BACH2.md
... ...
@@ -27,11 +27,7 @@ timeline
27 27
28 28
## Mutation pattern and selective pressure estimates
29 29
30
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
31
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
32
-|BL |Yes |No |0.652 | 0.000 |
33
-|DLBCL |Yes |No |0.949 | 0.000 |
34
-|FL |Yes |No |0.000 |28.997 |
30
+[[include:dnds_BACH2.md]]
35 31
36 32
## aSHM regions
37 33
BCL6.md
... ...
@@ -40,11 +40,7 @@ timeline
40 40
41 41
## Mutation pattern and selective pressure estimates
42 42
43
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
44
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
45
-|BL |Yes |No | 7.427 | 0.000 |
46
-|DLBCL |Yes |Yes |25.672 |60.803 |
47
-|FL |Yes |Yes |27.215 |62.162 |
43
+[[include:dnds_BACH2.md]]
48 44
49 45
## aSHM regions
50 46
BCL7A.md
... ...
@@ -43,11 +43,7 @@ timeline
43 43
44 44
## Mutation pattern and selective pressure estimates
45 45
46
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
47
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
48
-|BL |Yes |Yes | 9.127 | 46.248 |
49
-|DLBCL |Yes |Yes |22.635 | 0.000 |
50
-|FL |Yes |Yes |55.348 |146.110 |
46
+[[include:dnds_BCL7A.md]]
51 47
52 48
## aSHM regions
53 49
test1.md
... ...
@@ -0,0 +1,1777 @@
1
+# Supplemental Methods and Results
2
+
3
+## Sources of B-cell lymphoma genes
4
+
5
+Any study that described at least one gene as recurrently mutated in
6
+DLBCL, FL or BL was eligible to contribute to the gene lists. The
7
+current lists relied on a total of 37 studies for DLBCL,^1--37^ 15
8
+studies for FL,^7,10,16,19,22,26,36,38--45^ and 13 studies for
9
+BL.^43,46--57^
10
+
11
+## Procedure for gene retirement (Tier 3)
12
+
13
+The pattern of mutations in Tier 2 genes has, by definition, not been
14
+independently reproduced. To counteract the continued growth of Tier 2
15
+over time, genes can be retired to Tier 3 in certain scenarios.
16
+Specifically, when a new analysis or scrutiny of the original data draws
17
+the validity of a gene or study into question, Tier 2 genes from a study
18
+may be retired idividually or *en masse*, depending on the situation.
19
+Ideally, the entire set of mutations that led to the original nomination
20
+of each gene will be reviewed individually to reduce the likelihood that
21
+a gene is retired unnecessarily. However, when systematic manual review
22
+is impossible, genes may be retired when the originating study is deemd
23
+to have low reproducibility. In these rare situations, all Tier 2 genes
24
+from that study can be moved to Tier 3.
25
+
26
+1. Where feasible, all variants reported in the original study are
27
+ subjected to manual review using the primary data and each mutation
28
+ is rated on a five-point scale. Following review, any Tier 2 gene
29
+ with an average quality score less than 3 for all variants is moved
30
+ to Tier 3 and the other genes remain in their current Tier. The
31
+ results from applying this procedure to genes from six studies are
32
+ included in the [subsequent section](#manual), focusing on
33
+ representative examples of mutations in genes that were retired.
34
+
35
+2. In scenarios where only some of the data are available, the quality
36
+ of a study may instead be used to retire genes *en masse*. If a
37
+ separate analysis of the data from the study or re-sequencing of
38
+ samples from the study cumulatively replicates less than 50% the
39
+ variants in Tier 2 genes, all genes arising from that study can be
40
+ assigned to Tier 3 (unless they are already in Tier 1). This
41
+ procedure is described in more detail at the [end of this
42
+ document](#replicability). This study-wide retirement is an
43
+ alternative to the first approach and should only be performed when
44
+ all Tier 2 genes from the study cannot be individually reviewed due
45
+ to lack of access to some or all the primary data.
46
+
47
+## Procedure 1: Manual review `<a name="manual">`{=html}`</a>`{=html}
48
+
49
+While establishing the current gene lists, six studies were selected for
50
+manual review of the primary data. Studies were chosen based on data
51
+availability and the relative proportion of orphan genes. For each
52
+study, bam files were obtained from the European Genome-Phenome Archive
53
+(EGA) or dbGAP. The positions reported as mutated in each patient sample
54
+were visualized in the corresponding sequence data using IGV or
55
+[igv-reports](https://github.com/igvteam/igv-reports). When available,
56
+the data from the tumor and matched normal sample was visualized in
57
+parallel. As described
58
+[previously](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1.full),
59
+each variant was assigned a rating on a 5-point scale with 1 reserved
60
+for variants having the minimal support (one molecule) and 5
61
+representing variants with the best support. For every novel gene
62
+reported in a study, all mutations in that gene were rated. A gene was
63
+considered to have inadequate support (failed) if the average rating of
64
+all variants reviewed was less than 3. Representative visualizations and
65
+the average rating for each of these genes and studies are included
66
+below. For each study, a single example of a gene that passed manual
67
+review is shown for comparison. The table below summarises these
68
+studies.
69
+
70
+::: {style="page-break-after: always;"}
71
+:::
72
+
73
+ -----------------------------------------------------------------------
74
+ Study Methodology Entity
75
+ ----------------------------- ----------------------- -----------------
76
+ [Love *et al*, Exome BL
77
+ 2012^50^](#love)
78
+
79
+ [Morin *et al*, WGS DLBCL
80
+ 2013^18^](#morin)
81
+
82
+ [Reddy *et al*, Exome DLBCL
83
+ 2017^28^](#reddy)
84
+
85
+ [Panea *et al*, Exome/RNA-seq BL
86
+ 2019^52^](#panea)
87
+
88
+ [Chapuy *et al*, Exome DLBCL
89
+ 2018^4^](#chapuy)
90
+
91
+ [Hübschmann *et al*, WGS DLBCL,FL
92
+ 2021^10^](#icgc)
93
+ -----------------------------------------------------------------------
94
+
95
+## Procedure 2: Assessing reproducibility `<a name="replicability">`{=html}`</a>`{=html}
96
+
97
+It is often not feasible to scrutinze each mutation in the primary data.
98
+In lieu of this, Tier 3 status can also be applied study-wide.
