Self-paced tutorial · UCSC Genome Browser
Tutorial 3: Clinical Examples & Variant Interpretation — Contents
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Welcome
1
Title
2
A thread for today: three cancer variants
3
Interpreting a variant = asking questions (germline)
Recommended Track Sets
5
Recommended Track Sets: The problem they solve
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Seven sets on hg38
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Demo 1: Clinical SNVs (coding) (1/2)
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Demo 1 · cont: validating a BRCA2 variant (2/2)
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Demo 2: Non-coding SNVs → epigenetics (1/2)
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Demo 2 · cont: a non-coding variant at TERT (2/2)
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Demo 3: expert-panel gene sets
Somatic interpretation
13
Interpreting a variant = asking questions (somatic)
14
Worked example: BRAF V600E
Expression
16
Three expression datasets on hg38
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Expression: what tissue is it expressed in?
Regulation & epigenetics
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Picking up from “Non-coding SNVs”
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Enhancers & promoters: cCREs
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Histone marks & open chromatin
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Worked locus: the TERT promoter (1/2)
23
TERT: the data say “active promoter” (2/2)
Variant-interpretation toolkit
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AlphaMissense: AI missense pathogenicity
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SpliceAI: predicting splice disruption
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Variant frequencies: how common, everywhere
Wrap-up
28
What you can now do
29
Where to get help
30
Thank you