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 @@ <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>UCSC Genome Browser · Tutorial 2: Cancer Data</title> -<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/reveal.js@5.1.0/dist/reveal.css"> -<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/reveal.js@5.1.0/dist/theme/white.css" id="theme"> +<link rel="stylesheet" href="../../reveal.js/dist/reveal.css"> +<link rel="stylesheet" href="../../reveal.js/dist/theme/white.css" id="theme"> <style> :root{ --ucsc-blue:#1f3a5f; --ucsc-accent:#0b5394; --ucsc-gold:#e6a817; } .reveal { font-size: 32px; } .reveal h1,.reveal h2,.reveal h3 { color: var(--ucsc-blue); text-transform:none; letter-spacing:normal; } .reveal h1 { font-size: 1.9em; } .reveal h2 { font-size: 1.32em; } .reveal section img { border:none; box-shadow:none; } .reveal a { color: var(--ucsc-accent); } .reveal ul { width: 100%; box-sizing: border-box; } .reveal li { margin: 0.16em 0; } @@ -78,64 +78,64 @@ font-size:0.62em; font-weight:700; box-shadow:0 1px 4px rgba(0,0,0,.4); } .navkey { font-size:0.64em; text-align:left; gap:1.6em; } .navkey p { margin:0.22em 0; } .navkey .keybadge { display:inline-block; width:1.5em; height:1.5em; line-height:1.5em; text-align:center; background:var(--ucsc-blue); color:#fff; border-radius:50%; font-weight:700; margin-right:0.35em; } </style> </head> <body> <div class="reveal"> <div class="footer">UCSC Genome Browser · Tutorial 2: Cancer Data</div> <div class="slides"> <section class="divider" data-background-color="#1f3a5f"> <p class="kicker">UCSC Genome Browser · Tutorial 2</p> <h1>Cancer Data</h1> - <h2 style="color:#fff;font-weight:400;">The cancer & clinical databases, worked on BRAF V600E</h2> + <h2 style="color:#fff;font-weight:400;">The cancer & clinical databases, a worked BRAF V600E example</h2> <p class="timing">A hands-on tour of the oncology tracks · genome.ucsc.edu</p> </section> <section> <h2>What we'll cover</h2> <ul class="small"> - <li>How to analyse variants using the <strong>cancer database tracks</strong>.</li> + <li>How to analyze variants using the <strong>cancer database tracks</strong>.</li> <li>The main tracks: <strong>CIViC, COSMIC, ClinVar, TCGA</strong> (somatic) and <strong>GenCC, OMIM, gnomAD</strong> (germline).</li> - <li>A running example throughout: <strong>BRAF V600E</strong>, the well-known melanoma driver.</li> + <li>A running example: <strong>BRAF V600E</strong>, the well-known melanoma driver.</li> <li>Where each database fits when you ask “is this variant real, and does it matter?”</li> </ul> <div class="callout demo"><span class="lbl">Two kinds of question</span> We split the databases into <strong>somatic</strong> (acquired, in cancer) and <strong>germline</strong> (inherited) diagnosis.</div> </section> <section> <h2>Where the cancer data lives</h2> <p class="small">The key datasets and what each is good for. Click a name for its track description page.</p> <div class="twocol"> <div> <p class="small"><strong>Clinical & cancer databases</strong></p> <ul class="small"> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinvar">ClinVar</a>: archive of lab and expert-panel variant classifications. Is it already called pathogenic, benign, or VUS (and now its somatic oncogenicity)?</li> - <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cosmicRegions">COSMIC</a>: catalogue of somatic mutations in cancer. Shows how recurrently a site is mutated across tumours, flagging likely drivers.</li> + <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cosmicRegions">COSMIC</a>: catalog of somatic mutations in cancer. Shows how recurrently a site is mutated across tumors, flagging likely drivers.</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=civic">CIViC</a>: crowd-sourced, expert-curated clinical interpretations. Is the variant oncogenic and linked to a therapy?</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=genCC">GenCC</a>: curated gene-disease validity with evidence strength. Is the gene genuinely tied to a heritable disease?</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=omimGene2">OMIM</a>: genes and Mendelian phenotypes. The reference for known gene-disease relationships and disease alleles.</li> </ul> </div> <div> <p class="small"><strong>Population frequency & evidence</strong></p> <ul class="small"> - <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gdcCancer">TCGA Pan-Cancer</a>: somatic mutations across ~10,000 tumours of many types, drawn as a lollipop. Shows recurrence and hotspots by cancer type.