BCL7A.md
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@@ -73,13 +73,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
73 73
<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
74 74
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
75 75
## References
76
-1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972
77
-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
78
-3. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379
79
-4. Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.
76
+1. *Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972*
77
+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*
78
+3. *Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379*
79
+4. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
80 80
5. *Ramos-Medina R, Montes-Moreno S, Maestre L, Cañamero M, Rodríguez-Pinilla M, Martínez-Torrecuadrada J, Piris MÁ, Majid A, Dyer MJ, Pulford K, Roncador G. BCL7A protein expression in normal and malignant lymphoid tissues. Br J Haematol. 2013 Jan;160(1):106-9. doi: 10.1111/bjh.12080. Epub 2012 Oct 9. PMID: 23043359.*
81 81
6. *Baliñas-Gavira C, Rodríguez MI, Andrades A, Cuadros M, Álvarez-Pérez JC, Álvarez-Prado ÁF, de Yébenes VG, Sánchez-Hernández S, Fernández-Vigo E, Muñoz J, Martín F, Ramiro AR, Martínez-Climent JA, Medina PP. Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL. Leukemia. 2020 Oct;34(10):2722-2735. doi: 10.1038/s41375-020-0919-5. Epub 2020 Jun 24. PMID: 32576963.*
82
-7. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379
83 82
84 83
85 84
BIRC6.md
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@@ -2,8 +2,15 @@
2 2
3 3
## Overview
4 4
BIRC6, as a negative regulator of non-canonical NF-κB signaling, is implicated in lymphomagenesis. Mutations in the BIRC6 have been found in DLBCL and grey zone lymphoma (GZL).<sup>1,2</sup>
5
-
6
-
5
+## History
6
+
7
+```mermaid
8
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
9
+timeline
10
+ title Publication timing
11
+ 2017-10-10 : Reddy : DLBCL
12
+ 2021-04-01 : Sarkozy : PMBL
13
+```
7 14
## Relevance tier by entity
8 15
9 16
|Entity|Tier|Description |
BMP7.md
... ...
@@ -1,5 +1,11 @@
1 1
# BMP7
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
BMP7.pdf
... ...
Binary files /dev/null and b/BMP7.pdf differ
BRINP3.md
... ...
@@ -7,6 +7,12 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup
7 7
> Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1)
8 8
9 9
10
+```mermaid
11
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
12
+timeline
13
+ title Publication timing
14
+ 2017-10-10 : Reddy : DLBCL
15
+```
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## Relevance tier by entity
11 17
12 18
|Entity|Tier|Description |
BTBD3.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
10
+```
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## Relevance tier by entity
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7 13
|Entity|Tier|Description |
BTG2.md
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@@ -1,7 +1,15 @@
1 1
# BTG2
2 2
## Overview
3 3
BTG2 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. Mutations in the BTG2 gene have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL), contributing to the development and progression of the disease. These mutations are a feature of the MCD genetic subgroup of DLBCL.<sup>1</sup> The biological function of BTG2 mutations and their role in lymphomagenesis remains poorly understood. A potential prognostic association with BTG2 mutations in primary testicular DLBCL has been reported but this has not yet been reproduced.<sup>2</sup>
4
-
4
+## History
5
+
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2011-07-27 : Morin : DLBCL
11
+ 2012-12-01 : Love : BL
12
+```
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## Relevance tier by entity
6 14
7 15
|Entity|Tier|Description |
BTK.md
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@@ -1,6 +1,13 @@
1 1
# BTK
2 2
One study reported BTK mutations in approximately 7% of FL and 11% of transformed FL cases.<sup>1</sup> Another showed these mutations were more common, and typically co-occur in tumours with BCL2 translocations. Despite the known role of certain BTK mutations in acquired resistance to BTK inhibitors, these mutations were found in BTK inhibitor-naïve patients.<sup>2</sup> These mutations often occur in treatment-naive patients and lead to inactivation of the BTK protein through destabilization or by altering key residues involved in enzymatic activity.<sup>1</sup> The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations*. No notable hot spots have been described in this gene in the context of the cancers listed below.
