ACTB.md
... ...
@@ -7,10 +7,11 @@ ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
7 7
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|Entity|Tier|Description |
9 9
|:------:|:----:|--------------------------|
10
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
11
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
10 12
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated|
11 13
|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated |
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13
-
14 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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|Entity|source |frequency (%)|
ACTG1.md
... ...
@@ -8,8 +8,11 @@ Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschma
8 8
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|Entity|Tier|Description |
10 10
|:------:|:----:|--------------------------------------|
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+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
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+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
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+|![FL](images/icons/FL_tier2.png)|2|relevance in FL not firmly established|
11 14
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
12
-|![DLBCL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
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+
13 16
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
15 18
ARID1A.md
... ...
@@ -7,9 +7,10 @@ ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes
7 7
> Mutations in this gene were first described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597) and first described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
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## Relevance tier by entity
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-
11 10
|Entity|Tier|Description |
12 11
|:------:|:----:|--------------------------|
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+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
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+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
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|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
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|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
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|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
ARID5B.md
... ...
@@ -9,6 +9,7 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup
9 9
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|Entity|Tier|Description |
11 11
|:------:|:----:|-----------------------------------------|
12
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
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|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
13 14
14 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
B2M.md
... ...
@@ -9,6 +9,7 @@ The B2M (β2-microglobulin) gene plays a crucial role in the function of the maj
9 9
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|Entity|Tier|Description |
11 11
|:------:|:----:|---------------------------------------|
12
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
12 13
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
13 14
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
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|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
BCL2_tmp.html
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+<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>
BCL7A.md
... ...
@@ -11,6 +11,8 @@ Mutations in this gene were first described in FL in 2017 by Krysiak et al.<sup>
11 11
12 12
|Entity|Tier|Description |
13 13
|:------:|:----:|--------------------------------------|
14
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
15
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
14 16
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
15 17
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
16 18
|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
BIRC3.md
... ...
@@ -4,6 +4,8 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
8
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
7 9
|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 10
|![MCL](images/icons/MCL_tier1.png) |1-a | aSHM target and high-confidence MCL gene |
9 11
BIRC6.md
... ...
@@ -8,6 +8,7 @@ BIRC6, as a negative regulator of non-canonical NF-κB signaling, is implicated
8 8
9 9
|Entity|Tier|Description |
10 10
|:------:|:----:|--------------------------------------|
11
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
11 12
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
12 13
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
13 14
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
BTG1.md
... ...
@@ -6,6 +6,8 @@ BTG1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
10
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
9 11
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
10 12
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
11 13
|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
CCND3.md
... ...
@@ -6,6 +6,8 @@ CCND3 (Cyclin D3) is a gene that encodes a protein involved in the regulation of
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
10
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
9 11
|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
10 12
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
11 13
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
CIITA.md
... ...
@@ -6,6 +6,7 @@ CIITA encodes the major histocompatibility complex (MHC) class II transactivator
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
9 10
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
10 11
11 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)