</li> + <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gdcCancer">TCGA Pan-Cancer</a>: somatic mutations across ~10,000 tumors of many types, drawn as a lollipop. Shows recurrence and hotspots by cancer type.</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants">gnomAD</a>: population allele frequencies from large healthy cohorts. Common implies benign, and it filters germline variants out of somatic calls.</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=uniprot">UniProt</a>: protein domains and key residues. Does the variant fall in a functional region (ACMG PM1)?</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=revel">REVEL</a>: ensemble missense pathogenicity score (0 to 1). High values support a damaging computational call (PP3).</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cons100way">Conservation</a> (100-way): cross-species constraint. Conserved positions are more likely functionally important.</li> </ul> </div> </div> <aside class="notes"> Frame the two relevant groups. This section is about the datasets themselves; the NEXT section shows the curated sets that combine them. Name-drop each database briefly; we click through them on BRAF V600E next. </aside> </section> <section class="divider" data-background-color="#0b5394"> <p class="kicker">Somatic diagnosis</p> @@ -177,113 +177,113 @@ </section> <section> <h2>CIViC: the evidence behind each call</h2> <figure class="fig"><img class="shotbig" src="/images/slideDecks/tutorial2-cancer/civic_evidence_annot.png" alt="Clicking an Evidence ID opens its detailed evidence record"> <figcaption class="capbig">Click an Evidence ID (EID) in the list to open its full evidence record.</figcaption></figure> <p class="small" style="text-align:center;max-width:80%;margin:0.5em auto 0;">Each disease and therapy links to <strong>Evidence Items (EIDs)</strong>; each EID cites the supporting publication and rates its strength: the “show me the evidence” layer behind actionability.</p> <aside class="notes">Drill into Evidence IDs (EIDs): the literature and evidence level behind each clinical claim.</aside> </section> <section> <h2>COSMIC: Catalogue of Somatic Mutations in Cancer</h2> <div class="split"> <div class="txt"> <ul class="small"> - <li>The reference catalogue of somatic mutations seen across tumours.</li> + <li>The reference catalog of somatic mutations seen across tumors.</li> <li>Shows how recurrently a position is mutated, and in which cancer types.</li> <li>Best for: spotting recurrent hotspots and likely drivers.</li> </ul> <div class="callout exercise"><span class="lbl">Try it, <a href="https://genome.ucsc.edu/s/Lou/cosmicBRAF">▶ open COSMIC at the BRAF hotspot</a></span> The V600 hotspot stands out by recurrence.</div> </div> <div class="figwrap"><figure class="fig"><img class="shot" src="/images/slideDecks/tutorial2-cancer/cosmic_track.png" alt="COSMIC track in the Genome Browser"><figcaption>COSMIC in the Browser: recurrent somatic mutations across cancer types.</figcaption></figure></div> </div> - <aside class="notes">COSMIC = recurrence catalogue of somatic mutations; the breadth tool for how often a site is hit in cancer.</aside> + <aside class="notes">COSMIC = recurrence catalog of somatic mutations; the breadth tool for how often a site is hit in cancer.</aside> </section> <section> <h2>ClinVar: variant-disease classifications</h2> <div class="split"> <div class="txt"> <ul class="small"> <li>Public archive of submitted clinical classifications, pathogenic to benign, with review status.</li> <li>Increasingly carries <strong>somatic</strong> oncogenicity and clinical-impact calls.</li> <li>Click a variant for its interpretation and submitters.</li> </ul> <div class="callout exercise"><span class="lbl">Try it, <a href="https://genome.ucsc.edu/s/Lou/clinvarInterp">▶ open the BRAF ClinVar interpretation track</a></span> - Variants coloured by clinical significance.</div> + Variants colored by clinical significance.</div> </div> - <div class="figwrap stack"><figure class="fig"><img class="shot" src="/images/slideDecks/tutorial2-cancer/clinvar_track.png" alt="ClinVar track across a gene"><figcaption>The ClinVar track across a gene, coloured by clinical significance.