ACAD9.md
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# ACAD9
2
-
2
+## History
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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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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+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
ARHGEF1_tmp.html
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+ </script>
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+<h1 id="arhgef1">ARHGEF1</h1>
369
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
370
+<table>
371
+<thead>
372
+<tr>
373
+<th style="text-align:center">Entity</th>
374
+<th style="text-align:center">Tier</th>
375
+<th>Description</th>
376
+</tr>
377
+</thead>
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+<tbody>
379
+<tr>
380
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
381
+<td style="text-align:center">2</td>
382
+<td>relevance in BL not firmly established</td>
383
+</tr>
384
+</tbody>
385
+</table>
386
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
387
+<table>
388
+<thead>
389
+<tr>
390
+<th style="text-align:center">Entity</th>
391
+<th style="text-align:center">source</th>
392
+<th style="text-align:center">frequency (%)</th>
393
+</tr>
394
+</thead>
395
+<tbody>
396
+<tr>
397
+<td style="text-align:center">BL</td>
398
+<td style="text-align:center">GAMBL genomes+capture</td>
399
+<td style="text-align:center">3.93</td>
400
+</tr>
401
+<tr>
402
+<td style="text-align:center">BL</td>
403
+<td style="text-align:center">Thomas cohort</td>
404
+<td style="text-align:center">2.00</td>
405
+</tr>
406
+<tr>
407
+<td style="text-align:center">BL</td>
408
+<td style="text-align:center">Panea cohort</td>
409
+<td style="text-align:center">NA</td>
410
+</tr>
411
+</tbody>
412
+</table>
413
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
414
+<table>
415
+<thead>
416
+<tr>
417
+<th style="text-align:center">Entity</th>
418
+<th style="text-align:center">aSHM</th>
419
+<th style="text-align:center">Significant selection</th>
420
+<th style="text-align:center">dN/dS (missense)</th>
421
+<th style="text-align:center">dN/dS (nonsense)</th>
422
+</tr>
423
+</thead>
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+<tbody>
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+<tr>
426
+<td style="text-align:center">BL</td>
427
+<td style="text-align:center">No</td>
428
+<td style="text-align:center">No</td>
429
+<td style="text-align:center">2.954</td>
430
+<td style="text-align:center">0.000</td>
431
+</tr>
432
+<tr>
433
+<td style="text-align:center">DLBCL</td>
434
+<td style="text-align:center">No</td>
435
+<td style="text-align:center">No</td>
436
+<td style="text-align:center">2.662</td>
437
+<td style="text-align:center">9.372</td>
438
+</tr>
439
+<tr>
440
+<td style="text-align:center">FL</td>
441
+<td style="text-align:center">No</td>
442
+<td style="text-align:center">No</td>
443
+<td style="text-align:center">3.865</td>
444
+<td style="text-align:center">0.000</td>
445
+</tr>
446
+</tbody>
447
+</table>
448
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1_protein_hg38.html">hg38</a></p>
449
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARHGEF1_NM_199002.svg" alt="image"></p>
450
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ARHGEF1_hg38.html">hg38</a></p>
451
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARHGEF1.svg" alt="image"></p>
452
+<h2 id="arhgef1-expression">ARHGEF1 Expression</h2>
453
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ARHGEF1_by_pathology.svg" alt="image"></p>
454
+<!-- ORIGIN: muppidiLossSignalingGa132014b -->
455
+<!-- BL: muppidiLossSignalingGa132014b -->
456
+<h2 id="references">References</h2>
457
+<ol>
458
+<li>Muppidi J, Schmitz R, Green JA, Green JA, Xiao W, Larsen AB, Braun S, An J, Xu Y, Rosenwald A, Ott G, Gascoyne R, Rimsza L, Campo E, Jaffe E, Delabie J, Smeland E, Braziel R, Tubbs R, Cook J, Weisenburger D, Chan W, Vaidehi N, Staudt L, Cyster J. Loss of signaling via Gα13 in germinal center B cell-derived lymphoma. Nature. 2014;516:254–258.</li>
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+</ol>
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+
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+</body>
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+</html>
BCL10_tmp.html
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- </script>
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-<h1 id="bcl10">BCL10</h1>
369
-<h2 id="overview">Overview</h2>
370
-<p>BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling and immune response regulation. Mutations in BCL10 have been implicated in the pathogenesis of various lymphomas, particularly mucosa-associated lymphoid tissue (MALT) lymphomas. They have also been reproducibly observed in a smaller proportion of DLBCLs with the frequency in non-MALT lymphomas under some debate.<sup>1</sup></p>
371
-<h2 id="history">History</h2>
372
-<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
373
-timeline
374
- title Publication timing
375
- 2011-07-27 : Morin : DLBCL
376
- 2016-09-08 : Spina : MZL
377
- 2023-07-26 : Russler : FL
378
-</div></code></pre>
379
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
380
-<table>
381
-<thead>
382
-<tr>
383
-<th style="text-align:center">Entity</th>
384
-<th style="text-align:center">Tier</th>
385
-<th>Description</th>
386
-</tr>
387
-</thead>
388
-<tbody>
389
-<tr>
390
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/MZL_tier1.png" alt="MZL"></td>
391
-<td style="text-align:center">1</td>
392
-<td>high-confidence MZL gene</td>
393
-</tr>
394
-<tr>
395
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier1.png" alt="DLBCL"></td>
