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-<h1 id="atr">ATR</h1>
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-<h2 id="history">History</h2>
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-<p>Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.</p>
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-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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-timeline
373
- title Publication timing
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- 2017-10-10 : Reddy : DLBCL
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-</div></code></pre>
376
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">Tier</th>
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-<th>Description</th>
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-</tr>
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-</thead>
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-<tbody>
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-<tr>
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-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
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-<td style="text-align:center">2</td>
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-<td>relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]</td>
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-</tr>
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-</tbody>
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-</table>
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-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">source</th>
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-<th style="text-align:center">frequency (%)</th>
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-</tr>
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-</thead>
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-<tbody>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">GAMBL genomes</td>
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-<td style="text-align:center">2.68</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">Schmitz cohort</td>
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-<td style="text-align:center">4.89</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">Reddy cohort</td>
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-<td style="text-align:center">2.80</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">Chapuy cohort</td>
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-<td style="text-align:center">3.85</td>
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-</tr>
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-</tbody>
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-</table>
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-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
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-<table>
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-<thead>
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-<tr>
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-<th style="text-align:center">Entity</th>
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-<th style="text-align:center">aSHM</th>
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-<th style="text-align:center">Significant selection</th>
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-<th style="text-align:center">dN/dS (missense)</th>
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-<th style="text-align:center">dN/dS (nonsense)</th>
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-</tr>
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-</thead>
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-<tbody>
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-<tr>
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-<td style="text-align:center">BL</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">0.459</td>
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-<td style="text-align:center">0.000</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">No</td>
448
-<td style="text-align:center">1.146</td>
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-<td style="text-align:center">3.261</td>
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-</tr>
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-<tr>
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-<td style="text-align:center">FL</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">No</td>
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-<td style="text-align:center">0.000</td>
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-<td style="text-align:center">0.000</td>
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-</tr>
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-</tbody>
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-</table>
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-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR_protein_hg38.html">hg38</a></p>
461
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ATR_NM_001184.svg" alt=""></p>
462
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR_hg38.html">hg38</a></p>
463
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ATR.svg" alt=""></p>
464
-<h2 id="atr-expression">ATR Expression</h2>
465
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ATR_by_pathology.svg" alt=""></p>
466
-<h2 id="representative-mutations">Representative Mutations</h2>
467
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Reddy_ATR_1.svg" alt="">
468
-<strong>Rating</strong>
469
-★ ★ ★ ★ ★</p>
470
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Reddy_ATR_2.svg" alt="">
471
-<strong>Rating</strong>
472
-★ ★ ☆ ☆ ☆</p>
473
-<h2 id="all-mutations">All Mutations</h2>
474
-<p><a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2121T.html">Reddy_2121T</a>
475
-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2150T.html">Reddy_2150T</a>
476
-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2163T.html">Reddy_2163T</a>
477
-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2192T.html">Reddy_2192T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2195T.html">Reddy_2195T</a>
479