3
-
3
+## History
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2017-01-26 : Krysiak : FL
9
+ 2017-05-01 : Albuquerque : DLBCL
10
+```
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## Relevance tier by entity
5 12
6 13
|Entity|Tier|Description |
... ...
@@ -36,11 +43,15 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
36 43
37 44
![image](images/proteinpaint/BTK.svg)
38 45
39
-## References
40
-1. *Hu N, Wang F, Sun T, Xu Z, Zhang J, Bernard D, Xu S, Wang S, Kaminski M, Devata S, Phillips T, Malek SN. Follicular Lymphoma-associated BTK Mutations are Inactivating Resulting in Augmented AKT Activation. Clin Cancer Res. 2021 Apr 15;27(8):2301-2313. doi: 10.1158/1078-0432.CCR-20-3741. Epub 2021 Jan 8. PMID: 33419778; PMCID: PMC8046715.*
41
-2. *Schejbel L, Breinholt MF, Gang AO, Nielsen TH, Pedersen LM, Høgdall E, Nørgaard P. Inactivating BTK mutations in large B-cell lymphoma in a real-world cohort: Strong correlation with BCL2 translocation. EJHaem. 2022 Jun 24;3(3):936-939. doi: 10.1002/jha2.489. PMID: 36051027; PMCID: PMC9421985.*
46
+
42 47
## BTK Expression
43 48
![image](images/gene_expression/BTK_by_pathology.svg)
44 49
<!-- ORIGIN: albuquerqueEnhancingKnowledgeDiscovery2017a -->
45 50
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
46 51
<!-- DLBCL: albuquerqueEnhancingKnowledgeDiscovery2017a -->
52
+## References
53
+1. 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
54
+2. Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience. 2017 May 1;6(5):1–13. PMCID: PMC5437943
55
+
56
+3. *Hu N, Wang F, Sun T, Xu Z, Zhang J, Bernard D, Xu S, Wang S, Kaminski M, Devata S, Phillips T, Malek SN. Follicular Lymphoma-associated BTK Mutations are Inactivating Resulting in Augmented AKT Activation. Clin Cancer Res. 2021 Apr 15;27(8):2301-2313. doi: 10.1158/1078-0432.CCR-20-3741. Epub 2021 Jan 8. PMID: 33419778; PMCID: PMC8046715.*
57
+4. *Schejbel L, Breinholt MF, Gang AO, Nielsen TH, Pedersen LM, Høgdall E, Nørgaard P. Inactivating BTK mutations in large B-cell lymphoma in a real-world cohort: Strong correlation with BCL2 translocation. EJHaem. 2022 Jun 24;3(3):936-939. doi: 10.1002/jha2.489. PMID: 36051027; PMCID: PMC9421985.*
CASP8.md
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@@ -1,5 +1,4 @@
1 1
# CASP8
2
-
3 2
## Overview
4 3
5 4
Caspase-8 mutations are relatively rare but have been documented in various non-Hodgkin lymphomas (NHLs). One study found no CASP8 mutations in gastrointestinal lymphomas, suggesting that these mutations may not be prevalent in all lymphoma types.<sup>1</sup> Due to the rarity of these mutations, their role remains poorly understood. Loss of caspase-8 may promote lymphomagenesis by impairing cytokinesis and increasing chromosomal aberrations.<sup>2</sup>
... ...