396
-<td style="text-align:center">1</td>
397
-<td>high-confidence DLBCL gene</td>
398
-</tr>
399
-<tr>
400
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/FL_tier2.png" alt="FL"></td>
401
-<td style="text-align:center">2</td>
402
-<td>relevance in FL not firmly established</td>
403
-</tr>
404
-<tr>
405
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
406
-<td style="text-align:center">2</td>
407
-<td>relevance in BL not firmly established</td>
408
-</tr>
409
-</tbody>
410
-</table>
411
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
412
-<table>
413
-<thead>
414
-<tr>
415
-<th style="text-align:center">Entity</th>
416
-<th style="text-align:center">source</th>
417
-<th style="text-align:center">frequency (%)</th>
418
-</tr>
419
-</thead>
420
-<tbody>
421
-<tr>
422
-<td style="text-align:center">DLBCL</td>
423
-<td style="text-align:center">GAMBL genomes</td>
424
-<td style="text-align:center">3.82</td>
425
-</tr>
426
-<tr>
427
-<td style="text-align:center">DLBCL</td>
428
-<td style="text-align:center">Schmitz cohort</td>
429
-<td style="text-align:center">7.66</td>
430
-</tr>
431
-<tr>
432
-<td style="text-align:center">DLBCL</td>
433
-<td style="text-align:center">Reddy cohort</td>
434
-<td style="text-align:center">3.10</td>
435
-</tr>
436
-<tr>
437
-<td style="text-align:center">DLBCL</td>
438
-<td style="text-align:center">Chapuy cohort</td>
439
-<td style="text-align:center">6.41</td>
440
-</tr>
441
-<tr>
442
-<td style="text-align:center">FL</td>
443
-<td style="text-align:center">GAMBL genomes</td>
444
-<td style="text-align:center">2.31</td>
445
-</tr>
446
-<tr>
447
-<td style="text-align:center">BL</td>
448
-<td style="text-align:center">GAMBL genomes+capture</td>
449
-<td style="text-align:center">0.23</td>
450
-</tr>
451
-<tr>
452
-<td style="text-align:center">BL</td>
453
-<td style="text-align:center">Thomas cohort</td>
454
-<td style="text-align:center">0.40</td>
455
-</tr>
456
-<tr>
457
-<td style="text-align:center">BL</td>
458
-<td style="text-align:center">Panea cohort</td>
459
-<td style="text-align:center">NA</td>
460
-</tr>
461
-</tbody>
462
-</table>
463
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
464
-<table>
465
-<thead>
466
-<tr>
467
-<th style="text-align:center">Entity</th>
468
-<th style="text-align:center">aSHM</th>
469
-<th style="text-align:center">Significant selection</th>
470
-<th style="text-align:center">dN/dS (missense)</th>
471
-<th style="text-align:center">dN/dS (nonsense)</th>
472
-</tr>
473
-</thead>
474
-<tbody>
475
-<tr>
476
-<td style="text-align:center">BL</td>
477
-<td style="text-align:center">No</td>
478
-<td style="text-align:center">No</td>
479
-<td style="text-align:center">3.224</td>
480
-<td style="text-align:center">0.000</td>
481
-</tr>
482
-<tr>
483
-<td style="text-align:center">DLBCL</td>
484
-<td style="text-align:center">No</td>
485
-<td style="text-align:center">Yes</td>
486
-<td style="text-align:center">13.754</td>
487
-<td style="text-align:center">106.692</td>
488
-</tr>
489
-<tr>
490
-<td style="text-align:center">FL</td>
491
-<td style="text-align:center">No</td>
492
-<td style="text-align:center">Yes</td>
493
-<td style="text-align:center">0.000</td>
494
-<td style="text-align:center">223.832</td>
495
-</tr>
496
-</tbody>
497
-</table>
498
-<h2 id="bcl10-hotspots">BCL10 Hotspots</h2>
499
-<table>
500
-<thead>
501
-<tr>
502
-<th style="text-align:center">Chromosome</th>
503
-<th style="text-align:center">Coordinate (hg19)</th>
504
-<th style="text-align:center">ref&gt;alt</th>
505
-<th style="text-align:center">HGVSp</th>
506
-</tr>
507
-</thead>
508
-<tbody>
509
-<tr>
510
-<td style="text-align:center">chr1</td>
511
-<td style="text-align:center">85736474</td>
512
-<td style="text-align:center">C&gt;T</td>
513
-<td style="text-align:center">R58Q</td>
514
-</tr>
515
-<tr>
516
-<td style="text-align:center">chr1</td>
517
-<td style="text-align:center">85733390</td>
518
-<td style="text-align:center">G&gt;A</td>
519
-<td style="text-align:center">Q208*</td>
520
-</tr>
521
-<tr>
522
-<td style="text-align:center">chr1</td>
523
-<td style="text-align:center">85733386</td>
524
-<td style="text-align:center">A&gt;C</td>
525
-<td style="text-align:center">L209*</td>
526
-</tr>
527
-</tbody>
528
-</table>
529
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL10_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL10_protein_hg38.html">hg38</a></p>
530
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BCL10_NM_003921.svg" alt="image"></p>
531
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL10.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL10_hg38.html">hg38</a></p>
532
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BCL10.svg" alt="image"></p>
533
-<h2 id="bcl10-expression">BCL10 Expression</h2>
534
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BCL10_by_pathology.svg" alt="image"></p>
535
-<h2 id="references">References</h2>
536
-<ol>
537
-<li>
538
-<p><em>Luminari S, Intini D, Baldini L, Berti E, Bertoni F, Zucca E, Cro L, Maiolo AT, Cavalli F, Neri A. BCL10 gene mutations rarely occur in lymphoid malignancies. Leukemia. 2000 May;14(5):905-8. doi: 10.1038/sj.leu.2401747. PMID: 10803524.</em></p>
539
-</li>
540
-<li>
541
-<p><em>Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.</em></p>
542
-</li>
543
-</ol>
544
-<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
545
-<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
546
-<!-- MZL: spinaGeneticsNodalMarginal2016b -->
547
-<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
548
-
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-</body>
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-</html>
BCL2L11.md
... ...