-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2206T.html">Reddy_2206T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2236T.html">Reddy_2236T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2475T.html">Reddy_2475T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2476T.html">Reddy_2476T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2585T.html">Reddy_2585T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2594T.html">Reddy_2594T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2758T.html">Reddy_2758T</a>
486
-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2768T.html">Reddy_2768T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2775T.html">Reddy_2775T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2779T.html">Reddy_2779T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2805T.html">Reddy_2805T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2828T.html">Reddy_2828T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2838T.html">Reddy_2838T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2898T.html">Reddy_2898T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2933T.html">Reddy_2933T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2947T.html">Reddy_2947T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3384T.html">Reddy_3384T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3385T.html">Reddy_3385T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3405T.html">Reddy_3405T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3489T.html">Reddy_3489T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3502T.html">Reddy_3502T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3520T.html">Reddy_3520T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3548T.html">Reddy_3548T</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3549T.html">Reddy_3549T</a>
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-<h1 id="bach2">BACH2</h1>
369
-<h2 id="history">History</h2>
370
-<p>Mutations in this gene were first described in BL in 2019 by Grande et al.<sup>1</sup></p>
371
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
372
-timeline
373
- title Publication timing
374
- 2019-03-21 : Grande : BL
375
-</div></code></pre>
376
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
377
-<table>
378
-<thead>
379
-<tr>
380
-<th style="text-align:center">Entity</th>
381
-<th style="text-align:center">Tier</th>
382
-<th>Description</th>
383
-</tr>
384
-</thead>
385
-<tbody>
386
-<tr>
387
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
388
-<td style="text-align:center">2-a</td>
389
-<td>aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@grandeGenomewideDiscoverySomatic2019]</td>
390
-</tr>
391
-</tbody>
392
-</table>
393
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
394
-<table>
395
-<thead>
396
-<tr>
397
-<th style="text-align:center">Entity</th>
398
-<th style="text-align:center">source</th>
399
-<th style="text-align:center">frequency (%)</th>
400
-</tr>
401
-</thead>
402
-<tbody>
403
-<tr>
404
-<td style="text-align:center">BL</td>
405
-<td style="text-align:center">GAMBL genomes+capture</td>
406
-<td style="text-align:center">1.85</td>
407
-</tr>
408
-<tr>
409
-<td style="text-align:center">BL</td>
410
-<td style="text-align:center">Thomas cohort</td>
411
-<td style="text-align:center">0.40</td>
412
-</tr>
413
-<tr>
414
-<td style="text-align:center">BL</td>
415
-<td style="text-align:center">Panea cohort</td>
416
-<td style="text-align:center">5.00</td>
417
-</tr>
418
-</tbody>
419
-</table>
420
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
421
-<table>
422
-<thead>
423
-<tr>
424
-<th style="text-align:center">Entity</th>
425
-<th style="text-align:center">aSHM</th>
426
-<th style="text-align:center">Significant selection</th>
427
-<th style="text-align:center">dN/dS (missense)</th>
428
-<th style="text-align:center">dN/dS (nonsense)</th>
429
-</tr>
430
-</thead>
431
-<tbody>
432
-<tr>
433
-<td style="text-align:center">BL</td>
434
-<td style="text-align:center">Yes</td>
435
-<td style="text-align:center">No</td>
436
-<td style="text-align:center">0.652</td>
437
-<td style="text-align:center">0.000</td>
438
-</tr>
439
-<tr>
440
-<td style="text-align:center">DLBCL</td>
441
-<td style="text-align:center">Yes</td>
442
-<td style="text-align:center">No</td>
443
-<td style="text-align:center">0.949</td>
444
-<td style="text-align:center">0.000</td>
445
-</tr>
446
-<tr>
447
-<td style="text-align:center">FL</td>
448
-<td style="text-align:center">Yes</td>
449
-<td style="text-align:center">No</td>
450
-<td style="text-align:center">0.000</td>
451
-<td style="text-align:center">28.997</td>
452
-</tr>
453
-</tbody>
454
-</table>
455
-<h2 id="ashm-regions">aSHM regions</h2>
456
-<table>
457
-<thead>
458
-<tr>
459
-<th style="text-align:center">chr_name</th>
460
-<th style="text-align:center">hg19_start</th>
461
-<th style="text-align:center">hg19_end</th>
462
-<th style="text-align:center">region</th>
463
-<th style="text-align:center">regulatory_comment</th>
464
-</tr>
465
-</thead>
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-<tbody>
467
-<tr>
468
-<td style="text-align:center">chr6</td>
469
-<td style="text-align:center">90981034</td>
470
-<td style="text-align:center">91016134</td>
471
-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134">TSS</a></td>
472
-<td style="text-align:center">NA</td>
473
-</tr>
474
-</tbody>
475
-</table>
476
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein_hg38.html">hg38</a></p>
477
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BACH2_NM_021813.svg" alt=""></p>
478
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2_hg38.html">hg38</a></p>
479
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BACH2.svg" alt=""></p>
480
-<h2 id="bach2-expression">BACH2 Expression</h2>
481
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BACH2_by_pathology.svg" alt=""></p>
482
-<h2 id="references">References</h2>
483
-<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
484
-<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
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-<h1 id="birc3">BIRC3</h1>
369
-<h2 id="history">History</h2>
370
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
-timeline
372
- title Publication timing
373
- 2011-11-03 : Rossi : MZL
374
- 2013-11-05 : Be : MCL
375
- 2018-10-01 : Arthur : DLBCL
376
- 2021-07-15 : Duns : PMBL
377
-</div></code></pre>
378
