Changes in 03bf8b5: more history

				JUP.md
			
          @@ -1,4 +1,6 @@

           # JUP

          +## History

          +Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>

           ## Relevance tier by entity

          @@ -21,10 +23,6 @@

           |FL    |No  |No                   |8.023           |0.000           |

          -> [!NOTE]

          -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/JUP_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/JUP_protein_hg38.html)

           ![image](images/proteinpaint/JUP_NM_002230.svg)

          @@ -34,4 +32,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/J

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

           ## JUP Expression

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

          +

          +## References

          +1.  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

          +

           <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->

          +<!-- FL: hubschmannMutationalMechanismsShaping2021b -->

				KLF2.md
			
          @@ -65,3 +65,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K

           3. *Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.*

           <!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->

          +<!-- PMBL: deschGenotypingCirculatingTumor2020 -->

          +<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->

          +<!-- MZL: jalladesExomeSequencingIdentifies2017 -->

				KLHL21.md
			
          @@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K

           ## KLHL21 Expression

           ![image](images/gene_expression/KLHL21_by_pathology.svg)

           <!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->

          +<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->

				KMT2D.md
			
          @@ -2,14 +2,18 @@

           ## Overview

           KMT2D (also known as MLL2) encodes a histone H3K4 methyltransferase, playing a crucial role in germinal center B cell development and function. Mutations in KMT2D are among the most common mutations in FL and are also common in DLBCL.<sup>1</sup> KMT2D mutations are recurrent but less common in BL and MCL and many other B-cell neoplasms. Mutations typically cause loss of KMT2D function, leading to diminished H3K4 methylation, impacting gene expression that favours lymphomagenesis. KMT2D mutations are associated with poor prognosis in DLBCL.<sup>2,3</sup>

          +## History

          +First identified as mutated in DLBCL and FL in 2011 by Morin et al.<sup>1</sup>

          +Mutations were later described in MCL in 2013 by Bea et al.<sup>4</sup> KMT2D mutations were later reported in BL by Grande et al.<sup>5</sup>

          +

           ## Relevance tier by entity

           |Entity|Tier|Description               |

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

          -|FL    |1   |high-confidence FL gene   |

          -|DLBCL |1   |high-confidence DLBCL gene|

          -|BL    |1   |high-confidence BL gene   |

          -|MCL   |1   |high-confidence MCL gene  |

          +|![FL](images/icons/FL_tier1.png)    |1   |high-confidence FL gene   |

          +|![DLBCL](images/icons/DLBCL_tier1.png) |1   |high-confidence DLBCL gene|

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

          +|![MCL](images/icons/MCL_tier1.png)   |1   |high-confidence MCL gene  |

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

          @@ -33,11 +37,6 @@ KMT2D (also known as MLL2) encodes a histone H3K4 methyltransferase, playing a c

           |DLBCL |No  |Yes                  | 3.731          | 104.190        |

           |FL    |No  |Yes                  |20.755          |1353.812        |

          -

          -> [!NOTE]

          -> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/KMT2D_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/KMT2D_protein_hg38.html)

           ![image](images/proteinpaint/KMT2D_NM_003482.svg)

          @@ -53,5 +52,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K

           1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*

           2. *You, H., Xu-Monette, Z., Wei, L., Nunns, H., Nagy, M., Bhagat, G., Fang, X., Zhu, F., Visco, C., Tzankov, A., Dybkaer, K., Chiu, A., Tam, W., Zu, Y., Hsi, E., Hagemeister, F., Huh, J., Ponzoni, M., Ferreri, A., Møller, M., Parsons, B., Krieken, J., Piris, M., Winter, J., Li, Y., Au, Q., Xu, B., Albitar, M., & Young, K. (2021). Genomic complexity is associated with epigenetic regulator mutations and poor prognosis in diffuse large B-cell lymphoma. Oncoimmunology, 10. https://doi.org/10.1080/2162402X.2021.1928365.*

           3. *Rushton CK, Arthur SE, Alcaide M, Cheung M, Jiang A, Coyle KM, Cleary KLS, Thomas N, Hilton LK, Michaud N, Daigle S, Davidson J, Bushell K, Yu S, Rys RN, Jain M, Shepherd L, Marra MA, Kuruvilla J, Crump M, Mann K, Assouline S, Connors JM, Steidl C, Cragg MS, Scott DW, Johnson NA, Morin RD. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv. 2020 Jul 14;4(13):2886-2898. doi: 10.1182/bloodadvances.2020001696. PMID: 32589730; PMCID: PMC7362366.*

          +4. *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*

          +5. *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.* 

          +

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

          +<!-- FL: morinFrequentMutationHistonemodifying2011 -->

          +<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

          +<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

          +<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

          +<!-- MCL: beaLandscapeSomaticMutations2013 -->

          +<!-- MZL: rossiCodingGenomeSplenic2012c -->

				KRAS.md
			
          @@ -55,3 +55,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K

           1. *Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.*

           <!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->

          +<!-- DLBCL: lohrDiscoveryPrioritizationSomatic2012a -->

				MYCBP2.md
			
          @@ -1,5 +1,8 @@

           # MYCBP2

          +## History

          +Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>

          +

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

          @@ -21,10 +24,6 @@

           |FL    |No  |No                   |0.850           |7.277           |

          -> [!NOTE]

          -> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYCBP2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYCBP2_protein_hg38.html)

           ![image](images/proteinpaint/MYCBP2_NM_015057.svg)

          @@ -34,4 +33,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M

           ![image](images/proteinpaint/MYCBP2.svg)

           ## MYCBP2 Expression

           ![image](images/gene_expression/MYCBP2_by_pathology.svg)