99
+Specifically, genes may be retired study-wide if a re-analysis of the
100
+same data (or new data from the same samples) does not reproduce at
101
+least 50% of the mutations in the Tier 2 genes from that study. Most
102
+commonly, we anticipate this scenario will arise when two separate
103
+studies (Study A and Study B) describe the analysis of some (or all) the
104
+same primary data and each study releases either their variant calls or
105
+per-gene mutation frequencies. For example, the 48 DLBCLs profiled by
106
+The Cancer Genome Atlas (TCGA) were used in several studies. Although
107
+each study performed their own variant calling, exome-wide variant calls
108
+from the central analysis pipelines in Genome Data Commons (GDC) are
109
+available from the GDC data portal.
110
+
111
+### Option A: Comprehensive assessment
112
+
113
+To quantify their reproducibility, three of the studies in the previous
114
+section were also re-analyzed using our in-house variant calling
115
+pipelines. The results are summarized in the table below. Importantly,
116
+the threshold for determining whether a study is sufficiently
117
+reproducible must accomodate a reasonable level of variability that
118
+could be attributed to different variant calling strategies. We selected
119
+the Chapuy study as a representative baseline for adequate
120
+reproducibility. This study reported 19 genes that have not yet been
121
+assigned to Tier 1 (Supplemental Table S7). Of the 75 mutations in these
122
+genes, 58 (77.3%) were also detected by our analysis. In contrast, far
123
+fewer of the mutations in the 37 and 54 genes respectively reported in
124
+the Panea and Reddy studies were reproduced (Supplemental Table S8).
125
+Based on this outcome, all Tier 2 genes from the Panea, Reddy and Fan
126
+studies could be retired from their respective lists (BL for Panea,
127
+DLBCL for the others). However, because the primary data were available
128
+for systematic manual review, procedure 1 applies. Hence, the Tier 2
129
+genes with a sufficiently high average variant score following review
130
+remain in Tier 2. Notably, the high proportion of novel genes from the
131
+Reddy and Panea study that failed manual review is consistent with a
132
+lower degree of overall reproducibility.
133
+
134
+### Option B: Partial assessment
135
+
136
+We used a less comprehensive approach to evaluate the two additional
137
+studies that each contributed a large number of Tier 2 genes (Fan *et
138
+al* and Zhang *et al*). For the former, which analyzed TCGA data, we
139
+relied on TCGA mutation calls from the same samples, which were obtained
140
+from GDC data portal. Because individual mutations were not reported in
141
+the Fan study, it was only feasible to compare the mutation incidence
142
+per-gene between the Fan study and the GDC results. For each of the 72
143
+Tier 2 genes from that study, we compared the total number of non-silent
144
+mutations in that gene between the study supplement and GDC results.
145
+Whereas Fan *et al* reported a total of 217 mutations in these genes,
146
+there were only 81 in the GDC results (Supplemental Table S9). Because
147
+the total number of mutations in these genes in the GDC results was less
148
+than half of the original study (37.3%), all Tier 2 genes from this
149
+study were retired. Notably, this approach is relatively lenient because
150
+it assumes that the 81 mutations in the GDC results were all present in
151
+the Fan results. If, in fact, some of the GDC variants were not
152
+identified in the Fan analysis, the number of shared variants would be
153
+lower.
154
+
155
+We used another approach to assess the reproducibility of the Zhang
156
+study. In this case, we relied on 16 samples from the Zhang study and
157
+assumed these would be representative of the full cohort. A more recent
158
+study by this group (Reddy *et al*) performed exome sequencing on 16 of
159
+the samples from the Zhang cohort. We reasoned that a set of samples
160
+subjected to whole exome sequencing by the same group should recover
161
+most of the mutations reported in the original study. To quantify the
162
+reproducibility of mutations in the genes reported in the Zhang study,
163
+we compared the mutation status of each Tier 2 gene in these patients to
164
+the results from our in-house reanalysis of these exomes, which was
165
+performed as part of our ongoing Genomic Analysis of Mature B-cell
166
+Lymphomas (GAMBL) project. A minority (48.7%) of the mutations in these
167
+genes were identified by our analysis of the more recent exomes
168
+(Supplemental Table S10). Owing to this, all Tier 2 genes from this
169
+study were migrated to Tier 3.
170
+
171
+ ---------------------------------------------------------------------------
172
+ Study Novel genes Failed review Mutations Mutations
173
+ reported reproduced
174
+ --------------- -------------- -------------- -------------- --------------
175
+ Chapuy^4^ 19 6 (31.5%) 75 58 (77.3%)
176
+
177
+ Panea^52^ 37 22 (59.4%) 365 145 (39.7%)
178
+
179
+ Reddy^28^ 54 26 (48%) 1398 484 (34.6%)
180
+
181
+ Fan\*^9^ 73 NA 217 81 (37.3%)
182
+
183
+ Zhang\*\*^37^ 280 NA 263 128 (48.7%)
184
+ ---------------------------------------------------------------------------
185
+
186
+\*Mutations from this study were not released. Only gene-level
187
+comparisons were performed.
188
+
189
+\*\*Gene-level comparisons were performed on 16 cases overlapping the
190
+Reddy cohort.
191
+
192
+## Potential contribution of rare germline variants
193
+
194
+As detailed in Supplemental Table S5, many of the studies contributing
195
+to our gene lists did not have matched germline DNA from every sample.
196
+It has been shown that some genes have disproportionately higher numbers
197
+of rare germline variants. The genes with the highest number of rare
198
+variants overall have been described in a recent study as FrequentLy
199
+mutAted GeneS (FLAGS)^58^. These genes should be considered with caution
200
+in any study that associates them with a phenotype. Insufficient removal
201
+of germline variants in the studies explored herein could explain some
202
+of the genes in Tiers 2 and 3. To evaluate this, we used the ranking of
203
+the frequency of rare mutations in all genes covered by common exome
204
+panels. This "FLAGS rank" assignes the lowest rank to genes with the
205
+highest number of rare variants (e.g. TTN = 1, MUC16 = 2, OBSCN = 3,
206
+etc). We used the distribution of ranks across the three tiers of DLBCL
207
+genes to evaluate the relative extent to which the genes on each list
208
+may be explained, in part, by inadequate removal of rare germline
209
+variants. If there is no influence on genes, the FLAGS_rank is expected
210
+to follow a uniform distribution. Accordingly, we compared each of the
211
+four gene lists to a uniform distribution using a negative binomial
212
+regression. Interestingly, the distributions of FLAGS_rank for Tier 2
213
+and Tier 3 and the Cosmic Cancer Gene Census (CGC)^59^ genes were
214
+significantly different than the uniform distribution. In contrast, the
215
+distribution for Tier 1 genes was not significantly different from a
216
+uniform distribution. This is consistent with the Tier 1 DLBCL genes
217
+having minimal contamination of genes due to rare germline variants. To
218
+evaluate whether the separation of genes into Tiers 2 and 3 offers some
219
+benefit in this regard, we compared the Tier 2 DLBCL genes to the other
220
+lists. Indeed, Tier 2 showed a significant difference when compared to
221
+Tier 3 (P=3.86e-06). Based on this, we conclude that the Tier 3 gene
222
+list is dominated by FLAGS whereas Tier 2 represents a mixture of true
223
+DLBCL genes and FLAGS.