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
379
-<table>
380
-<thead>
381
-<tr>
382
-<th style="text-align:center">Entity</th>
383
-<th style="text-align:center">Tier</th>
384
-<th>Description</th>
385
-</tr>
386
-</thead>
387
-<tbody>
388
-<tr>
389
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/PMBL_tier2.png" alt="PMBL"></td>
390
-<td style="text-align:center">2</td>
391
-<td>relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]</td>
392
-</tr>
393
-<tr>
394
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/MZL_tier1.png" alt="MZL"></td>
395
-<td style="text-align:center">1</td>
396
-<td>high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]</td>
397
-</tr>
398
-<tr>
399
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
400
-<td style="text-align:center">2-a</td>
401
-<td>aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]</td>
402
-</tr>
403
-<tr>
404
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/MCL_tier1.png" alt="MCL"></td>
405
-<td style="text-align:center">1-a</td>
406
-<td>aSHM target and high-confidence MCL gene [@beaLandscapeSomaticMutations2013]</td>
407
-</tr>
408
-</tbody>
409
-</table>
410
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
411
-<table>
412
-<thead>
413
-<tr>
414
-<th style="text-align:center">Entity</th>
415
-<th style="text-align:center">source</th>
416
-<th style="text-align:center">frequency (%)</th>
417
-</tr>
418
-</thead>
419
-<tbody>
420
-<tr>
421
-<td style="text-align:center">DLBCL</td>
422
-<td style="text-align:center">GAMBL genomes</td>
423
-<td style="text-align:center">1.53</td>
424
-</tr>
425
-<tr>
426
-<td style="text-align:center">DLBCL</td>
427
-<td style="text-align:center">Schmitz cohort</td>
428
-<td style="text-align:center">1.91</td>
429
-</tr>
430
-<tr>
431
-<td style="text-align:center">DLBCL</td>
432
-<td style="text-align:center">Reddy cohort</td>
433
-<td style="text-align:center">1.30</td>
434
-</tr>
435
-<tr>
436
-<td style="text-align:center">DLBCL</td>
437
-<td style="text-align:center">Chapuy cohort</td>
438
-<td style="text-align:center">1.71</td>
439
-</tr>
440
-<tr>
441
-<td style="text-align:center">MCL</td>
442
-<td style="text-align:center">GAMBL genomes</td>
443
-<td style="text-align:center">7.11</td>
444
-</tr>
445
-</tbody>
446
-</table>
447
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
448
-<table>
449
-<thead>
450
-<tr>
451
-<th style="text-align:center">Entity</th>
452
-<th style="text-align:center">aSHM</th>
453
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454
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455
-<th style="text-align:center">dN/dS (nonsense)</th>
456
-</tr>
457
-</thead>
458
-<tbody>
459
-<tr>
460
-<td style="text-align:center">BL</td>
461
-<td style="text-align:center">Yes</td>
462
-<td style="text-align:center">No</td>
463
-<td style="text-align:center">0.000</td>
464
-<td style="text-align:center">0</td>
465
-</tr>
466
-<tr>
467
-<td style="text-align:center">DLBCL</td>
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-<td style="text-align:center">Yes</td>
469
-<td style="text-align:center">No</td>
470
-<td style="text-align:center">1.404</td>
471
-<td style="text-align:center">0</td>
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-</tr>
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475
-<td style="text-align:center">Yes</td>
476
-<td style="text-align:center">No</td>
477
-<td style="text-align:center">2.427</td>
478
-<td style="text-align:center">0</td>
479
-</tr>
480
-</tbody>
481
-</table>
482
-<h2 id="ashm-regions">aSHM regions</h2>
483
-<table>
484
-<thead>
485
-<tr>
486
-<th style="text-align:center">chr_name</th>
487
-<th style="text-align:center">hg19_start</th>
488
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490
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496
-<td style="text-align:center">102188170</td>
497
-<td style="text-align:center">102190077</td>
498
-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A102188170%2D102190077">TSS</a></td>
499
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500
-</tr>
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-</tbody>
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-</table>
503
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3_protein_hg38.html">hg38</a></p>
504
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BIRC3_NM_001165.svg" alt=""></p>
505
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3_hg38.html">hg38</a></p>
506
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BIRC3.svg" alt=""></p>
507
-<h2 id="birc3-expression">BIRC3 Expression</h2>
508
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BIRC3_by_pathology.svg" alt=""></p>
509
-<!-- ORIGIN: rossiAlterationBIRC3Multiple2011a -->
510
-<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
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512
-<!-- MCL: beaLandscapeSomaticMutations2013 -->
513
-<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
514
-<h2 id="references">References</h2>
515
-
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-<h2 id="history">History</h2>
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-timeline
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- title Publication timing
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- 2012-12-01 : Love : BL
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-</div></code></pre>
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-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
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-<thead>
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-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4_protein_hg38.html">hg38</a></p>
422
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4_hg38.html">hg38</a></p>
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-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CARD4.svg" alt=""></p>
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-<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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-<!-- BL: loveGeneticLandscapeMutations2012 -->
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-<h2 id="representative-mutations">Representative Mutations</h2>
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-<strong>Rating</strong>
429
-★ ★ ★ ★ ☆</p>
430
