Changes in d841a5d: more history

				CCL4.md
			
          @@ -1,5 +1,12 @@

           # CCL4

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2018-05-01 : Chapuy : DLBCL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

          @@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CCL4_by_pathology.svg)

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## References

          +1.  Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387

				CCND1.md
			
          @@ -1,5 +1,11 @@

           # CCND1

          -

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-11-05 : Be : MCL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description             |

          @@ -36,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CCND1_by_pathology.svg)

           <!-- ORIGIN: beaLandscapeSomaticMutations2013 -->

           <!-- MCL: beaLandscapeSomaticMutations2013 -->

          +## References

          +1.  Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436

				CCNF.md
			
          @@ -1,5 +1,11 @@

           # CCNF

          -

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2015-10-15 : Abate : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -23,10 +29,6 @@

           |FL    |No  |No                   |0.000           |0               |

          -> [!NOTE]

          -> First described in BL in 2015 by [Abate F](https://pubmed.ncbi.nlm.nih.gov/26468873)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CCNF_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CCNF_protein_hg38.html)

           ![image](images/proteinpaint/CCNF_NM_001761.svg)

          @@ -38,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CCNF_by_pathology.svg)

           <!-- ORIGIN: abateDistinctViralMutational2015a -->

           <!-- BL: abateDistinctViralMutational2015a -->

          +## References

          +1.  Abate F, Ambrosio M, Mundo L, Laginestra M, Fuligni F, Rossi M, Zairis S, Gazaneo S, Falco GD, Lazzi S, Bellan C, Rocca BJ, Amato T, Marasco E, Etebari M, Ogwang M, Calbi V, Ndede I, Patel K, Chumba D, Piccaluga P, Pileri S, Leoncini L, Rabadán R. Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma. PLoS Pathogens. 2015;11.

				CCT6B.md
			
          @@ -1,5 +1,12 @@

           # CCT6B

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2012-12-01 : Love : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -38,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CCT6B_by_pathology.svg)

           <!-- ORIGIN: loveGeneticLandscapeMutations2012 -->

           <!-- BL: loveGeneticLandscapeMutations2012 -->

          +## References

          +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

				CD44.md
			
          @@ -1,5 +1,12 @@

           # CD44

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2018-10-01 : Arthur : DLBCL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

          @@ -44,3 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CD44_by_pathology.svg)

           <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->

           <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

          +## References

          +1.  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

				CD74.md
			
          @@ -1,5 +1,12 @@

           # CD74

          -

          +##History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2018-10-01 : Arthur : DLBCL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

          @@ -44,3 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CD74_by_pathology.svg)

           <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->

           <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

          +## References

          +1.  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

				CD79A.md
			
          @@ -1,9 +1,18 @@

           # CD79A

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2012-08-27 : Rossi : MZL

          +      2022-07-06 : Burkhardt : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

           |:------:|:----:|--------------------------------------|

          +|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|

           |![BL](images/icons/BL_tier2.png)    |2   |relevance in BL not firmly established|

           ## Mutation incidence in large patient cohorts (GAMBL reanalysis)

          @@ -46,3 +55,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           <!-- ORIGIN: rossiCodingGenomeSplenic2012c -->

           <!-- BL: burkhardtClinicalRelevanceMolecular2022b -->

           <!-- MZL: rossiCodingGenomeSplenic2012c -->

          +## References

          +1.  Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941

          +2.  Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584

				CDH17.md
			
          @@ -1,5 +1,11 @@

           # CDH17

          -

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2012-12-01 : Love : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CDH17_by_pathology.svg)

           <!-- ORIGIN: loveGeneticLandscapeMutations2012 -->

           <!-- BL: loveGeneticLandscapeMutations2012 -->

          +## References

          +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

				CDH8.md
			
          @@ -1,5 +1,12 @@

           # CDH8

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2014-05-08 : Zhang : MCL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                            |

          @@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CDH8_by_pathology.svg)

           <!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->

           <!-- MCL: zhangGenomicLandscapeMantle2014 -->

          +## References

          +1.  Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.

				CDH9.md
			
          @@ -1,5 +1,12 @@

           # CDH9

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-08-15 : Morin : DLBCL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

          @@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CDH9_by_pathology.svg)

           <!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->

           <!-- DLBCL: morinMutationalStructuralAnalysis2013 -->

          +## References

          +1.  Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992

				CDKN2C.md
			
          @@ -1,5 +1,11 @@

           # CDKN2C

          -

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2023-02-03 : Thomas : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CDKN2C_by_pathology.svg)

           <!-- ORIGIN: thomasGeneticSubgroupsInform2023 -->

           <!-- BL: thomasGeneticSubgroupsInform2023 -->

          +## References

          +1.  Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904–916.

