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/tutorial2-cancer/presentation/index.html docs/slideDecks/tutorial2-cancer/presentation/index.html index 3aab039876d..7ee9fe98fe1 100644 --- docs/slideDecks/tutorial2-cancer/presentation/index.html +++ docs/slideDecks/tutorial2-cancer/presentation/index.html @@ -1,24 +1,24 @@ UCSC Genome Browser · Tutorial 2: Cancer Data - - + +
UCSC Genome Browser · Tutorial 2: Cancer Data

UCSC Genome Browser · Tutorial 2

Cancer Data

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The cancer & clinical databases, worked on BRAF V600E

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The cancer & clinical databases, a worked BRAF V600E example

A hands-on tour of the oncology tracks · genome.ucsc.edu

What we'll cover

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  • How to analyse variants using the cancer database tracks.
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  • How to analyze variants using the cancer database tracks.
  • The main tracks: CIViC, COSMIC, ClinVar, TCGA (somatic) and GenCC, OMIM, gnomAD (germline).
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  • A running example throughout: BRAF V600E, the well-known melanoma driver.
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  • A running example: BRAF V600E, the well-known melanoma driver.
  • Where each database fits when you ask “is this variant real, and does it matter?”
Two kinds of question We split the databases into somatic (acquired, in cancer) and germline (inherited) diagnosis.

Where the cancer data lives

The key datasets and what each is good for. Click a name for its track description page.

Clinical & cancer databases

  • ClinVar: archive of lab and expert-panel variant classifications. Is it already called pathogenic, benign, or VUS (and now its somatic oncogenicity)?
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  • COSMIC: catalogue of somatic mutations in cancer. Shows how recurrently a site is mutated across tumours, flagging likely drivers.
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  • COSMIC: catalog of somatic mutations in cancer. Shows how recurrently a site is mutated across tumors, flagging likely drivers.
  • CIViC: crowd-sourced, expert-curated clinical interpretations. Is the variant oncogenic and linked to a therapy?
  • GenCC: curated gene-disease validity with evidence strength. Is the gene genuinely tied to a heritable disease?
  • OMIM: genes and Mendelian phenotypes. The reference for known gene-disease relationships and disease alleles.

Population frequency & evidence

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  • TCGA Pan-Cancer: somatic mutations across ~10,000 tumours of many types, drawn as a lollipop. Shows recurrence and hotspots by cancer type.
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  • TCGA Pan-Cancer: somatic mutations across ~10,000 tumors of many types, drawn as a lollipop. Shows recurrence and hotspots by cancer type.
  • gnomAD: population allele frequencies from large healthy cohorts. Common implies benign, and it filters germline variants out of somatic calls.
  • UniProt: protein domains and key residues. Does the variant fall in a functional region (ACMG PM1)?
  • REVEL: ensemble missense pathogenicity score (0 to 1). High values support a damaging computational call (PP3).
  • Conservation (100-way): cross-species constraint. Conserved positions are more likely functionally important.

Somatic diagnosis

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CIViC: the evidence behind each call

Clicking an Evidence ID opens its detailed evidence record
Click an Evidence ID (EID) in the list to open its full evidence record.

Each disease and therapy links to Evidence Items (EIDs); each EID cites the supporting publication and rates its strength: the “show me the evidence” layer behind actionability.

COSMIC: Catalogue of Somatic Mutations in Cancer

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  • The reference catalogue of somatic mutations seen across tumours.
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  • The reference catalog of somatic mutations seen across tumors.
  • Shows how recurrently a position is mutated, and in which cancer types.
  • Best for: spotting recurrent hotspots and likely drivers.
Try it, ▶ open COSMIC at the BRAF hotspot The V600 hotspot stands out by recurrence.
COSMIC track in the Genome Browser
COSMIC in the Browser: recurrent somatic mutations across cancer types.
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ClinVar: variant-disease classifications

  • Public archive of submitted clinical classifications, pathogenic to benign, with review status.
  • Increasingly carries somatic oncogenicity and clinical-impact calls.
  • Click a variant for its interpretation and submitters.
Try it, ▶ open the BRAF ClinVar interpretation track - Variants coloured by clinical significance.
+ Variants colored by clinical significance.
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ClinVar track across a gene
The ClinVar track across a gene, coloured by clinical significance.
ClinVar at BRAF V600E
At BRAF V600E: pathogenic submissions (T>A).
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ClinVar track across a gene
The ClinVar track across a gene, colored by clinical significance.
ClinVar at BRAF V600E
At BRAF V600E: pathogenic submissions (T>A).

ClinVar database link

Clicking a ClinVar interp item in the Browser opens its full ClinVar record
Click a variant in the ClinVar interp track for its details page, then follow the link out to the variant's full record on ClinVar.

TCGA Pan-Cancer

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TCGA lollipop track, with a click to a variant's mouse-over and details page +
TCGA lollipop track, with a click to a variant's mouse-over and details page
Lollipop track of somatic mutations; click a lollipop for its mouse-over and the item details (here C>T, seen in 38 samples).
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  • Somatic variants across thousands of tumours and many cancer types; useful for variant frequency by cancer type.
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  • Somatic variants across thousands of tumors and many cancer types; useful for variant frequency by cancer type.
  • Drawn as a lollipop plot; mouse-over identifies the variant and its sample count.
COSMIC vs TCGA - Both show recurrence. TCGA is one uniform cohort with comparable, by-cancer-type frequencies; COSMIC is the broader aggregate catalogue (bigger counts plus the driver Census), but heterogeneous.
+ Both show recurrence. TCGA is one uniform cohort with comparable, by-cancer-type frequencies; COSMIC is the broader aggregate catalog (bigger counts plus the driver Census), but heterogeneous.
Try it, ▶ open TCGA Pan-Cancer at BRAF
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Germline diagnosis

Germline variants

inherited disease: gene-level validity and population frequency

GenCC: the Gene Curation Coalition

GenCC track in the Genome Browser -
The GenCC track: gene-disease links coloured by evidence strength.
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The GenCC track: gene-disease links colored by evidence strength.
Try it, ▶ open the GenCC BRAF session - The gene-disease links for BRAF, coloured by evidence.
- + The gene-disease links for BRAF, colored by evidence. +

GenCC: click through to the source

Clicking a GenCC feature opens its details, with a link to the GenCC page
Click a feature for its details, then follow the boxed link straight to the GenCC page for the gene.

OMIM: Online Mendelian Inheritance in Man

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  • The classic catalogue of human genes and their phenotypes.
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  • The classic catalog of human genes and their phenotypes.
  • Mostly inherited disease; well-known genes (e.g. BRAF) can list somatic phenotypes too.
  • Covers whole-gene phenotype links and specific alleles.
OMIM vs GenCC OMIM gives per-gene depth (narrative biology and specific disease alleles); GenCC gives the standardized gene-disease validity tier and is fed partly by OMIM.
Try it, ▶ open OMIM at BRAF
OMIM information in the Genome Browser
OMIM in the Browser: gene-phenotype relationships and known disease alleles.

gnomAD: Genome Aggregation Database

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  • Help → Interactive Tutorials, or the docs at genome.ucsc.edu/docs.
  • Email the team: genome@soe.ucsc.edu.

    • Thank you!

    Questions? · genome@soe.ucsc.edu

    UCSC Genome Browser · genome.ucsc.edu

    UCSC Genome Browser team
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