224
+
225
+<figure>
226
+`<img src="FLAGS_rank_boxplot.png" alt="flags1" style="width:500px;"/>`{=html}
227
+<figcaption>
228
+`<strong>`{=html}Supplemental Figure S1. Comparing FLAGS rank in the
229
+DLBCL genes.`</strong>`{=html} `<br>`{=html} The FLAGS rank of DLBCL
230
+genes in Tier 1, 2 and 3 is compared. The genes in the COSMIC CGC list
231
+are included for comparison. Values closer to 1 indicate the gene has a
232
+higher number of rare germline variants.
233
+</figcaption>
234
+</figure>
235
+
236
+::: {style="page-break-after: always;"}
237
+:::
238
+
239
+## Representative results from manual review
240
+
241
+### [Love *et al*, 2012](https://www.nature.com/articles/ng.2468) `<a name="love">`{=html}`</a>`{=html}
242
+
243
+ Methodology Pairs Unpaired tumors Cell lines Tier 1 Tier 2 Tier 3
244
+ ------------- ------- ----------------- ------------ -------- -------- ----------
245
+ Exome 14 37 8 5 7 48 (80%)
246
+
247
+*See also:* [IGV
248
+reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/)
249
+
250
+### CARD4 - pass
251
+
252
+![CARD4](primary/Love_CARD4.svg)
253
+
254
+Average rating: ★ ★ ★ ★ ☆
255
+
256
+### ACAD9 - fail (insufficient support)
257
+
258
+![ACAD9](primary/Love_ACAD9.svg)
259
+
260
+Average rating: ★ ☆ ☆ ☆ ☆
261
+
262
+::: {style="page-break-after: always;"}
263
+:::
264
+
265
+### ACE - fail (insufficient support)
266
+
267
+![ACE](primary/Love_ACE.svg)
268
+
269
+Average rating: ★ ☆ ☆ ☆ ☆
270
+
271
+### ATP2C2 - fail (insufficient support)
272
+
273
+![ATP2C2](primary/Love_ATP2C2.svg)
274
+
275
+Average rating: ★ ★ ☆ ☆ ☆
276
+
277
+::: {style="page-break-after: always;"}
278
+:::
279
+
280
+### BRAF - fail (insufficient support)
281
+
282
+![BRAF](primary/Love_BRAF.svg)
283
+
284
+Average rating: ★ ☆ ☆ ☆ ☆
285
+
286
+### c6orf27 - fail (germline)
287
+
288
+![c6orf27](primary/Love_C6orf27_germline.svg)
289
+
290
+Average rating: Germline
291
+
292
+::: {style="page-break-after: always;"}
293
+:::
294
+
295
+### BRD4 - fail (insufficient support)
296
+
297
+![BRD4](primary/Love_BRD4.svg)
298
+
299
+Average rating: ★ ☆ ☆ ☆ ☆
300
+
301
+### CYB5D1 - fail (insufficient support)
302
+
303
+![CYB5D1](primary/Love_CYB5D1.svg)
304
+
305
+Average rating: ★ ☆ ☆ ☆ ☆
306
+
307
+::: {style="page-break-after: always;"}
308
+:::
309
+
310
+### BTG2 - fail (insufficient support)
311
+
312
+![BTG2](primary/Love_BTG2.svg)
313
+
314
+Average rating: ★ ☆ ☆ ☆ ☆
315
+
316
+### CAD - fail (insufficient support)
317
+
318
+![CAD](primary/Love_CAD.svg)
319
+
320
+Average rating: ★ ☆ ☆ ☆ ☆
321
+
322
+::: {style="page-break-after: always;"}
323
+:::
324
+
325
+### CCT6B - fail (germline)
326
+
327
+![CCT6B](primary/Love_CCT6B.svg)
328
+
329
+Average rating: Gremline
330
+
331
+### CDH17 - fail (insufficient support)
332
+
333
+![CDH17](primary/Love_CDH17.svg)
334
+
335
+Average rating: ★ ☆ ☆ ☆ ☆
336
+
337
+::: {style="page-break-after: always;"}
338
+:::
339
+
340
+### COL4A2 - fail (insufficient support)
341
+
342
+![COL4A2](primary/Love_COL4A2.svg)
343
+
344
+Average rating: ★ ☆ ☆ ☆ ☆
345
+
346
+### CYP4F22 - fail (insufficient support)
347
+
348
+![CYP4F22](primary/Love_CYP4F22_15523136.png)
349
+
350
+Average rating: ★ ☆ ☆ ☆ ☆
351
+
352
+### DLGAP1 - fail (insufficient support)
353
+
354
+![DLGAP1](primary/Love_DLGAP_chr18_3869854.png)
355
+
356
+Average rating: ★ ☆ ☆ ☆ ☆
357
+
358
+::: {style="page-break-after: always;"}
359
+:::
360
+
361
+### DTX1 - fail (insufficient support)
362
+
363
+![DTX1](primary/Love_DTX1_chr12_112017255.png)
364
+
365
+Average rating: ★ ☆ ☆ ☆ ☆
366
+
367
+### EIF2C4 - fail (insufficient support)
368
+
369
+![EIF2C4](primary/Love_EIF2C4.svg)
370
+
371
+Average rating: ★ ☆ ☆ ☆ ☆
372
+
373
+::: {style="page-break-after: always;"}
374
+:::
375
+
376
+### EML2 - fail (insufficient support)
377
+
378
+![EML2](primary/Love_EML2_50816396.png)
379
+
380
+Average rating: ★ ☆ ☆ ☆ ☆
381
+
382
+### ENTPD3 - fail (insufficient support)
383
+
384
+![ENTPD3](primary/Love_ENTPD3.svg)
385
+
386
+Average rating: ★ ★ ☆ ☆ ☆
387
+
388
+::: {style="page-break-after: always;"}
389
+:::
390
+
391
+### EPHB2 - fail (insufficient support)
392
+
393
+![EPHB2](primary/Love_EPHB2.svg)
394
+
395
+Average rating: ★ ★ ☆ ☆ ☆
396
+
397
+### FAM129B - fail (insufficient support)
398
+
399
+![FAM129B](primary/Love_FAM129B.svg)
400
+
401
+Average rating: ★ ★ ☆ ☆ ☆
402
+
403
+::: {style="page-break-after: always;"}
404
+:::
405
+
406
+### FGFR3 - fail (insufficient support)
407
+
408
+![FGFR3](primary/Love_FGFR3.svg)
409
+
410
+Average rating: ★ ☆ ☆ ☆ ☆
411
+
412
+### FTCD - fail (germline)
413
+
414
+![FTCD](primary/Love_FTCD.svg)
415
+
416
+Average rating: Germline
417
+
418
+::: {style="page-break-after: always;"}