-<h2 id="all-mutations">All Mutations</h2>
431
-<p><a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/1092_reports.html">1092</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/674_reports.html">674</a>
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-<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html">747</a></p>
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-<h2 id="references">References</h2>
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-<h1 id="gpc5">GPC5</h1>
369
-<h2 id="history">History</h2>
370
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
-timeline
372
- title Publication timing
373
- 2018-04-12 : Schmitz : DLBCL
374
-</div></code></pre>
375
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
376
-<table>
377
-<thead>
378
-<tr>
379
-<th style="text-align:center">Entity</th>
380
-<th style="text-align:center">Tier</th>
381
-<th>Description</th>
382
-</tr>
383
-</thead>
384
-<tbody>
385
-<tr>
386
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
387
-<td style="text-align:center">2</td>
388
-<td>relevance in DLBCL not firmly established[@schmitzGeneticsPathogenesisDiffuse2018a]</td>
389
-</tr>
390
-</tbody>
391
-</table>
392
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
393
-<table>
394
-<thead>
395
-<tr>
396
-<th style="text-align:center">Entity</th>
397
-<th style="text-align:center">source</th>
398
-<th style="text-align:center">frequency (%)</th>
399
-</tr>
400
-</thead>
401
-<tbody>
402
-<tr>
403
-<td style="text-align:center">DLBCL</td>
404
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405
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406
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407
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409
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410
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411
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412
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414
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415
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416
-</tr>
417
-<tr>
418
-<td style="text-align:center">DLBCL</td>
419
-<td style="text-align:center">Chapuy cohort</td>
420
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421
-</tr>
422
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-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
425
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426
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432
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439
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440
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441
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446
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447
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448
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453
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454
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456
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-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5_protein_hg38.html">hg38</a></p>
460
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/GPC5_NM_004466.svg" alt=""></p>
461
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5_hg38.html">hg38</a></p>
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-<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
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370
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371
-timeline
372
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373
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374
- 2019-09-26 : Panea : BL
375
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376
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
377
-<table>
378
-<thead>
379
-<tr>
380
-<th style="text-align:center">Entity</th>
381
-<th style="text-align:center">Tier</th>
382
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383
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384
-</thead>
385
-<tbody>
386
-<tr>
387
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/PMBL_tier2.png" alt="PMBL"></td>
388
-<td style="text-align:center">2</td>
389
-<td>relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019b]</td>
390
-</tr>
391
-<tr>
392
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
393
-<td style="text-align:center">2</td>
394
-<td>relevance in BL not firmly established[@paneaWholeGenomeLandscape2019]</td>
395
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396
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397
-</table>
398
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
399
-<table>
400
-<thead>
401
-<tr>
402
-<th style="text-align:center">Entity</th>
403
-<th style="text-align:center">source</th>
404
-<th style="text-align:center">frequency (%)</th>
405
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406
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407
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408
-<tr>
409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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425
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426
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427
-<thead>
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-<tr>
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430
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431
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432
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433
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440
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441
-<td style="text-align:center">0.955</td>
442
-<td style="text-align:center">0</td>
443
-</tr>
444
-<tr>
445
-<td style="text-align:center">DLBCL</td>
446
-<td style="text-align:center">No</td>
447
-<td style="text-align:center">No</td>
448
-<td style="text-align:center">1.504</td>
449
-<td style="text-align:center">0</td>
450
-</tr>
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-<td style="text-align:center">FL</td>
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454
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456
-<td style="text-align:center">0</td>
457
-</tr>
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-</tbody>
