ATP2C2.md
... ...
@@ -1,5 +1,11 @@
1 1
# ATP2C2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
38 44
![image](images/gene_expression/ATP2C2_by_pathology.svg)
39 45
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 46
<!-- BL: loveGeneticLandscapeMutations2012 -->
47
+## References
48
+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
ATP6AP1.md
... ...
@@ -1,5 +1,11 @@
1 1
# ATP6AP1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2016-02-02 : Okosun : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -33,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
33 39
![image](images/gene_expression/ATP6AP1_by_pathology.svg)
34 40
<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
35 41
<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->
42
+## References
43
+1. Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016 Feb;48(2):183–188. PMCID: PMC4731318
ATP6V1B2.md
... ...
@@ -1,5 +1,11 @@
1 1
# ATP6V1B2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2016-02-02 : Okosun : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -40,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
40 46
![image](images/gene_expression/ATP6V1B2_by_pathology.svg)
41 47
<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
42 48
<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->
49
+## References
50
+1. Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016 Feb;48(2):183–188. PMCID: PMC4731318
BCL10.md
... ...
@@ -1,11 +1,20 @@
1 1
# BCL10
2 2
## Overview
3 3
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>
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-27 : Morin : DLBCL
10
+ 2016-09-08 : Spina : MZL
11
+ 2023-07-26 : Russler : FL
12
+```
5 13
## Relevance tier by entity
6 14
7 15
|Entity|Tier|Description |
8 16
|:------:|:----:|--------------------------------------|
17
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
9 18
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10 19
|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
11 20
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
BCL10_tmp.html
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+ </script>
368
+<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
+
549
+</body>
550
+</html>
BCOR.md
... ...
@@ -1,11 +1,20 @@
1 1
# BCOR
2 2
3 3
BCOR acts as a co-repressor of BCL6, and mutations in BCOR could impair its binding affinity to BCL6 and other partners. Overall, protein-altering mutations in BCOR seem to be rare in DLBCL and MCL.<sup>1,2</sup> One study reported a much higher prevalence of a hot spot mutation in BCOR but this result has not been reproduced.<sup>1</sup>
4
-
4
+## History
5
+
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2017-07-27 : Jallades : MZL
11
+ 2020-09-17 : Nadeu : MCL
12
+```
5 13
## Relevance tier by entity
6 14
7 15
|Entity|Tier|Description |
8 16
|:------:|:----:|--------------------------|
17
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
9 18
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10 19
|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
11 20