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- Download and install the Integrative Genome Viewer from the Broad Institute.
- Select "Human hg19" as the reference genome from the top left drop down (you may need to select "more" to have hg19 as an option)
- Get some data: File > Load from Server… > 1000 genomes > Alignments > ACB > exome > HG01880
- Navigate to the rightmost exons of the GABBR1 gene.
- Zoom in until you find some SNPs. (Hint look just to the left of the 2nd exon).
- What type of library is this? (Hint: zoom out)
- If you knew this was a cancer patient, consider how strongly you would think this may be a potentially causative mutation.
- Imagine it was actually in the exon rather than just into the intron... would that make you consider it more?
- Load and look at the SNP track: File > Load from server > Annotations > Variants and Repeats > dbSNP 1.3.7
- The track may load with the Refseq genes, making it useful to resize that window to view both the gene and the dbSNP information simultaneously.
- Consider if this makes you think it more likely or less likely that this is a causative mutation.
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