				CHD4.md
			
          @@ -1,5 +1,11 @@

           # CHD4

          -

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2022-07-06 : Burkhardt : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CHD4_by_pathology.svg)

           <!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->

           <!-- BL: burkhardtClinicalRelevanceMolecular2022b -->

          +## References

          +1.  Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584

				CHD8.md
			
          @@ -2,10 +2,18 @@

           ## History

           Mutations in this gene were first described in DLBCL in 2017 by Reddy et al<sup>1</sup> and in BL in 2019 by Grande et al.<sup>2</sup>

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2017-10-10 : Reddy : DLBCL

          +      2019-03-21 : Grande : BL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

           |:------:|:----:|-----------------------------------------|

          +|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|

           |![BL](images/icons/BL_tier1.png)    |1   |high-confidence BL gene                  |

           |![DLBCL](images/icons/DLBCL_tier2.png) |2   |relevance in DLBCL not firmly established|

				CILP.md
			
          @@ -1,5 +1,12 @@

           # CILP

          -

          +## History

          +

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2023-07-26 : Russler : FL

          +```

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/gene_expression/CILP_by_pathology.svg)

           <!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->

           <!-- FL: russler-germainMutationsAssociatedProgression2023a -->

          +## References

          +1.  Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.

...	...	@@ -1,5 +1,12 @@
1	1	# CCL4
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2018-05-01 : Chapuy : DLBCL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
39	46	![image](images/gene_expression/CCL4_by_pathology.svg)
40	47	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41	48	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
	49	+## References
	50	+1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387

...	...	@@ -1,5 +1,11 @@
1	1	# CCND1
2		-
	2	+## History
	3	+```mermaid
	4	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	5	+timeline
	6	+ title Publication timing
	7	+ 2013-11-05 : Be : MCL
	8	+```
3	9	## Relevance tier by entity
4	10
5	11	\|Entity\|Tier\|Description \|
...	...	@@ -36,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36	42	![image](images/gene_expression/CCND1_by_pathology.svg)
37	43	<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
38	44	<!-- MCL: beaLandscapeSomaticMutations2013 -->
	45	+## References
	46	+1. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436

...	...	@@ -1,5 +1,11 @@
1	1	# CCNF
2		-
	2	+## History
	3	+```mermaid
	4	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	5	+timeline
	6	+ title Publication timing
	7	+ 2015-10-15 : Abate : BL
	8	+```
3	9	## Relevance tier by entity
4	10
5	11	\|Entity\|Tier\|Description \|
...	...	@@ -23,10 +29,6 @@
23	29	\|FL \|No \|No \|0.000 \|0 \|
24	30
25	31
26		-> [!NOTE]
27		-> First described in BL in 2015 by [Abate F](https://pubmed.ncbi.nlm.nih.gov/26468873)
28		-
29		-
30	32	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CCNF_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CCNF_protein_hg38.html)
31	33
32	34	![image](images/proteinpaint/CCNF_NM_001761.svg)
...	...	@@ -38,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38	40	![image](images/gene_expression/CCNF_by_pathology.svg)
39	41	<!-- ORIGIN: abateDistinctViralMutational2015a -->
40	42	<!-- BL: abateDistinctViralMutational2015a -->
	43	+## References
	44	+1. Abate F, Ambrosio M, Mundo L, Laginestra M, Fuligni F, Rossi M, Zairis S, Gazaneo S, Falco GD, Lazzi S, Bellan C, Rocca BJ, Amato T, Marasco E, Etebari M, Ogwang M, Calbi V, Ndede I, Patel K, Chumba D, Piccaluga P, Pileri S, Leoncini L, Rabadán R. Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma. PLoS Pathogens. 2015;11.