@@ -7,6 +6,12 @@ Caspase-8 mutations are relatively rare but have been documented in various non-
7 6
## History
8 7
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup>
9 8
9
+```mermaid
10
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
11
+timeline
12
+ title Publication timing
13
+ 2017-10-10 : Reddy : DLBCL
14
+```
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## Relevance tier by entity
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|Entity|Tier|Description |
CCDC42BPB.md
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@@ -3,6 +3,12 @@
3 3
## History
4 4
Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
5 5
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+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2021-05-05 : Hübschmann : FL
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+```
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CCDC42BPB_tmp.html
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+.hljs-params,
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+.hljs-meta,
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+.hljs-link {
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+ color: #f5871f;
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+}
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+
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+/* Tomorrow Yellow */
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+.hljs-attribute {
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+ color: #eab700;
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+}
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+
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+/* Tomorrow Green */
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+.hljs-string,
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+.hljs-symbol,
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+.hljs-bullet,
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+.hljs-addition {
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+ color: #718c00;
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+}
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+
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+/* Tomorrow Blue */
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+.hljs-title,
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+.hljs-section {
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+ color: #4271ae;
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+}
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+
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+/* Tomorrow Purple */
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+.hljs-keyword,
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+.hljs-selector-tag {
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+ color: #8959a8;
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+}
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+
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+.hljs {
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+ display: block;
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+ overflow-x: auto;
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+ color: #4d4d4c;
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+ padding: 0.5em;
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+}
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+
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+.hljs-emphasis {
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+ font-style: italic;
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+}
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+
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+.hljs-strong {
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+ font-weight: bold;
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+}
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+</style>
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+
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+<style>
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+/*
307
+ * Markdown PDF CSS
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+ */
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+
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+ body {
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+ font-family: -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif, "Meiryo";
312
+ padding: 0 12px;
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+}
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+
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+pre {
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+ background-color: #f8f8f8;
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+ border: 1px solid #cccccc;
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+ border-radius: 3px;
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+ overflow-x: auto;
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+ white-space: pre-wrap;
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+ overflow-wrap: break-word;
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+}
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+
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+pre:not(.hljs) {
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+ padding: 23px;
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+ line-height: 19px;
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+}
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+
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+blockquote {
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+ background: rgba(127, 127, 127, 0.1);
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+ border-color: rgba(0, 122, 204, 0.5);
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+}
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+
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+.emoji {
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+ height: 1.4em;
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+}
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+
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+code {
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+ font-size: 14px;
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+ line-height: 19px;
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+}
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+
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+/* for inline code */
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+:not(pre):not(.hljs) > code {
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+ color: #C9AE75; /* Change the old color so it seems less like an error */
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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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+-------------------------------------------------------- */
351
+.page {
352
+ 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>
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+</head>
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+<body>
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+ <script>
361
+ mermaid.initialize({
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+ startOnLoad: true,
363
+ theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
364
+ ? 'dark'
365
+ : 'default'
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+ });
367
+ </script>
368
+<h1 id="ccdc42bpb">CCDC42BPB</h1>
369
+<h2 id="history">History</h2>
370
+<p>Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup></p>
371
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
372
+timeline
373
+ title Publication timing
374
+ 2021-05-05 : Hübschmann : FL
375
+</div></code></pre>
376
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
377
+<table>
378
+<thead>
379
+<tr>
380
+<th style="text-align:center">Entity</th>
381
+<th style="text-align:center">Tier</th>
382
+<th>Description</th>
383
+</tr>
384
+</thead>
385
+<tbody>
386
+<tr>
387
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/FL_tier2.png" alt="FL"></td>
388
+<td style="text-align:center">2</td>
389
+<td>relevance in FL not firmly established</td>
390
+</tr>
391
+</tbody>
392
+</table>
393
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
394
+<table>
395
+<thead>
396
+<tr>
397
+<th style="text-align:center">Entity</th>
398
+<th style="text-align:center">source</th>
399
+<th style="text-align:center">frequency (%)</th>
400
+</tr>
401
+</thead>
402
+<tbody>
403
+<tr>
404
+<td style="text-align:center">FL</td>
405
+<td style="text-align:center">GAMBL genomes</td>
406
+<td style="text-align:center">NA</td>
407
+</tr>
408
+</tbody>
409
+</table>
410
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
411
+<p>|</p>
412
+<blockquote>
413
+<p>[!NOTE]
414
+First described in FL in 2021 by <a href="https://pubmed.ncbi.nlm.nih.gov/33953289">Hübschmann D</a></p>
415
+</blockquote>
416
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_protein_hg38.html">hg38</a></p>
417
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CCDC42BPB_hg38.html">hg38</a></p>
418
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CCDC42BPB.svg" alt="image"></p>
419
+<h2 id="ccdc42bpb-expression">CCDC42BPB Expression</h2>
420
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/CCDC42BPB_by_pathology.svg" alt="image"></p>
421
+<h2 id="references">References</h2>
422
+<ol>
423
+<li>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</li>
424
+</ol>
425
+<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
426
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
427
+
428
+</body>
429
+</html>
CD22.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
CD274.md
... ...