@@ -1,41 +0,0 @@
1
-# BCL2L11
2
-
3
-## Relevance tier by entity
4
-
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-
9
-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10
-
11
-|Entity|source |frequency (%)|
12
-|:------:|:---------------------:|:-------------:|
13
-|BL |GAMBL genomes+capture|1.62 |
14
-|BL |Thomas cohort |2.10 |
15
-|BL |Panea cohort |1.00 |
16
-
17
-## Mutation pattern and selective pressure estimates
18
-
19
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
-|BL |Yes |Yes |15.763 |114.229 |
22
-|DLBCL |Yes |No | 5.483 | 0.000 |
23
-|FL |Yes |No | 0.000 | 0.000 |
24
-
25
-## aSHM regions
26
-
27
-|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
-|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
-|chr2 |111874854 |111882174|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A111874854%2D111882174)|active_promoter |
30
-
31
-
32
-View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2L11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2L11_protein_hg38.html)
33
-
34
-![image](images/proteinpaint/BCL2L11_NM_138621.svg)
35
-
36
-View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2L11.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2L11_hg38.html)
37
-
38
-![image](images/proteinpaint/BCL2L11.svg)
39
-## BCL2L11 Expression
40
-![image](images/gene_expression/BCL2L11_by_pathology.svg)
41
-<!-- ORIGIN: -->
BCL2_tmp.html
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368
-<h1 id="bcl2">BCL2</h1>
369
-<h2 id="overview">Overview</h2>
370
-<p>BCL2 mutations are frequently found in DLBCL, particularly in the germinal center B-cell (GCB) subtype, and are often located in the flexible loop domain and outside the BCL2-homology domains. These mutations are caused by the somatic hypermutation process.<sup>1</sup> The presence of these mutations are strongly correlated with the presence of a translocation between BCL2 and one of the immunoglobulin loci. <sup>2</sup> Although missense mutations may not be under positive selective pressure in the context of lymphomagenesis, some of these mutations may interfere with the function of BCL2 antagonists.<sup>3</sup></p>
371
-<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
372
-<table>
373
-<thead>
374
-<tr>
375
-<th style="text-align:center">Entity</th>
376
-<th style="text-align:center">Tier</th>
377
-<th>Description</th>
378
-</tr>
379
-</thead>
380
-<tbody>
381
-<tr>
382
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier1.png" alt="DLBCL"></td>
383
-<td style="text-align:center">1-a</td>
384
-<td>high-confidence DLBCL gene, hypermutated</td>
385
-</tr>
386
-<tr>
387
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/FL_tier1.png" alt="FL"></td>
388
-<td style="text-align:center">1-a</td>
389
-<td>high-confidence FL gene, hypermutated</td>
390
-</tr>
391
-<tr>
392
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/PMBL_tier2.png" alt="PMBL"></td>
393
-<td style="text-align:center">2</td>
394
-<td>relevance in PMBL/cHL/GZL not firmly established</td>
395
-</tr>
396
-<tr>
397
-<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
398
-<td style="text-align:center">2</td>
399
-<td>relevance in BL not firmly established</td>
400
-</tr>
401
-</tbody>
402
-</table>
403
-<pre><code> |
404
-</code></pre>
405
-<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
406
-<table>
407
-<thead>
408
-<tr>
409
-<th style="text-align:center">Entity</th>
410
-<th style="text-align:center">source</th>
411
-<th style="text-align:center">frequency (%)</th>
412
-</tr>
413
-</thead>
414
-<tbody>
415
-<tr>
416
-<td style="text-align:center">BL</td>
417
-<td style="text-align:center">GAMBL genomes+capture</td>
418
-<td style="text-align:center">0.46</td>
419
-</tr>
420
-<tr>
421
-<td style="text-align:center">BL</td>
422
-<td style="text-align:center">Thomas cohort</td>
423
-<td style="text-align:center">0.00</td>
424
-</tr>
425
-<tr>
426
-<td style="text-align:center">BL</td>
427
-<td style="text-align:center">Panea cohort</td>
428
-<td style="text-align:center">1.00</td>
429
-</tr>
430
-<tr>
431
-<td style="text-align:center">DLBCL</td>
432
-<td style="text-align:center">GAMBL genomes</td>
433
-<td style="text-align:center">23.71</td>
434
-</tr>
435
-<tr>
436
-<td style="text-align:center">DLBCL</td>
437
-<td style="text-align:center">Schmitz cohort</td>
438
-<td style="text-align:center">10.60</td>
439
-</tr>
440
-<tr>
441
-<td style="text-align:center">DLBCL</td>
442
-<td style="text-align:center">Reddy cohort</td>
443
-<td style="text-align:center">12.90</td>
444
-</tr>
445
-<tr>
446
-<td style="text-align:center">DLBCL</td>
447
-<td style="text-align:center">Chapuy cohort</td>
448
-<td style="text-align:center">15.80</td>
449
-</tr>
450
-<tr>
451
-<td style="text-align:center">FL</td>
452
-<td style="text-align:center">GAMBL genomes</td>
453
-<td style="text-align:center">50.35</td>
454
-</tr>
455
-</tbody>
456
-</table>
457
-<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
458
-<table>
459
-<thead>
460
-<tr>
461
-<th style="text-align:center">Entity</th>
462
-<th style="text-align:center">aSHM</th>
463
-<th style="text-align:center">Significant selection</th>
464
-<th style="text-align:center">dN/dS (missense)</th>
465
-<th style="text-align:center">dN/dS (nonsense)</th>
466
-</tr>
467
-</thead>
468
-<tbody>
469
-<tr>
470
-<td style="text-align:center">BL</td>
471
-<td style="text-align:center">Yes</td>
472
-<td style="text-align:center">No</td>
473
-<td style="text-align:center">0.000</td>
474
-<td style="text-align:center">0</td>
475
-</tr>
476
-<tr>
477
-<td style="text-align:center">DLBCL</td>
478
-<td style="text-align:center">Yes</td>
479