419
+:::
420
+
421
+### GRIK5 - fail (insufficient support)
422
+
423
+![GRIK5](primary/Love_GRIK5.svg)
424
+
425
+Average rating: ★ ☆ ☆ ☆ ☆
426
+
427
+### ICK - fail (insufficient support)
428
+
429
+![ICK](primary/Love_ICK.svg)
430
+
431
+Average rating: ★ ☆ ☆ ☆ ☆
432
+
433
+::: {style="page-break-after: always;"}
434
+:::
435
+
436
+### ITPR3 - fail (insufficient support)
437
+
438
+![ITPR3](primary/Love_ITPR3.svg)
439
+
440
+Average rating: ★ ☆ ☆ ☆ ☆
441
+
442
+### KIFC3 - fail (insufficient support)
443
+
444
+![KIFC3](primary/Love_KIFC3_2_56362071.png)
445
+
446
+Average rating: ★ ☆ ☆ ☆ ☆
447
+
448
+::: {style="page-break-after: always;"}
449
+:::
450
+
451
+### MAP3K6 - fail (insufficient support)
452
+
453
+![MAP3K6](primary/Love_MAP3K6.svg)
454
+
455
+Average rating: ★ ☆ ☆ ☆ ☆
456
+
457
+### MYH10 - fail (insufficient support)
458
+
459
+![MYH10](primary/Love_MYH10.svg)
460
+
461
+Average rating: ★ ☆ ☆ ☆ ☆
462
+
463
+::: {style="page-break-after: always;"}
464
+:::
465
+
466
+### NOTCH1 - fail (insufficient support)
467
+
468
+![NOTCH1](primary/Love_NOTCH1.svg)
469
+
470
+Average rating: ★ ☆ ☆ ☆ ☆
471
+
472
+### NRXN2 - fail (insufficient support)
473
+
474
+![NRXN2](primary/Love_NRXN2.svg)
475
+
476
+Average rating: ★ ☆ ☆ ☆ ☆
477
+
478
+::: {style="page-break-after: always;"}
479
+:::
480
+
481
+### PC - fail (insufficient support)
482
+
483
+![PC](primary/Love_PC_chr11_66374870.png)
484
+
485
+Average rating: ★ ☆ ☆ ☆ ☆
486
+
487
+### POLRMT - fail (insufficient support)
488
+
489
+![POLRMT](primary/Love_POLRMT.svg)
490
+
491
+Average rating: ★ ☆ ☆ ☆ ☆
492
+
493
+::: {style="page-break-after: always;"}
494
+:::
495
+
496
+### POR - fail (insufficient support)
497
+
498
+![POR](primary/Love_POR.svg)
499
+
500
+Average rating: ★ ☆ ☆ ☆ ☆
501
+
502
+### PRSS22 - fail (insufficient support)
503
+
504
+![PRSS22](primary/Love_PRSS22.svg)
505
+
506
+Average rating: ★ ☆ ☆ ☆ ☆
507
+
508
+::: {style="page-break-after: always;"}
509
+:::
510
+
511
+### PTPRN - fail (insufficient support)
512
+
513
+![PTPRN](primary/Love_PTPRN.svg)
514
+
515
+Average rating: ★ ☆ ☆ ☆ ☆
516
+
517
+### RBP3 - fail (insufficient support)
518
+
519
+![RBP3](primary/Love_RBP3.svg)
520
+
521
+Average rating: ★ ☆ ☆ ☆ ☆
522
+
523
+::: {style="page-break-after: always;"}
524
+:::
525
+
526
+### RET - fail (insufficient support)
527
+
528
+![RET](primary/Love_RET_42930092.png)
529
+
530
+Average rating: ★ ☆ ☆ ☆ ☆
531
+
532
+### SALL3 - fail (insufficient support)
533
+
534
+![SALL3](primary/Love_SALL3.svg)
535
+
536
+Average rating: ★ ★ ☆ ☆ ☆
537
+
538
+::: {style="page-break-after: always;"}
539
+:::
540
+
541
+### SAPS2 - fail (insufficient support)
542
+
543
+![SAPS2](primary/Love_SAPS2.svg)
544
+
545
+Average rating: ★ ☆ ☆ ☆ ☆
546
+
547
+### SBF1 - fail (insufficient support)
548
+
549
+![SBF1](primary/Love_SBF1.svg)
550
+
551
+Average rating: ★ ★ ☆ ☆ ☆
552
+
553
+::: {style="page-break-after: always;"}
554
+:::
555
+
556
+### SF3B1 - fail (insufficient support)
557
+
558
+![SF3B1](primary/Love_SF3B1.svg)
559
+
560
+Average rating: ★ ★ ★ ★ ☆
561
+
562
+### SLC29A2 - fail (insufficient support)
563
+
564
+![SLC29A2](primary/Love_SLC29A2.svg)
565
+
566
+Average rating: ★ ☆ ☆ ☆ ☆
567
+
568
+::: {style="page-break-after: always;"}
569
+:::
570
+
571
+### SHANK1 - fail (insufficient support)
572
+
573
+![SHANK1](primary/Love_SHANK1.svg)
574
+
575
+Average rating: ★ ☆ ☆ ☆ ☆
576
+
577
+### SYNGAP1 - fail (insufficient support)
578
+
579
+![SYNGAP1](primary/Love_SYNGAP1_33518868.png)
580
+
581
+Average rating: ★ ☆ ☆ ☆ ☆
582
+
583
+::: {style="page-break-after: always;"}
584
+:::
585
+
586
+### TBC1D9B - fail (insufficient support)
587
+
588
+![TBC1D9B](primary/Love_TBC1D9B.svg)
589
+
590
+Average rating: ★ ☆ ☆ ☆ ☆
591
+
592
+### TIGD6 - fail (insufficient support)
593
+
594
+![TIGD6](primary/Love_TIGD6.svg)
595
+
596
+Average rating: ★ ☆ ☆ ☆ ☆
597
+
598
+::: {style="page-break-after: always;"}
599
+:::
600
+
601
+### TPST2 - fail (insufficient support)
602
+
603
+![TPST2](primary/Love_TPST2.svg)
604
+
605
+Average rating: ★ ☆ ☆ ☆ ☆
606
+
607
+### ZNF229 - fail (germline)
608
+
609
+![ZNF229](primary/Love_ZNF229_chr19_49624750_also_in_germline.png)
610
+
611
+Average rating: Germline
612
+
613
+::: {style="page-break-after: always;"}
614
+:::
615
+
616
+### Reddy *et al*, 2017 `<a name="reddy">`{=html}`</a>`{=html}
617
+
618
+*See also:* [IGV
619
+reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/)
620
+
621
+ Methodology Pairs Unpaired tumors Cell lines Tier 1 Tier 2 Tier 3
622
+ ------------- ------- ----------------- ------------ -------- -------- ----------
623
+ Exome 400 601 0 13 28 26 (39%)
624
+
625
+### ARID5B - pass
626
+
627