@@ -1,7 +1,13 @@
1 1
# CD274
2 2
## Overview
3 3
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.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-27 : Morin : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
CD36.md
... ...
@@ -1,7 +1,13 @@
1 1
# CD36
2 2
3 3
CD36 is a transmembrane glycoprotein involved in fatty acid metabolism, glucose intolerance, and immune responses. It is expressed on various cell types, including platelets, monocytes, and some lymphocytes. One study showed higher rates of CD36 mutations in FL relative to DLBCLs.<sup>1</sup>
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-31 : Pasqualucci : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
CD58.md
... ...
@@ -2,7 +2,14 @@
2 2
## Overview
3 3
4 4
CD58, also known as lymphocyte function-associated antigen 3 (LFA-3), is crucial for immune recognition, facilitating interactions between tumor cells and cytotoxic T cells and natural killer (NK) cells. In DLBCL, mutations prevent the expression of CD58 on the cell surface, impairing the ability of T and NK cells to recognize and attack the tumor cells. This is often accompanied by mutations in the β2-Microglobulin gene, which further aids in immune evasion.<sup>1</sup>
5
-
5
+## History
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2011-07-27 : Morin : DLBCL
11
+ 2015-10-01 : Schneider : PMBL
12
+```
6 13
## Relevance tier by entity
7 14
8 15
|Entity|Tier|Description |
CD70.md
... ...
@@ -1,7 +1,14 @@
1 1
# CD70
2 2
## Overview
3 3
CD70 is a costimulatory molecule expressed on some activated lymphocytes and has a role in T-cell-mediated immune responses.<sup>1</sup> CD70 aberrations are relatively common in DLBCL and appear more frequent in certain DLBCL patient populations. For instance, in a Chinese DLBCL cohort, 24% of cases exhibited CD70 genetic changes, compared to 10.8% in a Swedish cohort.<sup>1</sup> CD70 mutations are associated with the BN2 genetic subtype of DLBCL.<sup>2</sup> The mutation pattern in CD70 is consistent with the preferential accumulation of *inactivating mutations*. Loss of CD70 protein expression has been described.<sup>1</sup> Genetic perturbation limits the development of an effective CD8+ T-cell immune response in Bcl6-driven DLBCL. In mouse models, CD70 loss promoted lymphomagenesis, consistent with its role as a tumor suppressor gene in B-cell lymphomas.<sup>1,3</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
+ 2023-07-26 : Russler : FL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
CD79B.md
... ...
@@ -1,7 +1,14 @@
1 1
# CD79B
2 2
## Overview
3 3
CD79B mutations significantly contribute to the pathogenesis of DLBCL by enhancing BCR signaling and promoting tumor survival. These mutations, especially when co-occurring with MYD88 mutations, define a unique molecular subtype.<sup>1</sup> This has clinical and therapeutic implications as it may contribute sensitivity to BTK inhibitors. In an inducible mouse model of MYD88-driven DLBCL, CD79B mutations did not accelerate lymphomagenesis but demonstrated an increased sensitivity to pharmacological BTK inhibition.<sup>2</sup> In a retrospective analysis, younger patients with MCD DLBCL that were treated with ibrutinib had significantly better outcomes.<sup>3</sup> The most common hotspot mutation in CD79B is at the tyrosine residue 196 (Y196). This and other common mutations primarily occur in the immunoreceptor tyrosine-based activation motif (ITAM) domain and prevent the negative regulatory feedback provided by Lyn kinase thereby enhancing BCR signaling.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-27 : Morin : DLBCL
10
+ 2019-09-26 : Panea : BL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
CD83.md
... ...
