Scroll up and down using scroll bar or Page-up/Page-down keys Hide some sample attributes View > Select Attributes to Show Uncheck DATA_FILE, KARNSCORE, and NAME Jump to gene MGMT Type MGMT in search box and click go Zoom out Click - box on railroad track control (upper right corner) or use mouse shortcut Alt-click Sort by sample attribute Click MGMT METHYLATED header above sample info panel Note: correlation of methylation status and gene expression

2 Zoom out further and explore region Zoom out using railroad track control Pan by click-dragging left and right Jump to other locus by clicking on the cytoband or by dragging the red box on the cytoband Set mutation overlay preference View > Preferences Click Overlays tab Check Overlay mutation tracks Uncheck Display mutation data as distinct tracks Load copy # and mutation data Open The Cancer Genome Atlas (hg8) Open GBM Subtypes (Verhaak et. al.) Select Copy Number and Non-silent Mutations Filter by sample attribute Tracks > Filter Tracks Set GENDER is equal to MALE Go to chromosome 7 Select chr7 from chromosome pulldown Note: focal amplification, narrow bright red region in copy number data Zoom in on focal amplification Double click over amplified region until window width is ~0mb Make sure to keep the cursor over the region when clicking

3 Define region of interest 7 Click region icon in tool bar Move mouse over data panel Click once to left of amplified region to define first boundary Click once to right of amplified region to define right boundary Sort by amplification Clock red region bar above data panel. Select Sort by amplfication Note: good correlation of copy # and expression Group by subtype Tracks > Group Tracks Select SUBTYPE in dropdown Note: frequency of EGFR amplification in Classical subtype relative to other subtypes Jump to gene NF Type NF in search box and click Go Zoom out Click - box twice on railroad track control Note: deletion of NF In Mesenchymal subtype Jump to gene MET Note: over-expression in Mesnchymal subtype Jump to gene TP Note: mutations in all subtypes except Classical Zoom in to base-pair level Shift-click until you see reference genome in the feature panel Note: protein residues displayed in exons

4 IGV Hands-on Exercise: SNP validation Step Action Load SNP call track File > Load from URL Load CEU Daughter data Open 000 Genomes > CEU Trio Select NA878 SLX and NA878 SOLID Adjust panel boundaries by grabbing and dragging horizontal borders Jump to first SNP call Enter the following into the search box and hit go chr:9,78,09-9,78, Click and drag view to center if necessary to center SNP (between vertical dashed lines). Sort alignments Right-click over alignment window and select Sort alignments > by base Does this SNP look real? High quality? Why or why not? Select SNP call track Click on track name ( SNP Calls ) Jump to next SNP call Hold ctrl key down and press f Adjust position if necessary to center SNP 7 Repeat for rest of SNPS, record score in table below Load validated SNP track File > Load from URL Validated SNPs are colored green Notes: You can right-click on the alignments and collapse the track to see more rows. Try the following options from the popup-menu: sort by base, sort by strand, shade by quality, show all reads.

5 SNP # T/F Comments