...	...	@@ -1,5 +1,12 @@
1	1	# CCT6B
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2012-12-01 : Love : BL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -38,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
38	45	![image](images/gene_expression/CCT6B_by_pathology.svg)
39	46	<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40	47	<!-- BL: loveGeneticLandscapeMutations2012 -->
	48	+## References
	49	+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561

...	...	@@ -1,5 +1,12 @@
1	1	# CD44
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2018-10-01 : Arthur : DLBCL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -44,3 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
44	51	![image](images/gene_expression/CD44_by_pathology.svg)
45	52	<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46	53	<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
	54	+## References
	55	+1. 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

...	...	@@ -1,5 +1,12 @@
1	1	# CD74
2		-
	2	+##History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2018-10-01 : Arthur : DLBCL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -44,3 +51,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
44	51	![image](images/gene_expression/CD74_by_pathology.svg)
45	52	<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46	53	<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
	54	+## References
	55	+1. 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

...	...	@@ -1,9 +1,18 @@
1	1	# CD79A
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2012-08-27 : Rossi : MZL
	9	+ 2022-07-06 : Burkhardt : BL
	10	+```
3	11	## Relevance tier by entity
4	12
5	13	\|Entity\|Tier\|Description \|
6	14	\|:------:\|:----:\|--------------------------------------\|
	15	+\|![MZL](images/icons/MZL_tier2.png)\|2\|relevance in MZL not firmly established\|
7	16	\|![BL](images/icons/BL_tier2.png) \|2 \|relevance in BL not firmly established\|
8	17
9	18	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
...	...	@@ -46,3 +55,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
46	55	<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
47	56	<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
48	57	<!-- MZL: rossiCodingGenomeSplenic2012c -->
	58	+## References
	59	+1. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941
	60	+2. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584

...	...	@@ -1,5 +1,11 @@
1	1	# CDH17
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/C
38	44	![image](images/gene_expression/CDH17_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

...	...	@@ -1,5 +1,12 @@
1	1	# CDH8
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2014-05-08 : Zhang : MCL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36	43	![image](images/gene_expression/CDH8_by_pathology.svg)
37	44	<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38	45	<!-- MCL: zhangGenomicLandscapeMantle2014 -->
	46	+## References
	47	+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.

...	...	@@ -1,5 +1,12 @@
1	1	# CDH9
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2013-08-15 : Morin : DLBCL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -39,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
39	46	![image](images/gene_expression/CDH9_by_pathology.svg)
40	47	<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41	48	<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
	49	+## References
	50	+1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992

...	...	@@ -1,5 +1,11 @@
1	1	# CDKN2C
2		-
	2	+## History
	3	+```mermaid
	4	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	5	+timeline
	6	+ title Publication timing
	7	+ 2023-02-03 : Thomas : 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/C
38	44	![image](images/gene_expression/CDKN2C_by_pathology.svg)
39	45	<!-- ORIGIN: thomasGeneticSubgroupsInform2023 -->
40	46	<!-- BL: thomasGeneticSubgroupsInform2023 -->
	47	+## References
	48	+1. Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904–916.

...	...	@@ -1,5 +1,11 @@
1	1	# CHD4
2		-
	2	+## History
	3	+```mermaid
	4	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	5	+timeline
	6	+ title Publication timing
	7	+ 2022-07-06 : Burkhardt : 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/C
38	44	![image](images/gene_expression/CHD4_by_pathology.svg)
39	45	<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40	46	<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
	47	+## References
	48	+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584

...	...	@@ -2,10 +2,18 @@
2	2	## History
3	3	Mutations in this gene were first described in DLBCL in 2017 by Reddy et al<sup>1</sup> and in BL in 2019 by Grande et al.<sup>2</sup>
4	4
	5	+```mermaid
	6	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	7	+timeline
	8	+ title Publication timing
	9	+ 2017-10-10 : Reddy : DLBCL
	10	+ 2019-03-21 : Grande : BL
	11	+```
5	12	## Relevance tier by entity
6	13
7	14	\|Entity\|Tier\|Description \|
8	15	\|:------:\|:----:\|-----------------------------------------\|
	16	+\|![PMBL](images/icons/PMBL_tier1.png)\|1\|high-confidence PMBL/cHL/GZL gene\|
9	17	\|![BL](images/icons/BL_tier1.png) \|1 \|high-confidence BL gene \|
10	18	\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
11	19

...	...	@@ -1,5 +1,12 @@
1	1	# CILP
2		-
	2	+## History
	3	+
	4	+```mermaid
	5	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	6	+timeline
	7	+ title Publication timing
	8	+ 2023-07-26 : Russler : FL
	9	+```
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
...	...	@@ -36,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
36	43	![image](images/gene_expression/CILP_by_pathology.svg)
37	44	<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38	45	<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
	46	+## References
	47	+1. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.