+![ARID5B](primary/Reddy_ARID5B_1.svg)
628
+
629
+Average rating: ★ ★ ★ ★ ☆
630
+
631
+### ARID1B - fail (insufficient support)
632
+
633
+![ARID1B](primary/Reddy_ARID1B_1.svg)
634
+
635
+Average rating: ★ ★ ☆ ☆ ☆
636
+
637
+::: {style="page-break-after: always;"}
638
+:::
639
+
640
+### CBLB - fail (insufficient support)
641
+
642
+![CBLB](primary/Reddy_CBLB_1.svg)
643
+
644
+Average rating: ★ ★ ☆ ☆ ☆
645
+
646
+::: {style="page-break-after: always;"}
647
+:::
648
+
649
+### CDC73 - fail (insufficient support)
650
+
651
+![CDC73](primary/Reddy_CDC73.svg)
652
+
653
+Average rating: ★ ★ ☆ ☆ ☆
654
+
655
+### CHD8 - fail (insufficient support)
656
+
657
+![CHD8](primary/Reddy_CHD8.svg)
658
+
659
+Average rating: ★ ★ ☆ ☆ ☆
660
+
661
+::: {style="page-break-after: always;"}
662
+:::
663
+
664
+### CHD1 - fail (insufficient support)
665
+
666
+![CHD1](primary/Reddy_CHD1.svg)
667
+
668
+Average rating: ★ ★ ☆ ☆ ☆
669
+
670
+::: {style="page-break-after: always;"}
671
+:::
672
+
673
+### CHST2 - fail (insufficient support)
674
+
675
+![CHST2](primary/Reddy_CHST2.svg)
676
+
677
+Average rating: ★ ★ ☆ ☆ ☆
678
+
679
+::: {style="page-break-after: always;"}
680
+:::
681
+
682
+### DCAF6 - fail (insufficient support)
683
+
684
+![DCAF6](primary/Reddy_DCAF6.svg)
685
+
686
+Average rating: ★ ★ ☆ ☆ ☆
687
+
688
+::: {style="page-break-after: always;"}
689
+:::
690
+
691
+### DICER1 - fail (insufficient support)
692
+
693
+![DICER1](primary/Reddy_DICER1.svg)
694
+
695
+Average rating: ★ ★ ☆ ☆ ☆
696
+
697
+::: {style="page-break-after: always;"}
698
+:::
699
+
700
+### DNMT3A - fail (insufficient support)
701
+
702
+![DNMT3A](primary/Reddy_DNMT3A.svg)
703
+
704
+Average rating: ★ ☆ ☆ ☆ ☆
705
+
706
+::: {style="page-break-after: always;"}
707
+:::
708
+
709
+### GNAS - fail (insufficient support)
710
+
711
+![GNAS](primary/Reddy_GNAS.svg)
712
+
713
+Average rating: ★ ★ ☆ ☆ ☆
714
+
715
+::: {style="page-break-after: always;"}
716
+:::
717
+
718
+### HRAS - fail (insufficient support)
719
+
720
+![HRAS](primary/Reddy_HRAS.svg)
721
+
722
+Average rating: ★ ★ ☆ ☆ ☆
723
+
724
+::: {style="page-break-after: always;"}
725
+:::
726
+
727
+### LIN54 - fail (insufficient support)
728
+
729
+![LIN54](primary/Reddy_LIN54.svg)
730
+
731
+Average rating: ★ ★ ☆ ☆ ☆
732
+
733
+::: {style="page-break-after: always;"}
734
+:::
735
+
736
+### MAP4K4 - fail (insufficient support)
737
+
738
+![MAP4K4](primary/Reddy_MAP4K4.svg)
739
+
740
+Average rating: ★ ★ ☆ ☆ ☆
741
+
742
+::: {style="page-break-after: always;"}
743
+:::
744
+
745
+### MARK1 - fail (insufficient support)
746
+
747
+![MARK1](primary/Reddy_MARK1.svg)
748
+
749
+Average rating: ★ ☆ ☆ ☆ ☆
750
+
751
+::: {style="page-break-after: always;"}
752
+:::
753
+
754
+### MSH2 - fail (insufficient support)
755
+
756
+![MSH2](primary/Reddy_MSH2.svg)
757
+
758
+Average rating: ★ ★ ☆ ☆ ☆
759
+
760
+::: {style="page-break-after: always;"}
761
+:::
762
+
763
+### MYB - fail (insufficient support)
764
+
765
+![MYB](primary/Reddy_MYB.svg)
766
+
767
+Average rating: ★ ★ ☆ ☆ ☆
768
+
769
+::: {style="page-break-after: always;"}
770
+:::
771
+
772
+### NCOR1 - fail (insufficient support)
773
+
774
+![NCOR1](primary/Reddy_NCOR1.svg)
775
+
776
+Average rating: ★ ★ ☆ ☆ ☆
777
+
778
+::: {style="page-break-after: always;"}
779
+:::
780
+
781
+### NFKB2 - fail (insufficient support)
782
+
783
+![NFKB2](primary/Reddy_NFKB2.svg)
784
+
785
+Average rating: ★ ★ ☆ ☆ ☆
786
+
787
+::: {style="page-break-after: always;"}
788
+:::
789
+
790
+### PHF6 - fail (insufficient support)
791
+
792
+![PHF6](primary/Reddy_PHF6.svg)
793
+
794
+Average rating: ★ ★ ☆ ☆ ☆
795
+
796
+::: {style="page-break-after: always;"}
797
+:::
798
+
799
+### PTPRK - fail (insufficient support)
800
+
801
+![PTPRK](primary/Reddy_PTPRK.svg)
802
+
803
+Average rating: ★ ★ ☆ ☆ ☆
804
+
805
+::: {style="page-break-after: always;"}
806
+:::
807
+
808
+### RARA - fail (insufficient support)
809
+
810
+![RARA](primary/Reddy_RARA.svg)
811
+
812
+Average rating: ★ ☆ ☆ ☆ ☆
813
+
814
+::: {style="page-break-after: always;"}
815
+:::
816
+
817
+### RUNX1 - fail (insufficient support)
818
+
819
+![RUNX1](primary/Reddy_RUNX1.svg)
820
+
821
+Average rating: ★ ★ ☆ ☆ ☆
822
+
823
+::: {style="page-break-after: always;"}
824
+:::
825
+
826
+### SYK - fail (insufficient support)
827
+
828
+![SYK](primary/Reddy_SYK.svg)
829
+
830
+Average rating: ★ ★ ☆ ☆ ☆
831
+
832
+::: {style="page-break-after: always;"}
833
+:::
834
+
835
+### WAC - fail (insufficient support)
836
+
837
+![WAC](primary/Reddy_WAC.svg)
838
+
839
+Average rating: ★ ★ ☆ ☆ ☆
840
+
841
+::: {style="page-break-after: always;"}
842
+:::
843
+
844
+### ZBTB7A - fail (insufficient support)
845
+
846
+![ZBTB7A](primary/Reddy_ZBTB7A.svg)
847
+
848