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-</table>
460
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J_protein_hg38.html">hg38</a></p>
461
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/HIST1H4J_NM_021968.svg" alt=""></p>
462
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J_hg38.html">hg38</a></p>
463
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/HIST1H4J.svg" alt=""></p>
464
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465
-<h3 id="blsup2sup">BL<sup>2</sup></h3>
466
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Panea_HIST1H4J.svg" alt="">
467
-<strong>Rating</strong>
468
-★ ★ ★ ☆ ☆</p>
469
-<h2 id="references">References</h2>
470
-<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
471
-<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
472
-<!-- BL: paneaWholeGenomeLandscape2019 -->
473
-<!-- BL: paneaWholeGenomeLandscape2019 -->
474
-
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-</body>
476
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-<h1 id="nlrp8">NLRP8</h1>
369
-<h2 id="history">History</h2>
370
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
-timeline
372
- title Publication timing
373
- 2018-05-01 : Chapuy : DLBCL
374
-</div></code></pre>
375
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
376
-<table>
377
-<thead>
378
-<tr>
379
-<th style="text-align:center">Entity</th>
380
-<th style="text-align:center">Tier</th>
381
-<th>Description</th>
382
-</tr>
383
-</thead>
384
-<tbody>
385
-<tr>
386
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
387
-<td style="text-align:center">2</td>
388
-<td>relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]</td>
389
-</tr>
390
-</tbody>
391
-</table>
392
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
393
-<table>
394
-<thead>
395
-<tr>
396
-<th style="text-align:center">Entity</th>
397
-<th style="text-align:center">source</th>
398
-<th style="text-align:center">frequency (%)</th>
399
-</tr>
400
-</thead>
401
-<tbody>
402
-<tr>
403
-<td style="text-align:center">DLBCL</td>
404
-<td style="text-align:center">GAMBL genomes</td>
405
-<td style="text-align:center">0.38</td>
406
-</tr>
407
-<tr>
408
-<td style="text-align:center">DLBCL</td>
409
-<td style="text-align:center">Schmitz cohort</td>
410
-<td style="text-align:center">3.40</td>
411
-</tr>
412
-<tr>
413
-<td style="text-align:center">DLBCL</td>
414
-<td style="text-align:center">Reddy cohort</td>
415
-<td style="text-align:center">2.10</td>
416
-</tr>
417
-<tr>
418
-<td style="text-align:center">DLBCL</td>
419
-<td style="text-align:center">Chapuy cohort</td>
420
-<td style="text-align:center">3.42</td>
421
-</tr>
422
-</tbody>
423
-</table>
424
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
425
-<table>
426
-<thead>
427
-<tr>
428
-<th style="text-align:center">Entity</th>
429
-<th style="text-align:center">aSHM</th>
430
-<th style="text-align:center">Significant selection</th>
431
-<th style="text-align:center">dN/dS (missense)</th>
432
-<th style="text-align:center">dN/dS (nonsense)</th>
433
-</tr>
434
-</thead>
435
-<tbody>
436
-<tr>
437
-<td style="text-align:center">BL</td>
438
-<td style="text-align:center">No</td>
439
-<td style="text-align:center">No</td>
440
-<td style="text-align:center">2.456</td>
441
-<td style="text-align:center">7.316</td>
442
-</tr>
443
-<tr>
444
-<td style="text-align:center">DLBCL</td>
445
-<td style="text-align:center">No</td>
446
-<td style="text-align:center">No</td>
447
-<td style="text-align:center">2.731</td>
448
-<td style="text-align:center">0.000</td>
449
-</tr>
450
-<tr>
451
-<td style="text-align:center">FL</td>
452
-<td style="text-align:center">No</td>
453
-<td style="text-align:center">No</td>
454
-<td style="text-align:center">0.000</td>
455
-<td style="text-align:center">0.000</td>
456
-</tr>
457
-</tbody>
458
-</table>
459
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/NLRP8_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/NLRP8_protein_hg38.html">hg38</a></p>
460
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/NLRP8_NM_176811.svg" alt=""></p>
461
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/NLRP8.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/NLRP8_hg38.html">hg38</a></p>
462
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/NLRP8.svg" alt=""></p>
463
-<h2 id="nlrp8-expression">NLRP8 Expression</h2>
464
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/NLRP8_by_pathology.svg" alt=""></p>
465
-<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
466
-<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
467
-<h2 id="references">References</h2>
468
-
469
-</body>
470
-</html>
TIGD6.md
... ...
@@ -5,6 +5,8 @@ link-citations: true
5 5
---
6 6
# TIGD6
7 7
8
+<<Warn("The variants reported in this gene failed QC")>>
9
+
8 10
## History
9 11
```mermaid
10 12
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -17,7 +19,7 @@ timeline
17 19
18 20
|Entity|Tier|Description |
19 21
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
22
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
21 23
22 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 25
TPST2.md
... ...
@@ -5,6 +5,8 @@ link-citations: true
5 5
---
6 6
# TPST2
7 7
8
+<<Warn("The variants reported in this gene failed QC")>>
9
+
8 10
## History
9 11
```mermaid
10 12
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -17,7 +19,7 @@ timeline
17 19
18 20
|Entity|Tier|Description |
19 21
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
22
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
21 23
22 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 25
ZNF229.md
... ...
@@ -7,6 +7,7 @@ link-citations: true
7 7
8 8
Due to [minimal support](ZNF229#representative-mutation) in the original primary data, [low expression in BL](ZNF229#znf229-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL.
9 9
10
+<<Warn("The variants reported in this gene failed QC")>>
10 11
11 12
## History
12 13
```mermaid
... ...
@@ -20,7 +21,7 @@ timeline
20 21
21 22
|Entity|Tier|Description |
22 23
|:------:|:----:|--------------------------------------|
23
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
24
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
24 25
25 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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