@@ -7,6 +7,15 @@ CD83 is a transmembrane protein that plays a role in the immune system, particul
7 7
Mutations in this gene were first described in DLBCL in 2013 by Morin et al<sup>2</sup>, in BL in 2019 by Panea et al<sup>3</sup> and in FL in 2023 by Russler-Germain et al.<sup>4</sup>
8 8
9 9
10
+```mermaid
11
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
12
+timeline
13
+ title Publication timing
14
+ 2013-08-15 : Morin : DLBCL
15
+ 2019-09-26 : Panea : BL
16
+ 2021-07-15 : Duns : PMBL
17
+ 2023-07-26 : Russler : FL
18
+```
10 19
## Relevance tier by entity
11 20
12 21
|Entity|Tier|Description |
CDC73.md
... ...
@@ -2,6 +2,13 @@
2 2
## History
3 3
Mutations in this gene were first described in BL in 2012 by Love et al<sup>1</sup> and subsequently in DLBCL by Reddy et al.<sup>2</sup> Subsequent exome and genome-wide studies of DLBCL and BL did not reproduce these observations.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2012-12-01 : Love : BL
10
+ 2017-10-10 : Reddy : DLBCL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
CDKN2A.md
... ...
@@ -6,6 +6,14 @@ Although CDKN2A aberrations are common in DLBCL, this gene is predominantly affe
6 6
Mutations in this gene were first described in DLBCL and FL in 2013 by Morin et al<sup>2</sup> and in BL in 2019 by Grande et al.<sup>3</sup>
7 7
8 8
9
+```mermaid
10
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
11
+timeline
12
+ title Publication timing
13
+ 2013-08-15 : Morin : DLBCL
14
+ 2016-09-08 : Spina : MZL
15
+ 2019-03-21 : Grande : BL
16
+```
9 17
## Relevance tier by entity
10 18
11 19
|Entity|Tier|Description |
CHD1.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
CHST2.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
CIITA.md
... ...
@@ -2,6 +2,13 @@
2 2
## Overview
3 3
CIITA encodes the major histocompatibility complex (MHC) class II transactivator. CIITA mutations are frequent in PMBCL. These mutations often include structural genomic rearrangements, missense, nonsense, and frameshift mutations. In PMBCL, these mutations are thought to contribute to loss of MHC expression.<sup>1</sup> Although loss of CIITA and MHC Class II Expression is commonly observed in DLBCL, the role of mutations and methylation affecting this locus remains unclear.<sup>2</sup> CIITA 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.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2011-07-27 : Morin : DLBCL
10
+ 2015-11-17 : Mottok : PMBL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
CNOT2.md
... ...
@@ -3,6 +3,12 @@
3 3
## History
4 4
Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
5 5
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2021-05-05 : H : DLBCL
11
+```
6 12
## Relevance tier by entity
7 13
8 14
|Entity|Tier|Description |
CNTNAP5.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2013 by Morin et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2013-08-15 : Morin : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
CPNE8.md
... ...
@@ -3,6 +3,12 @@
3 3
## History
4 4
Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
5 5
6
+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
9
+ title Publication timing
10
+ 2021-05-05 : H : FL
11
+```
6 12
## Relevance tier by entity
7 13
8 14
|Entity|Tier|Description |
CYP4F22.md
... ...
@@ -1,6 +1,12 @@
1 1
# CYP4F22
2 2
## History
3 3
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2012-12-01 : Love : BL
9
+```
4 10
## Relevance tier by entity
5 11
6 12
|Entity|Tier|Description |
DAZAP1.md
... ...
@@ -1,7 +1,13 @@
1 1
# DAZAP1
2 2
## Overview
3 3
This gene has some recurrent sites of mutations (hot spots). The mutation pattern in DLBCL and FL implies the preferential accumulation of *inactivating mutations* however the pattern is notable. These mutations often result in truncations affecting the DAZAP1 C-terminus, which are predicted to alter protein sub-cellular localization and disrupt protein-protein interactions.<sup>1</sup>
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2020-07-30 : Pararajalingam : MCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
DCAF6.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
DDX10.md
... ...