+Average rating: ★ ☆ ☆ ☆ ☆
849
+
850
+::: {style="page-break-after: always;"}
851
+:::
852
+
853
+### ZFAT - fail (insufficient support)
854
+
855
+![ZFAT](primary/Reddy_ZFAT.svg)
856
+
857
+Average rating: ★ ★ ☆ ☆ ☆
858
+
859
+::: {style="page-break-after: always;"}
860
+:::
861
+
862
+### [Morin *et al*, 2013](https://ashpublications.org/blood/article/122/7/1256/32425/Mutational-and-structural-analysis-of-diffuse) `<a name="morin">`{=html}`</a>`{=html}
863
+
864
+ Methodology Pairs Unpaired tumors Cell lines Tier 1 Tier 2 Tier 3
865
+ ------------- ------- ----------------- ------------ -------- -------- ---------
866
+ WGS 40 0 13 9 23 7 (18%)
867
+
868
+*See also:* [IGV
869
+reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Morin_2013/)
870
+
871
+### HDAC7 - pass
872
+
873
+![HDAC7](primary/Morin_HDAC7.svg)
874
+
875
+Average rating: ★ ★ ★ ☆ ☆
876
+
877
+::: {style="page-break-after: always;"}
878
+:::
879
+
880
+### FAM38B - fail (insufficient support)
881
+
882
+![FAM38B](primary/Morin_FAM38B.svg)
883
+
884
+::: {style="page-break-after: always;"}
885
+:::
886
+
887
+### FNDC1 - fail (insufficient support)
888
+
889
+![FNDC1](primary/Morin_FNDC1.svg)
890
+
891
+::: {style="page-break-after: always;"}
892
+:::
893
+
894
+### IER2 - fail (insufficient support)
895
+
896
+![IER2](primary/Morin_IER2.svg)
897
+
898
+::: {style="page-break-after: always;"}
899
+:::
900
+
901
+### PKD1 - fail (insufficient support)
902
+
903
+![PKD1](primary/Morin_PKD1.svg)
904
+
905
+::: {style="page-break-after: always;"}
906
+:::
907
+
908
+### POGZ - fail (insufficient support)
909
+
910
+![POGZ](primary/Morin_POGZ.svg)
911
+
912
+::: {style="page-break-after: always;"}
913
+:::
914
+
915
+### PTPN23 - fail (insufficient support)
916
+
917
+![PTPN23](primary/Morin_PTPN23.svg)
918
+
919
+::: {style="page-break-after: always;"}
920
+:::
921
+
922
+### SARM1 - fail (insufficient support)
923
+
924
+![SARM1](primary/Morin_SARM1.svg)
925
+
926
+::: {style="page-break-after: always;"}
927
+:::
928
+
929
+### Panea *et al*, 2019 `<a name="panea">`{=html}`</a>`{=html}
930
+
931
+*See also:* [IGV
932
+reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Panea/)
933
+
934
+ Methodology Pairs Unpaired tumors Cell lines Tier 1 Tier 2 Tier 3
935
+ ------------- ------- ----------------- ------------ -------- -------- ----------
936
+ WGS 101 0 0 2 15 22 (56%)
937
+
938
+### CXCR4 - pass
939
+
940
+![CXCR4](primary/Panea_CXCR4_1.svg)
941
+
942
+### ALPK2 - fail (insufficient support)
943
+
944
+![ALPK2](primary/Panea_ALPK2.svg)
945
+
946
+::: {style="page-break-after: always;"}
947
+:::
948
+
949
+### CD79B - fail (insufficient support, RNA-only)
950
+
951
+![CD79B](primary/Panea_CD79B.svg)
952
+
953
+### CTCF - fail (insufficient support)
954
+
955
+![CTCF](primary/Panea_CTCF_1.svg)
956
+
957
+::: {style="page-break-after: always;"}
958
+:::
959
+
960
+### DNMT1 - fail (insufficient support)
961
+
962
+![DNMT1](primary/Panea_DNMT1_1.svg)
963
+
964
+### ETS1 - fail (insufficient support, RNA-only)
965
+
966
+![ETS1](primary/Panea_ETS1_1.svg)
967
+
968
+::: {style="page-break-after: always;"}
969
+:::
970
+
971
+### FZD3 - fail (insufficient support)
972
+
973
+![FZD3](primary/Panea_FZD3_1.svg)
974
+
975
+::: {style="page-break-after: always;"}
976
+:::
977
+
978
+### HIST1H1C - fail (insufficient support)
979
+
980
+![HIST1H1C](primary/Panea_HIST1H1C_3.svg)
981
+
982
+::: {style="page-break-after: always;"}
983
+:::
984
+
985
+### HIST1H2AG - fail (insufficient support)
986
+
987
+![HIST1H2AG](primary/Panea_HIST1H2AG_3.svg)
988
+
989
+### HIST1H2AM - fail (insufficient support, RNA-only)
990
+
991
+![HIST1H2AM](primary/Panea_HIST1H2AM_1.svg)
992
+
993
+::: {style="page-break-after: always;"}
994
+:::
995
+
996
+### HIST1H2BK - fail (insufficient support)
997
+
998
+![HIST1H2BK](primary/Panea_HIST1H2BK_1.svg)
999
+
1000
+### HIST1H3H - fail (insufficient support)
1001
+
1002
+![HIST1H3H](primary/Panea_HIST1H3H_1.svg)
1003
+
1004
+::: {style="page-break-after: always;"}
1005
+:::
1006
+
1007
+### HIST1H3J - fail (insufficient support)
1008
+
1009
+![HIST1H3J](primary/Panea_HIST1H3J_1.svg)
1010
+
1011
+### KCNK10 - fail (insufficient support)
1012
+
1013
+![KCNK10](primary/Panea_KCNK10_1.svg)
1014
+
1015
+### MME - fail (insufficient support)
1016
+
1017
+![MME](primary/Panea_MME_1.svg)
1018
+
1019
+::: {style="page-break-after: always;"}
1020
+:::
1021
+
1022
+### MTOR - fail (insufficient support)
1023
+
1024
+![MTOR](primary/Panea_MTOR_1.svg)
1025
+
1026
+### PABPC4L - fail (insufficient support)
1027
+
1028
+![PABPC4L](primary/Panea_PABPC4L_1.svg)
1029
+
1030
+### PCDHA11 - fail (insufficient support)
1031
+
1032
+![PCDHA11](primary/Panea_PCDHA11_1.svg)