-<td style="text-align:center">Yes</td>
480
-<td style="text-align:center">2.645</td>
481
-<td style="text-align:center">0</td>
482
-</tr>
483
-<tr>
484
-<td style="text-align:center">FL</td>
485
-<td style="text-align:center">Yes</td>
486
-<td style="text-align:center">No</td>
487
-<td style="text-align:center">1.197</td>
488
-<td style="text-align:center">0</td>
489
-</tr>
490
-</tbody>
491
-</table>
492
-<h2 id="ashm-regions">aSHM regions</h2>
493
-<table>
494
-<thead>
495
-<tr>
496
-<th style="text-align:center">chr_name</th>
497
-<th style="text-align:center">hg19_start</th>
498
-<th style="text-align:center">hg19_end</th>
499
-<th style="text-align:center">region</th>
500
-<th style="text-align:center">regulatory_comment</th>
501
-</tr>
502
-</thead>
503
-<tbody>
504
-<tr>
505
-<td style="text-align:center">chr18</td>
506
-<td style="text-align:center">60796984</td>
507
-<td style="text-align:center">60814103</td>
508
-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60796984%2D60814103">intron</a></td>
509
-<td style="text-align:center">strong_enhancer</td>
510
-</tr>
511
-<tr>
512
-<td style="text-align:center">chr18</td>
513
-<td style="text-align:center">60982728</td>
514
-<td style="text-align:center">60988342</td>
515
-<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342">TSS</a></td>
516
-<td style="text-align:center">active_promoter</td>
517
-</tr>
518
-</tbody>
519
-</table>
520
-<blockquote>
521
-<p>[!NOTE]
522
-First described in FL in 2011 by <a href="https://pubmed.ncbi.nlm.nih.gov/21796119">Morin RD</a></p>
523
-</blockquote>
524
-<h2 id="bcl2-hotspots">BCL2 Hotspots</h2>
525
-<table>
526
-<thead>
527
-<tr>
528
-<th style="text-align:center">Chromosome</th>
529
-<th style="text-align:center">Coordinate (hg19)</th>
530
-<th style="text-align:center">ref&gt;alt</th>
531
-<th style="text-align:center">HGVSp</th>
532
-</tr>
533
-</thead>
534
-<tbody>
535
-<tr>
536
-<td style="text-align:center">chr18</td>
537
-<td style="text-align:center">60985854</td>
538
-<td style="text-align:center">T&gt;C</td>
539
-<td style="text-align:center">M16V</td>
540
-</tr>
541
-<tr>
542
-<td style="text-align:center">chr18</td>
543
-<td style="text-align:center">60985854</td>
544
-<td style="text-align:center">T&gt;A</td>
545
-<td style="text-align:center">M16L</td>
546
-</tr>
547
-<tr>
548
-<td style="text-align:center">chr18</td>
549
-<td style="text-align:center">60985853</td>
550
-<td style="text-align:center">A&gt;T</td>
551
-<td style="text-align:center">M16K</td>
552
-</tr>
553
-<tr>
554
-<td style="text-align:center">chr18</td>
555
-<td style="text-align:center">60985852</td>
556
-<td style="text-align:center">C&gt;T</td>
557
-<td style="text-align:center">M16I</td>
558
-</tr>
559
-<tr>
560
-<td style="text-align:center">chr18</td>
561
-<td style="text-align:center">60985849</td>
562
-<td style="text-align:center">C&gt;G</td>
563
-<td style="text-align:center">K17N</td>
564
-</tr>
565
-<tr>
566
-<td style="text-align:center">chr18</td>
567
-<td style="text-align:center">60985842</td>
568
-<td style="text-align:center">G&gt;A</td>
569
-<td style="text-align:center">H20Y</td>
570
-</tr>
571
-<tr>
572
-<td style="text-align:center">chr18</td>
573
-<td style="text-align:center">60985840</td>
574
-<td style="text-align:center">A&gt;C</td>
575
-<td style="text-align:center">H20Q</td>
576
-</tr>
577
-<tr>
578
-<td style="text-align:center">chr18</td>
579
-<td style="text-align:center">60985838</td>
580
-<td style="text-align:center">T&gt;G</td>
581
-<td style="text-align:center">Y21S</td>
582
-</tr>
583
-<tr>
584
-<td style="text-align:center">chr18</td>
585
-<td style="text-align:center">60985835</td>
586
-<td style="text-align:center">T&gt;C</td>
587
-<td style="text-align:center">K22R</td>
588
-</tr>
589
-<tr>
590
-<td style="text-align:center">chr18</td>
591
-<td style="text-align:center">60985834</td>
592
-<td style="text-align:center">CT&gt;TC</td>
593
-<td style="text-align:center">K22R</td>
594
-</tr>
595
-</tbody>
596
-</table>
597
-<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein_hg38.html">hg38</a></p>
598
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BCL2_NM_000633.svg" alt="image"></p>
599
-<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL2.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BCL2_hg38.html">hg38</a></p>
600
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BCL2.svg" alt="image"></p>
601
-<h2 id="references">References</h2>
602
-<ol>
603
-<li><em>Schuetz JM, Johnson NA, Morin RD, Scott DW, Tan K, Ben-Nierah S, Boyle M, Slack GW, Marra MA, Connors JM, Brooks-Wilson AR, Gascoyne RD. BCL2 mutations in diffuse large B-cell lymphoma. Leukemia. 2012 Jun;26(6):1383-90. doi: 10.1038/leu.2011.378. Epub 2011 Dec 22. PMID: 22189900.</em></li>
604
-<li><em>Hilton L et al. Motive and Opportunity: MYC rearrangements in high-grade B-cell lymphoma with MYC
605
-and BCL2 rearrangements-an LLMPP study. Blood. 2024. Epub May 3.</em></li>
606
-<li><em>Singh K, Briggs JM. Functional Implications of the spectrum of BCL2 mutations in Lymphoma. Mutat Res Rev Mutat Res. 2016 Jul-Sep;769:1-18. doi: 10.1016/j.mrrev.2016.06.001. Epub 2016 Jun 16. PMID: 27543313.</em></li>
607
-</ol>
608
-<h2 id="bcl2-expression">BCL2 Expression</h2>
609
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BCL2_by_pathology.svg" alt="image"></p>
610
-<!-- ORIGIN: 1339299 -->
611
-<!-- FL: morinFrequentMutationHistonemodifying2011 -->
612
-<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
613
-<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
614
-<!-- DLBCL: tanakaFrequentIncidenceSomatic1992 -->
615
-
616
-</body>
617
-</html>
C10orf12.md
... ...