@@ -2,6 +2,12 @@
2 2
3 3
## History
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
DDX3X.md
... ...
@@ -1,7 +1,15 @@
1 1
# DDX3X
2 2
## Overview
3 3
Mutations in the DDX3X gene, which encodes an RNA helicase involved in various aspects of RNA metabolism, have significant implications in B-cell lymphomas, including BL, DLBCL, and other related malignancies and are particularly enriched within MYC-translocated tumors and those expressing the dark zone signature (DZsig).<sup>1</sup> These mutations are predominantly loss-of-function (LOF) mutations, affecting the helicase domain of the protein.<sup>2</sup> Missense mutations are predominantly found in male patients and rarely in females, hence showing a sex-specific pattern.<sup>3</sup>
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2012-10-04 : Schmitz : BL
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 |
DHDH.md
... ...
@@ -2,6 +2,12 @@
2 2
3 3
## History
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2014-05-08 : Zhang : MCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
DHX15.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2021-05-05 : H : FL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
DHX16.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2021-05-05 : H : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
DICER1.md
... ...
@@ -2,6 +2,12 @@
2 2
3 3
## History
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
9
+ 2017-10-10 : Reddy : DLBCL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |
DLC1.md
... ...
@@ -1,5 +1,11 @@
1 1
# DLC1
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-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
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+```
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## Relevance tier by entity
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5 11
|Entity|Tier|Description |
DLGAP1.md
... ...
@@ -1,5 +1,11 @@
1 1
# DLGAP1
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-
2
+## History
3
+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
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+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
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## Relevance tier by entity
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5 11
|Entity|Tier|Description |
DNM2.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
4 4
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+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2021-05-05 : H : DLBCL
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+```
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## Relevance tier by entity
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7 13
|Entity|Tier|Description |
DTX1.md
... ...
@@ -1,7 +1,16 @@
1 1
# DTX1
2 2
## Overview
3 3
Mutations in the DTX1 gene, which encodes the E3 ubiquitin ligase Deltex 1, have been identified in various B-cell lymphomas, including diffuse large B-cell lymphoma (DLBCL). DTX1 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. These mutations are associated with the BN2 genetic subgroup of DLBCL.<sup>1</sup> There are numerous mutation hotspots in this gene with some leading to a truncated protein. DTX1 functions as a negative regulator of the Notch signaling pathway. Some DTX1 mutations impair its function, thereby dysregulating Notch signaling, which is crucial for normal B-cell development and function. <sup>2</sup>
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-
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+## History
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+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
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+ title Publication timing
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+ 2012-08-27 : Rossi : MZL
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+ 2018-04-12 : Schmitz : DLBCL
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+ 2019-09-26 : Panea : BL
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+ 2023-11-15 : Gomez : PMBL
13
+```
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## Relevance tier by entity
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|Entity|Tier|Description |
DUSP2.md
... ...
@@ -2,7 +2,14 @@
2 2
## Overview
3 3
4 4
DUSP2 functions as a negative regulator of MAPK signaling, particularly affecting the ERK1/2 pathway. DUSP2 mutations have been reported in nodular lymphocyte predominant Hodgkin lymphoma (NLPHL),<sup>1</sup> T-cell/histiocyte-rich large B-cell lymphoma (T/HRLBCL)<sup>2</sup> and they are relatively frequent in DLBCL. DUSP2 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. These mutations are associated with the ST2 genetic subgroup of DLBCL. This gene has some recurrent sites of mutations (hot spots). The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*.
5
-
5
+## History
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+```mermaid
7
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
8
+timeline
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+ title Publication timing
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+ 2013-08-15 : Morin : DLBCL
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+ 2021-07-15 : Duns : PMBL
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+```
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## Relevance tier by entity
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|Entity|Tier|Description |