</figcaption></figure><figure class="fig"><img class="shot" src="/images/slideDecks/tutorial2-cancer/clinvar_braf.png" alt="ClinVar at BRAF V600E" style="width:auto;max-width:78%;margin:0.35em auto 0;"><figcaption>At BRAF V600E: pathogenic submissions (T>A).</figcaption></figure></div> + <div class="figwrap stack"><figure class="fig"><img class="shot" src="/images/slideDecks/tutorial2-cancer/clinvar_track.png" alt="ClinVar track across a gene"><figcaption>The ClinVar track across a gene, colored by clinical significance.</figcaption></figure><figure class="fig"><img class="shot" src="/images/slideDecks/tutorial2-cancer/clinvar_braf.png" alt="ClinVar at BRAF V600E" style="width:auto;max-width:78%;margin:0.35em auto 0;"><figcaption>At BRAF V600E: pathogenic submissions (T>A).</figcaption></figure></div> </div> <aside class="notes">ClinVar = aggregated lab and expert-panel classifications with star review status; now also somatic fields.</aside> </section> <section> <h2>ClinVar database link</h2> <figure class="fig"><img class="shotbig" src="/images/slideDecks/tutorial2-cancer/clinvar_link.png" alt="Clicking a ClinVar interp item in the Browser opens its full ClinVar record"> <figcaption class="capbig">Click a variant in the <strong>ClinVar interp</strong> track for its details page, then follow the link out to the variant's full record on ClinVar.</figcaption></figure> <aside class="notes">Show the click path on BRAF: the ClinVar interp item details page in the Browser links straight to the variant's ClinVar page at NCBI (VCV000013961).</aside> </section> <section> <h2>TCGA Pan-Cancer</h2> - <figure class="fig"><img class="shotbig" src="/images/slideDecks/tutorial2-cancer/tcga_annot.png" alt="TCGA lollipop track, with a click to a variant's mouse-over and details page"> + <figure class="fig"><img class="shotbig" style="max-height:38vh;" src="/images/slideDecks/tutorial2-cancer/tcga_annot.png" alt="TCGA lollipop track, with a click to a variant's mouse-over and details page"> <figcaption class="capbig">Lollipop track of somatic mutations; click a lollipop for its mouse-over and the item details (here C>T, seen in 38 samples).</figcaption></figure> <ul class="small" style="max-width:84%;margin:0.4em auto 0;text-align:left;"> - <li>Somatic variants across thousands of tumours and many cancer types; useful for <strong>variant frequency</strong> by cancer type.</li> + <li>Somatic variants across thousands of tumors and many cancer types; useful for <strong>variant frequency</strong> by cancer type.</li> <li>Drawn as a lollipop plot; mouse-over identifies the variant and its sample count.</li> </ul> <div class="callout caution" style="max-width:84%;margin:0.4em auto 0;font-size:0.64em;"><span class="lbl">COSMIC vs TCGA</span> - Both show recurrence. TCGA is <strong>one uniform cohort</strong> with comparable, by-cancer-type frequencies; COSMIC is the <strong>broader aggregate</strong> catalogue (bigger counts plus the driver Census), but heterogeneous.</div> + Both show recurrence. TCGA is <strong>one uniform cohort</strong> with comparable, by-cancer-type frequencies; COSMIC is the <strong>broader aggregate</strong> catalog (bigger counts plus the driver Census), but heterogeneous.</div> <div class="callout exercise" style="max-width:84%;margin:0.4em auto 0;"><span class="lbl">Try it, <a href="https://genome.ucsc.edu/s/Lou/TCGAbraf">▶ open TCGA Pan-Cancer at BRAF</a></span></div> - <aside class="notes">TCGA Pan-Cancer (via the NCI GDC): somatic variants across ~10,000 tumours, drawn as a lollipop; recurrence by cancer type. Click a lollipop for the mouse-over and item details (sample count, variant frequency).</aside> + <aside class="notes">TCGA Pan-Cancer (via the NCI GDC): somatic variants across ~10,000 tumors, drawn as a lollipop; recurrence by cancer type. Click a lollipop for the mouse-over and item details (sample count, variant frequency).</aside> </section> <section class="divider" data-background-color="#0b5394"> <p class="kicker">Germline diagnosis</p> <h1>Germline variants</h1> <p class="timing">inherited disease: gene-level validity and population frequency</p> </section> <section> <h2>GenCC: the Gene Curation Coalition</h2> <figure class="fig"><img class="shotbig" src="/images/slideDecks/tutorial2-cancer/gencc_track.png" alt="GenCC track in the Genome Browser"> - <figcaption class="capbig">The GenCC track: gene-disease links coloured by evidence strength.