603a734862321da4d9bde067c47a4a13175acc02 mspeir Thu Jul 23 09:24:22 2026 -0700 Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904 diff --git docs/slideDecks/tutorial3-clinical/tableOfContents/index.html docs/slideDecks/tutorial3-clinical/tableOfContents/index.html index f953260e25b..455d15a0cf2 100644 --- docs/slideDecks/tutorial3-clinical/tableOfContents/index.html +++ docs/slideDecks/tutorial3-clinical/tableOfContents/index.html @@ -1,102 +1,102 @@ Contents · UCSC Genome Browser · Tutorial 3: Clinical Examples & Variant Interpretation

Self-paced tutorial · UCSC Genome Browser

Tutorial 3: Clinical Examples & Variant Interpretation — Contents

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Welcome

1Title
2A thread for today: three cancer variants
2A set of clear examples: three cancer variants
3Interpreting a variant = asking questions (germline)

Recommended Track Sets

5Recommended Track Sets: The problem they solve
6Seven sets on hg38
7Demo 1: Clinical SNVs (coding) (1/2)
8Demo 1 · cont: validating a BRCA2 variant (2/2)
9Demo 2: Non-coding SNVs → epigenetics (1/2)
10Demo 2 · cont: a non-coding variant at TERT (2/2)
11Demo 3: expert-panel gene sets

Somatic interpretation

13Interpreting a variant = asking questions (somatic)
14Worked example: BRAF V600E

Expression

16Three expression datasets on hg38
17Expression: what tissue is it expressed in?

Regulation & epigenetics

19Picking up from “Non-coding SNVs”
20Enhancers & promoters: cCREs
21Histone marks & open chromatin
22Worked locus: the TERT promoter (1/2)
23TERT: the data say “active promoter” (2/2)

Variant-interpretation toolkit

25AlphaMissense: AI missense pathogenicity
26SpliceAI: predicting splice disruption
27Variant frequencies: how common, everywhere

Wrap-up

28What you can now do
29Where to get help
30Thank you