@@ -1,37 +0,0 @@
1
-# C10orf12
2
-
3
-## Relevance tier by entity
4
-
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-
9
-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10
-
11
-|Entity|source |frequency (%)|
12
-|:------:|:---------------------:|:-------------:|
13
-|BL |GAMBL genomes+capture|3.46 |
14
-|BL |Thomas cohort |0.00 |
15
-|BL |Panea cohort | NA |
16
-
17
-## Mutation pattern and selective pressure estimates
18
-
19
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
-|BL |No |No |1.452 |27.236 |
22
-|DLBCL |No |Yes |1.140 |38.506 |
23
-|FL |No |Yes |3.190 |81.421 |
24
-
25
-
26
-
27
-
28
-View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_protein_hg38.html)
29
-
30
-![image](images/proteinpaint/C10orf12_NM_001346516.svg
31
-images/proteinpaint/C10orf12_NM_032440.svg)
32
-
33
-View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_hg38.html)
34
-
35
-![image](images/proteinpaint/C10orf12.svg)
36
-## C10orf12 Expression
37
-![image](images/gene_expression/C10orf12_by_pathology.svg)
CCL4_tmp.html
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+
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+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
358
+</head>
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+ ? 'dark'
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+ });
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+ </script>
368
+<h1 id="ccl4">CCL4</h1>
369
+<h2 id="history">History</h2>
370
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
371
+<table>
372
+<thead>
373
+<tr>
374
+<th style="text-align:center">Entity</th>
375
+<th style="text-align:center">Tier</th>
376
+<th>Description</th>
377
+</tr>
378
+</thead>
379
+<tbody>
380
+<tr>
381
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
382
+<td style="text-align:center">2</td>
383
+<td>relevance in DLBCL not firmly established</td>
384
+</tr>
385
+</tbody>
386
+</table>
387
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
388
+<table>
389
+<thead>
390
+<tr>
391
+<th style="text-align:center">Entity</th>
392
+<th style="text-align:center">source</th>
393
+<th style="text-align:center">frequency (%)</th>
394
+</tr>
395
+</thead>
396
+<tbody>
397
+<tr>
398
+<td style="text-align:center">DLBCL</td>
399
+<td style="text-align:center">GAMBL genomes</td>
400
+<td style="text-align:center">0.19</td>
401
+</tr>
402
+<tr>
403
+<td style="text-align:center">DLBCL</td>
404
+<td style="text-align:center">Schmitz cohort</td>
405
+<td style="text-align:center">1.49</td>
406
+</tr>
407
+<tr>
408
+<td style="text-align:center">DLBCL</td>
409
+<td style="text-align:center">Reddy cohort</td>
410
+<td style="text-align:center">0.60</td>
411
+</tr>
412
+<tr>
413
+<td style="text-align:center">DLBCL</td>
414
+<td style="text-align:center">Chapuy cohort</td>
415
+<td style="text-align:center">1.28</td>
416
+</tr>
417
+</tbody>
418
+</table>
419
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
420
+<table>
421
+<thead>
422
+<tr>
423
+<th style="text-align:center">Entity</th>
424
+<th style="text-align:center">aSHM</th>
425
+<th style="text-align:center">Significant selection</th>
426
+<th style="text-align:center">dN/dS (missense)</th>
427
+<th style="text-align:center">dN/dS (nonsense)</th>
428
+</tr>
429
+</thead>
430
+<tbody>
431
+<tr>
432
+<td style="text-align:center">BL</td>
433
+<td style="text-align:center">No</td>
434
+<td style="text-align:center">No</td>
435
+<td style="text-align:center">0.000</td>
436
+<td style="text-align:center">0</td>
437
+</tr>
438
+<tr>
439
+<td style="text-align:center">DLBCL</td>
440
+<td style="text-align:center">No</td>
441
+<td style="text-align:center">No</td>
442
+<td style="text-align:center">3.891</td>
443
+<td style="text-align:center">0</td>
444
+</tr>
445
+<tr>
446
+<td style="text-align:center">FL</td>
447
+<td style="text-align:center">No</td>
448
+<td style="text-align:center">No</td>
449
+<td style="text-align:center">0.000</td>
450
+<td style="text-align:center">0</td>
451
+</tr>
452
+</tbody>
453
+</table>
454
+<blockquote>
455
+<p>[!NOTE]
456
+First described in DLBCL in 2018 by <a href="https://pubmed.ncbi.nlm.nih.gov/29713087">Chapuy B</a></p>
457
+</blockquote>
458
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4_protein_hg38.html">hg38</a></p>
459
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CCL4_NM_002984.svg" alt="image"></p>
460
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCL4_hg38.html">hg38</a></p>
461
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CCL4.svg" alt="image"></p>
462
+<h2 id="ccl4-expression">CCL4 Expression</h2>
463
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/CCL4_by_pathology.svg" alt="image"></p>
464
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
465
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
466
+<h2 id="references">References</h2>
467
+<ol>
468
+<li>Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387</li>
469
+</ol>
470
+
471
+</body>
472
+</html>
CD274_tmp.html
... ...