</figcaption></figure> + <figcaption class="capbig">The GenCC track: gene-disease links colored by evidence strength.</figcaption></figure> <ul class="small" style="max-width:84%;margin:0.4em auto 0;text-align:left;"> <li>Aggregates <strong>gene-disease validity</strong> from many expert groups.</li> <li>Germline / Mendelian focus: genes to inherited diseases, not specific variants or somatic mutations.</li> - <li>Colour = strength of the link (definitive, strong, moderate, limited); spans the whole gene, mouse-over for the curated detail.</li> + <li>Color = strength of the link (definitive, strong, moderate, limited); spans the whole gene, mouse-over for the curated detail.</li> </ul> <div class="callout exercise" style="max-width:84%;margin:0.4em auto 0;"><span class="lbl">Try it, <a href="https://genome.ucsc.edu/s/Lou/GenCCbraf">▶ open the GenCC BRAF session</a></span> - The gene-disease links for BRAF, coloured by evidence.</div> - <aside class="notes">GenCC = curated gene-disease validity (germline). Whole-gene features, colour by evidence strength. Not variant-specific or somatic.</aside> + The gene-disease links for BRAF, colored by evidence.</div> + <aside class="notes">GenCC = curated gene-disease validity (germline). Whole-gene features, color by evidence strength. Not variant-specific or somatic.</aside> </section> <section> <h2>GenCC: click through to the source</h2> <figure class="fig"><img class="shotbig" src="/images/slideDecks/tutorial2-cancer/gencc_click_annot.png" alt="Clicking a GenCC feature opens its details, with a link to the GenCC page"> <figcaption class="capbig">Click a feature for its details, then follow the boxed link straight to the GenCC page for the gene.</figcaption></figure> <aside class="notes">Same click path as CIViC: feature to details page to the external GenCC entry. The red box marks the link out to GenCC.</aside> </section> <section> <h2>OMIM: Online Mendelian Inheritance in Man</h2> <div class="split"> <div class="txt"> <ul class="small"> - <li>The classic catalogue of human genes and their phenotypes.</li> + <li>The classic catalog of human genes and their phenotypes.</li> <li>Mostly inherited disease; well-known genes (e.g. BRAF) can list somatic phenotypes too.</li> <li>Covers whole-gene phenotype links and specific alleles.</li> </ul> <div class="callout caution"><span class="lbl">OMIM vs GenCC</span> OMIM gives per-gene <strong>depth</strong> (narrative biology and specific disease alleles); GenCC gives the standardized gene-disease <strong>validity tier</strong> and is fed partly by OMIM.</div> <div class="callout exercise"><span class="lbl">Try it, <a href="https://genome.ucsc.edu/s/Lou/omimBraf">▶ open OMIM at BRAF</a></span></div> </div> <div class="figwrap"><figure class="fig"><img class="shot" src="/images/slideDecks/tutorial2-cancer/omim.png" alt="OMIM information in the Genome Browser"><figcaption>OMIM in the Browser: gene-phenotype relationships and known disease alleles.</figcaption></figure></div> </div> <aside class="notes">OMIM = genes and Mendelian phenotypes; the reference for gene-disease relationships and known alleles.</aside> </section> <section> <h2>gnomAD: Genome Aggregation Database</h2> <div class="split"> @@ -306,30 +306,30 @@ <li>Help → <strong>Interactive Tutorials</strong>, or the docs at <a href="https://genome.ucsc.edu/docs/">genome.ucsc.edu/docs</a>.</li> <li>Email the team: <strong>genome@soe.ucsc.edu</strong>.</li> </ul> </section> <section class="divider" data-background-color="#1f3a5f"> <h1 style="color:#fff;margin-bottom:0.12em;">Thank you!</h1> <p style="color:#fff;font-size:0.72em;margin:0.05em 0;">Questions? · genome@soe.ucsc.edu</p> <p style="color:#cdd9e8;font-size:0.55em;margin:0.05em 0 0.45em;">UCSC Genome Browser · genome.ucsc.edu</p> <figure class="fig" style="margin:0 auto;"><img src="/images/slideDecks/tutorial2-cancer/gb_team.jpg" alt="UCSC Genome Browser team" style="max-height:360px;width:auto;border-radius:8px;"></figure> </section> </div> </div> -<script src="https://cdn.jsdelivr.net/npm/reveal.js@5.1.0/dist/reveal.js"></script> -<script src="https://cdn.jsdelivr.net/npm/reveal.js@5.1.0/plugin/notes/notes.js"></script> +<script src="../../reveal.js/dist/reveal.js"></script> +<script src="../../reveal.js/plugin/notes/notes.js"></script> <script> Reveal.initialize({ hash: true, slideNumber: 'c/t', transition: 'fade', width: 1280, height: 800, margin: 0.06, plugins: [ RevealNotes ] }); </script> </body> </html>