1033
+
1034
+### PDZRN3 - fail (insufficient support)
1035
+
1036
+![PDZRN3](primary/Panea_PDZRN3_1.svg)
1037
+
1038
+::: {style="page-break-after: always;"}
1039
+:::
1040
+
1041
+### PIK3R1 - fail (insufficient support)
1042
+
1043
+![PIK3R1](primary/Panea_PIK3R1_1.svg)
1044
+
1045
+### PXDNL - fail (insufficient support)
1046
+
1047
+![PXDNL](primary/Panea_PXDNL_1.svg)
1048
+
1049
+### SNTB2 - fail (insufficient support)
1050
+
1051
+![SNTB2](primary/Panea_SNTB2_1.svg)
1052
+
1053
+::: {style="page-break-after: always;"}
1054
+:::
1055
+
1056
+### WDR7 - fail (insufficient support)
1057
+
1058
+![WDR7](primary/Panea_WDR7_3.svg)
1059
+
1060
+::: {style="page-break-after: always;"}
1061
+:::
1062
+
1063
+### Chapuy *et al*, 2018 `<a name="chapuy">`{=html}`</a>`{=html}
1064
+
1065
+*See also:* [IGV
1066
+reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/)
1067
+
1068
+ Methodology Pairs Unpaired tumors Cell lines Tier 1 Tier 2 Tier 3
1069
+ ------------- ------- ----------------- ------------ -------- -------- --------
1070
+ Exome 137 167 0 10 13 6(21%)
1071
+
1072
+### DOCK1 - pass
1073
+
1074
+![DOCK1](primary/Chapuy_DOCK1.svg)
1075
+
1076
+::: {style="page-break-after: always;"}
1077
+:::
1078
+
1079
+### FUT5 - fail (insufficient support)
1080
+
1081
+![FUT5](primary/Chapuy_FUT5.svg)
1082
+
1083
+::: {style="page-break-after: always;"}
1084
+:::
1085
+
1086
+### NLRP8 - fail (insufficient support)
1087
+
1088
+![NLRP8](primary/Chapuy_NLRP8.svg)
1089
+
1090
+::: {style="page-break-after: always;"}
1091
+:::
1092
+
1093
+### PDE4DIP - fail (insufficient support)
1094
+
1095
+![PDE4DIP](primary/Chapuy_PDE4DIP.svg)
1096
+
1097
+::: {style="page-break-after: always;"}
1098
+:::
1099
+
1100
+### Hübschmann *et al*, 2021 `<a name="icgc">`{=html}`</a>`{=html}
1101
+
1102
+*See also:* [IGV
1103
+reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/)
1104
+
1105
+ Methodology Pairs Unpaired tumors Cell lines Tier 1 Tier 2 Tier 3
1106
+ ------------- ------- ----------------- ------------ -------- -------- ----------
1107
+ WGS 179 2 0 5 31 3 (7.7%)
1108
+
1109
+### IKBKE - pass
1110
+
1111
+![IKBKE](primary/ICGC_IKBKE.svg)
1112
+
1113
+::: {style="page-break-after: always;"}
1114
+:::
1115
+
1116
+### GAK - fail (insufficient support)
1117
+
1118
+![GAK](primary/ICGC_GAK.svg)
1119
+
1120
+::: {style="page-break-after: always;"}
1121
+:::
1122
+
1123
+### HLA-DQA1 - fail (insufficient support)
1124
+
1125
+![HLA-DQA1](primary/ICGC_HLA-DQA1.svg)
1126
+
1127
+::: {style="page-break-after: always;"}
1128
+:::
1129
+
1130
+### NR2F2 - fail (insufficient support)
1131
+
1132
+![NR2F2](primary/ICGC_NR2F2.svg)
1133
+
1134
+::: {style="page-break-after: always;"}
1135
+:::
1136
+
1137
+## References {#references .unnumbered}
1138
+
1139
+:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: {#refs .references .csl-bib-body}
1140
+::: {#ref-albuquerqueEnhancingKnowledgeDiscovery2017 .csl-entry}
1141
+[1. ]{.csl-left-margin}[Albuquerque MA, Grande BM, Ritch EJ,
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+Morin RD. Enhancing knowledge discovery from cancer genomics data with
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1146
+:::
1147
+
1148
+::: {#ref-arthurGenomewideDiscoverySomatic2018 .csl-entry}
1149
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+Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L,
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+Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B,
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+Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB,
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+Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P,
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+Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide
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1158
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1159
+
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1161
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1165
+:::
1166
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1167
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1168
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1177
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1179
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1180
+
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1182
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+Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L. Mutations of
1185
+multiple genes cause deregulation of [NF-kappaB]{.nocase} in diffuse
1186
+large [B-cell]{.nocase} lymphoma. Nature. 2009 Jun 4;459(7247):717--721.