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+/* https://github.com/microsoft/vscode/blob/master/extensions/markdown-language-features/media/markdown.css */
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+ * Copyright (c) Microsoft Corporation. All rights reserved.
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+ * Licensed under the MIT License. See License.txt in the project root for license information.
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+ *--------------------------------------------------------------------------------------------*/
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+
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+<style>
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+ * Markdown PDF CSS
308
+ */
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+ body {
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+ font-family: -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif, "Meiryo";
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+:not(pre):not(.hljs) > code {
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+ font-size: inherit;
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+}
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+
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+/* Page Break : use <div class="page"/> to insert page break
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+-------------------------------------------------------- */
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+.page {
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+ page-break-after: always;
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+}
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+
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+</style>
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+
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+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
358
+</head>
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+<body>
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+ <script>
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+ mermaid.initialize({
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+ startOnLoad: true,
363
+ theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
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+ ? 'dark'
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+ : 'default'
366
+ });
367
+ </script>
368
+<h1 id="cd274">CD274</h1>
369
+<h2 id="overview">Overview</h2>
370
+<p>the CD274 gene encodes the programmed death-ligand 1 (PD-L1). Mutations in B-cell lymphomas, such as DLBCL, are relatively rare.<sup>1</sup> Although rare, mutations have the potential to impact PD-L1 expression and could be relevant in the context of immune checkpoint inhibitors.</p>
371
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
372
+<table>
373
+<thead>
374
+<tr>
375
+<th style="text-align:center">Entity</th>
376
+<th style="text-align:center">Tier</th>
377
+<th>Description</th>
378
+</tr>
379
+</thead>
380
+<tbody>
381
+<tr>
382
+<td style="text-align:center">DLBCL</td>
383
+<td style="text-align:center">1</td>
384
+<td>high-confidence DLBCL gene</td>
385
+</tr>
386
+</tbody>
387
+</table>
388
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
389
+<table>
390
+<thead>
391
+<tr>
392
+<th style="text-align:center">Entity</th>
393
+<th style="text-align:center">source</th>
394
+<th style="text-align:center">frequency (%)</th>
395
+</tr>
396
+</thead>
397
+<tbody>
398
+<tr>
399
+<td style="text-align:center">DLBCL</td>
400
+<td style="text-align:center">GAMBL genomes</td>
401
+<td style="text-align:center">0.96</td>
402
+</tr>
403
+<tr>
404
+<td style="text-align:center">DLBCL</td>
405
+<td style="text-align:center">Schmitz cohort</td>
406
+<td style="text-align:center">2.34</td>
407
+</tr>
408
+<tr>
409
+<td style="text-align:center">DLBCL</td>
410
+<td style="text-align:center">Reddy cohort</td>
411
+<td style="text-align:center">1.30</td>
412
+</tr>
413
+<tr>
414
+<td style="text-align:center">DLBCL</td>
415
+<td style="text-align:center">Chapuy cohort</td>
416
+<td style="text-align:center">2.56</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">No</td>
435
+<td style="text-align:center">No</td>
436
+<td style="text-align:center">5.538</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">No</td>
442
+<td style="text-align:center">No</td>
443
+<td style="text-align:center">2.633</td>
444
+<td style="text-align:center">49.045</td>
445
+</tr>
446
+<tr>
447
+<td style="text-align:center">FL</td>
448
+<td style="text-align:center">No</td>
449
+<td style="text-align:center">No</td>
450
+<td style="text-align:center">4.631</td>
451
+<td style="text-align:center">42.709</td>
452
+</tr>
453
+</tbody>
454
+</table>
455
+<blockquote>
456
+<p>[!NOTE]
457
+First described in DLBCL in 2011 by <a href="https://pubmed.ncbi.nlm.nih.gov/21796119">Morin RD</a></p>
458
+</blockquote>
459
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274_protein_hg38.html">hg38</a></p>
460
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CD274_NM_014143.svg" alt="image"></p>
461
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CD274_hg38.html">hg38</a></p>
462
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CD274.svg" alt="image"></p>
463
+<h2 id="references">References</h2>
464
+<ol>
465
+<li><em>Huang RSP, Decker B, Murugesan K, Hiemenz M, Mata DA, Li G, Creeden J, Ramkissoon SH, Ross JS. Pan-cancer analysis of CD274 (PD-L1) mutations in 314,631 patient samples and subset correlation with PD-L1 protein expression. J Immunother Cancer. 2021 Jun;9(6):e002558. doi: 10.1136/jitc-2021-002558. PMID: 34130989; PMCID: PMC8207995.</em></li>
466
+<li><em>Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.</em></li>
467
+</ol>
468
+
469
+</body>
470
+</html>
COL11A1.md
... ...
@@ -1,5 +1,12 @@
1 1
# COL11A1
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2014-05-08 : Zhang : MCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36 43
![image](images/gene_expression/COL11A1_by_pathology.svg)
37 44
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 45
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
46
+## References
47
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
COL16A1.md
... ...
@@ -1,5 +1,12 @@
1 1
# COL16A1
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2014-05-08 : Zhang : MCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36 43
![image](images/gene_expression/COL16A1_by_pathology.svg)
37 44
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 45
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
46
+## References
47
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
COL4A2.md
... ...
@@ -1,5 +1,12 @@
1 1
# COL4A2
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2012-12-01 : Love : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -38,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 45
![image](images/gene_expression/COL4A2_by_pathology.svg)
39 46
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 47
<!-- BL: loveGeneticLandscapeMutations2012 -->
48
+## References
49
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
COQ7.md
... ...
@@ -1,5 +1,12 @@
1 1
# COQ7
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2018-05-01 : Chapuy : DLBCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
39 46
![image](images/gene_expression/COQ7_by_pathology.svg)
40 47
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 48
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
49
+## References
50
+1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
CPXM2.md
... ...
@@ -1,5 +1,12 @@
1 1
# CPXM2
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2022-07-06 : Burkhardt : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -38,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 45
![image](images/gene_expression/CPXM2_by_pathology.svg)
39 46
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40 47
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
48
+## References
49
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
CRIP1.md
... ...
@@ -1,5 +1,12 @@
1 1
# CRIP1
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2018-05-01 : Chapuy : DLBCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
39 46
![image](images/gene_expression/CRIP1_by_pathology.svg)
40 47
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 48
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
49
+## References
50
+1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
CTCF.md
... ...
@@ -1,5 +1,12 @@
1 1
# CTCF
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2019-09-26 : Panea : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -38,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 45
![image](images/gene_expression/CTCF_by_pathology.svg)
39 46
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40 47
<!-- BL: paneaWholeGenomeLandscape2019 -->
48
+## References
49
+1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
CTNNA2.md
... ...
@@ -1,5 +1,12 @@
1 1
# CTNNA2
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2014-05-08 : Zhang : MCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36 43
![image](images/gene_expression/CTNNA2_by_pathology.svg)
37 44
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 45
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
46
+## References
47
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
CTSS.md
... ...
@@ -1,5 +1,12 @@
1 1
# CTSS
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2020-05-05 : Bararia : FL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -41,3 +48,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
41 48
![image](images/gene_expression/CTSS_by_pathology.svg)
42 49
<!-- ORIGIN: barariaCathepsinAlterationsInduce2020c -->
43 50
<!-- FL: barariaCathepsinAlterationsInduce2020c -->
51
+## References
52
+1. Bararia D, Hildebrand JA, Stolz S, Haebe S, Alig S, Trevisani CP, Osorio-Barrios F, Bartoschek MD, Mentz M, Pastore A, Gaitzsch E, Heide M, Jurinovic V, Rautter K, Gunawardana J, Sabdia MB, Szczepanowski M, Richter J, Klapper W, Louissaint A, Ludwig C, Bultmann S, Leonhardt H, Eustermann S, Hopfner KP, Hiddemann W, von Bergwelt-Baildon M, Steidl C, Kridel R, Tobin JWD, Gandhi MK, Weinstock DM, Schmidt-Supprian M, Sárosi MB, Rudelius M, Passerini V, Mautner J, Weigert O. Cathepsin S Alterations Induce a Tumor-Promoting Immune Microenvironment in Follicular Lymphoma. Cell Rep. 2020 May 5;31(5):107522. PMID: 32330423
CXCR4.md
... ...
@@ -7,10 +7,19 @@ CXCR4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
7 7
Mutations in this gene were first described in DLBCL in 2012 by Khodabakhshi et al,<sup>1</sup> in FL in 2021 by Hübschmann et al<sup>2</sup> and in BL in 2019 by Panea et al.<sup>3</sup>
8 8
9 9
10
+```mermaid
11
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
12
+timeline
13
+ title Publication timing
14
+ 2012-11-12 : Khodabakhshi : DLBCL
15
+ 2017-01-26 : Krysiak : FL
16
+ 2019-09-26 : Panea : BL
17
+```
10 18
## Relevance tier by entity
11 19
12 20
|Entity|Tier|Description |
13 21
|:------:|:----:|--------------------------------------|
22
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
14 23
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
15 24
|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
16 25
|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
CXCR5.md
... ...
@@ -1,7 +1,15 @@
1 1
# CXCR5
2 2
## Overview
3 3
CXCR5 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. No notable hot spots have been described in this gene in the context of the cancers listed below. The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*.
4
-
4
+## History
5
+
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2018-04-12 : Schmitz : DLBCL
11
+ 2019-09-05 : Mottok : PMBL
12
+```
5 13
## Relevance tier by entity
6 14
7 15
|Entity|Tier|Description |
... ...
@@ -48,3 +56,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
48 56
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
49 57
<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
50 58
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
59
+## References
60
+1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183
61
+2. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115
CYB5D1.md
... ...
@@ -1,5 +1,12 @@
1 1
# CYB5D1
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2012-12-01 : Love : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -38,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 45
![image](images/gene_expression/CYB5D1_by_pathology.svg)
39 46
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 47
<!-- BL: loveGeneticLandscapeMutations2012 -->
48
+## References
49
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
CYP2A6.md
... ...
@@ -1,5 +1,12 @@
1 1
# CYP2A6
2
-
2
+## History
3
+
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2023-07-26 : Russler : FL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36 43
![image](images/gene_expression/CYP2A6_by_pathology.svg)
37 44
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38 45
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
46
+## References
47
+1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.