1187
+PMCID:
1188
+[PMC2973325](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2973325)]{.csl-right-inline}
1189
+:::
1190
+
1191
+::: {#ref-davisChronicActiveBcellreceptor2010 .csl-entry}
1192
+[6. ]{.csl-left-margin}[Davis RE, Ngo VN, Lenz G, Tolar P, Young RM,
1193
+Romesser PB, Kohlhammer H, Lamy L, Zhao H, Yang Y, Xu W, Shaffer AL,
1194
+Wright G, Xiao W, Powell J, Jiang JK, Thomas CJ, Rosenwald A, Ott G,
1195
+Müller-Hermelink HK, Gascoyne RD, Connors JM, Johnson NA, Rimsza LM,
1196
+Campo E, Jaffe ES, Wilson WH, Delabie J, Smeland EB, Fisher RI, Braziel
1197
+RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pierce SK, Staudt LM.
1198
+Chronic active [B-cell-receptor]{.nocase} signalling in diffuse large
1199
+[B-cell]{.nocase} lymphoma. Nature. 2010 Jan;463(7277):88--92. PMCID:
1200
+[PMC2845535](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845535)]{.csl-right-inline}
1201
+:::
1202
+
1203
+::: {#ref-drevalGeneticSubdivisionsFollicular2023 .csl-entry}
1204
+[7. ]{.csl-left-margin}[Dreval K, Hilton LK, Cruz M, Shaalan H,
1205
+Ben-Neriah S, Boyle M, Collinge B, Coyle KM, Duns G, Farinha P, Grande
1206
+BM, Meissner B, Pararajalingam P, Rushton CK, Slack GW, Wong J, Mungall
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+AJ, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genetic
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+subdivisions of follicular lymphoma defined by distinct coding and
1209
+noncoding mutation patterns. Blood. 2023 Aug 10;142(6):561--573. PMCID:
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+[PMC10644066](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10644066)]{.csl-right-inline}
1211
+:::
1212
+
1213
+::: {#ref-dunsCharacterizationDLBCLPMBL2021 .csl-entry}
1214
+[8. ]{.csl-left-margin}[Duns G, Viganò E, Ennishi D, Sarkozy C, Hung SS,
1215
+Chavez E, Takata K, Rushton C, Jiang A, Ben-Neriah S, Woolcock BW, Slack
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+GW, Hsi ED, Craig JW, Hilton LK, Shah SP, Farinha P, Mottok A, Gascoyne
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+RD, Morin RD, Savage KJ, Scott DW, Steidl C. [Characterization of DLBCL
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+with a PMBL gene expression
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1220
+15;138(2):136--148. ]{.csl-right-inline}
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+:::
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1228
+:::
1229
+
1230
+::: {#ref-hubschmannMutationalMechanismsShaping2021 .csl-entry}
1231
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+Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann
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+AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo
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+JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A,
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+Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W,
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+Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining
1243
+consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R.
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+Mutational mechanisms shaping the coding and noncoding genome of
1245
+germinal center derived [B-cell]{.nocase} lymphomas. Leukemia. 2021
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+Jul;35(7):2002--2016. PMCID:
1247
+[PMC8257491](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8257491)]{.csl-right-inline}
1248
+:::
1249
+
1250
+::: {#ref-khodabakhshiRecurrentTargetsAberrant2012 .csl-entry}
1251
+[11. ]{.csl-left-margin}[Khodabakhshi AH, Morin RD, Fejes AP, Mungall
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+AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors JM, Gascoyne RD,
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+Marra MA, Birol I, Jones SJM. Recurrent targets of aberrant somatic
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+[PMC3717795](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717795)]{.csl-right-inline}
1256
+:::
1257
+
1258
+::: {#ref-kwanhianMicroRNA142Mutated202012 .csl-entry}
1259
+[12. ]{.csl-left-margin}[Kwanhian W, Lenze D, Alles J, Motsch N, Barth
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+S, Döll C, Imig J, Hummel M, Tinguely M, Trivedi P, Lulitanond V,
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+Meister G, Renner C, Grässer FA. MicroRNA-142 is mutated in about 20% of
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+diffuse large [B-cell]{.nocase} lymphoma. Cancer Med. 2012
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+Oct;1(2):141--155. PMCID:
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+[PMC3544448](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544448)]{.csl-right-inline}
1265
+:::
1266
+
1267
+::: {#ref-lenzOncogenicCARD11Mutations2008 .csl-entry}
1268
+[13. ]{.csl-left-margin}[Lenz G, Davis RE, Ngo VN, Lam L, George TC,
1269
+Wright GW, Dave SS, Zhao H, Xu W, Rosenwald A, Ott G, Müller-Hermelink
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+HK, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J,
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+Smeland EB, Fisher RI, Chan WC, Staudt LM. [Oncogenic CARD11 mutations
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+in human diffuse large B cell
1273
+lymphoma.](https://doi.org/10.1126/science.1153629) Science. 2008
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+Mar;319(5870):1676--1679. ]{.csl-right-inline}
1275
+:::
1276
+
1277
+::: {#ref-lohrDiscoveryPrioritizationSomatic2012 .csl-entry}
1278
+[14. ]{.csl-left-margin}[Lohr JG, Stojanov P, Lawrence MS, Auclair D,
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+Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL,
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+Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G,
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+:::
1290
+
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+::: {#ref-mareschalWholeExomeSequencing2016 .csl-entry}
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+2016 Mar;55(3):251--267. ]{.csl-right-inline}
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+
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1339
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+:::
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1387
+
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+Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G,
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+::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::