CYP4F22.md
... ...
@@ -1,4 +1,5 @@
1 1
# CYP4F22
2
+## History
2 3
3 4
## Relevance tier by entity
4 5
... ...
@@ -38,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38 39
![image](images/gene_expression/CYP4F22_by_pathology.svg)
39 40
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 41
<!-- BL: loveGeneticLandscapeMutations2012 -->
42
+## References
43
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
DDX10.md
... ...
@@ -1,5 +1,7 @@
1 1
# DDX10
2 2
3
+## History
4
+
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
... ...
@@ -39,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
39 41
![image](images/gene_expression/DDX10_by_pathology.svg)
40 42
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41 43
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
44
+## References
45
+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
DHDH.md
... ...
@@ -1,5 +1,7 @@
1 1
# DHDH
2 2
3
+## History
4
+
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
... ...
@@ -36,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
36 38
![image](images/gene_expression/DHDH_by_pathology.svg)
37 39
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 40
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
41
+## References
42
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
DHX15.md
... ...
@@ -41,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
41 41
42 42
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
43 43
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
44
+## References
45
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
DICER1.md
... ...
@@ -1,5 +1,7 @@
1 1
# DICER1
2 2
3
+## History
4
+
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
... ...
@@ -42,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
42 44
![image](images/gene_expression/DICER1_by_pathology.svg)
43 45
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
44 46
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
47
+## References
48
+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
DLC1.md
... ...
@@ -36,3 +36,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
36 36
![image](images/gene_expression/DLC1_by_pathology.svg)
37 37
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 38
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
39
+## References
40
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
DLGAP1.md
... ...
@@ -38,3 +38,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
38 38
![image](images/gene_expression/DLGAP1_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 40
<!-- BL: loveGeneticLandscapeMutations2012 -->
41
+## References
42
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
ZNF423.md
... ...
@@ -1,5 +1,11 @@
1 1
# ZNF423
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2018-05-01 : Chapuy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -39,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
39 45
![image](images/gene_expression/ZNF423_by_pathology.svg)
40 46
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 47
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
48
+## References
49
+1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
ZNF423_tmp.html
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+<!DOCTYPE html>
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+<html>
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+<head>
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+<title>ZNF423.md</title>
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+<meta http-equiv="Content-type" content="text/html;charset=UTF-8">
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+
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+<style>
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+/* https://github.com/microsoft/vscode/blob/master/extensions/markdown-language-features/media/markdown.css */
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+/*---------------------------------------------------------------------------------------------
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+ * Copyright (c) Microsoft Corporation. All rights reserved.
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+ * Licensed under the MIT License. See License.txt in the project root for license information.
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+ *--------------------------------------------------------------------------------------------*/
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+
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+body {
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+ font-family: var(--vscode-markdown-font-family, -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif);
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+ font-size: var(--vscode-markdown-font-size, 14px);
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+ padding: 0 26px;
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+ line-height: var(--vscode-markdown-line-height, 22px);
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+ word-wrap: break-word;
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+}
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+
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+#code-csp-warning {
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+ position: fixed;
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+ top: 0;
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+ right: 0;
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+ color: white;
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+ margin: 16px;
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+ text-align: center;
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+ font-size: 12px;
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+ font-family: sans-serif;
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+ background-color:#444444;
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+ cursor: pointer;
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+ padding: 6px;
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+ box-shadow: 1px 1px 1px rgba(0,0,0,.25);
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+}
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+
37
+#code-csp-warning:hover {
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+ text-decoration: none;
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+ background-color:#007acc;
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+ box-shadow: 2px 2px 2px rgba(0,0,0,.25);
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+}
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+
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+body.scrollBeyondLastLine {
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+ margin-bottom: calc(100vh - 22px);
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+}
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+
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+body.showEditorSelection .code-line {
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+ position: relative;
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+}
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+
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+body.showEditorSelection .code-active-line:before,
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+body.showEditorSelection .code-line:hover:before {
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+ content: "";
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+ display: block;
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+ position: absolute;
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+ top: 0;
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+ left: -12px;
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+ height: 100%;
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+}
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+
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+ ? 'dark'
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+ });
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+ </script>
368
+<h1 id="znf423">ZNF423</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</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">1.91</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">0.594</td>
441
+<td style="text-align:center">0</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">1.430</td>
448
+<td style="text-align:center">0</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">0.836</td>
455
+<td style="text-align:center">0</td>
456
+</tr>
457
+</tbody>
458
+</table>
459
+<blockquote>
460
+<p>[!NOTE]
461
+First described in DLBCL in 2018 by <a href="https://pubmed.ncbi.nlm.nih.gov/29713087">Chapuy B</a></p>
462
+</blockquote>
463
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423_protein_hg38.html">hg38</a></p>
464
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ZNF423_NM_015069.svg" alt="image"></p>
465
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ZNF423_hg38.html">hg38</a></p>
466
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ZNF423.svg" alt="image"></p>
467
+<h2 id="znf423-expression">ZNF423 Expression</h2>
468
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ZNF423_by_pathology.svg" alt="image"></p>
469
+<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
470
+<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
471
+<h2 id="references">References</h2>
472
+<ol>
473
+<li>Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387</li>
474
+</ol>
475
+
476
+</body>
477
+</html>
ZNF608.md
... ...
@@ -4,6 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
+|![FL](images/icons/FL_tier2.png)|2|relevance in FL not firmly established|
7 8
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
8 9
9 10
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -40,3 +41,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
40 41
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
41 42
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
42 43
<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
44
+## References
45
+1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan;
46
+2. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390