          +

          +

          +## References

          +1.  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

          +

           <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->

          +<!-- FL: hubschmannMutationalMechanismsShaping2021b -->

				PNPO.md
			
          @@ -1,4 +1,6 @@

           # PNPO

          +## History

          +Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>

           ## Relevance tier by entity

          @@ -24,10 +26,6 @@

           |FL    |No  |No                   |0.000           |0               |

          -> [!NOTE]

          -> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PNPO_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PNPO_protein_hg38.html)

           ![image](images/proteinpaint/PNPO_NM_018129.svg)

          @@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P

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

           ## PNPO Expression

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

          +

          +## References

          +1.  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

          +

           <!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->

          +<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

				SIAH2.md
			
          @@ -37,4 +37,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S

           ![image](images/proteinpaint/SIAH2.svg)

           ## SIAH2 Expression

           ![image](images/gene_expression/SIAH2_by_pathology.svg)

          -<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->

          +<!-- ORIGIN: reichelFlowSortingExome2015a -->

          +<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

          +<!-- PMBL: reichelFlowSortingExome2015a -->

...	...	@@ -1,4 +1,6 @@
1	1	# JUP
	2	+## History
	3	+Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
2	4
3	5	## Relevance tier by entity
4	6
...	...	@@ -21,10 +23,6 @@
21	23	\|FL \|No \|No \|8.023 \|0.000 \|
22	24
23	25
24		-> [!NOTE]
25		-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
26		-
27		-
28	26	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/JUP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/JUP_protein_hg38.html)
29	27
30	28	![image](images/proteinpaint/JUP_NM_002230.svg)
...	...	@@ -34,4 +32,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/J
34	32	![image](images/proteinpaint/JUP.svg)
35	33	## JUP Expression
36	34	![image](images/gene_expression/JUP_by_pathology.svg)
	35	+
	36	+## References
	37	+1. 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
	38	+
37	39	<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	40	+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -65,3 +65,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
65	65	3. Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.
66	66
67	67	<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
	68	+<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
	69	+<!-- DLBCL: pasqualucciAnalysisCodingGenome2011 -->
	70	+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->

...	...	@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
43	43	## KLHL21 Expression
44	44	![image](images/gene_expression/KLHL21_by_pathology.svg)
45	45	<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
	46	+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->

...	...	@@ -2,14 +2,18 @@
2	2	## Overview
3	3	KMT2D (also known as MLL2) encodes a histone H3K4 methyltransferase, playing a crucial role in germinal center B cell development and function. Mutations in KMT2D are among the most common mutations in FL and are also common in DLBCL.<sup>1</sup> KMT2D mutations are recurrent but less common in BL and MCL and many other B-cell neoplasms. Mutations typically cause loss of KMT2D function, leading to diminished H3K4 methylation, impacting gene expression that favours lymphomagenesis. KMT2D mutations are associated with poor prognosis in DLBCL.<sup>2,3</sup>
4	4
	5	+## History
	6	+First identified as mutated in DLBCL and FL in 2011 by Morin et al.<sup>1</sup>
	7	+Mutations were later described in MCL in 2013 by Bea et al.<sup>4</sup> KMT2D mutations were later reported in BL by Grande et al.<sup>5</sup>
	8	+
5	9	## Relevance tier by entity
6	10
7	11	\|Entity\|Tier\|Description \|
8	12	\|:------:\|:----:\|--------------------------\|
9		-\|FL \|1 \|high-confidence FL gene \|
10		-\|DLBCL \|1 \|high-confidence DLBCL gene\|
11		-\|BL \|1 \|high-confidence BL gene \|
12		-\|MCL \|1 \|high-confidence MCL gene \|
	13	+\|![FL](images/icons/FL_tier1.png) \|1 \|high-confidence FL gene \|
	14	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene\|
	15	+\|![BL](images/icons/BL_tier1.png) \|1 \|high-confidence BL gene \|
	16	+\|![MCL](images/icons/MCL_tier1.png) \|1 \|high-confidence MCL gene \|
13	17
14	18	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
15	19
...	...	@@ -33,11 +37,6 @@ KMT2D (also known as MLL2) encodes a histone H3K4 methyltransferase, playing a c
33	37	\|DLBCL \|No \|Yes \| 3.731 \| 104.190 \|
34	38	\|FL \|No \|Yes \|20.755 \|1353.812 \|
35	39
36		-
37		-> [!NOTE]
38		-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
39		-
40		-
41	40	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/KMT2D_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/KMT2D_protein_hg38.html)
42	41
43	42	![image](images/proteinpaint/KMT2D_NM_003482.svg)
...	...	@@ -53,5 +52,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
53	52	1. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.
54	53	2. You, H., Xu-Monette, Z., Wei, L., Nunns, H., Nagy, M., Bhagat, G., Fang, X., Zhu, F., Visco, C., Tzankov, A., Dybkaer, K., Chiu, A., Tam, W., Zu, Y., Hsi, E., Hagemeister, F., Huh, J., Ponzoni, M., Ferreri, A., Møller, M., Parsons, B., Krieken, J., Piris, M., Winter, J., Li, Y., Au, Q., Xu, B., Albitar, M., & Young, K. (2021). Genomic complexity is associated with epigenetic regulator mutations and poor prognosis in diffuse large B-cell lymphoma. Oncoimmunology, 10. https://doi.org/10.1080/2162402X.2021.1928365.
55	54	3. Rushton CK, Arthur SE, Alcaide M, Cheung M, Jiang A, Coyle KM, Cleary KLS, Thomas N, Hilton LK, Michaud N, Daigle S, Davidson J, Bushell K, Yu S, Rys RN, Jain M, Shepherd L, Marra MA, Kuruvilla J, Crump M, Mann K, Assouline S, Connors JM, Steidl C, Cragg MS, Scott DW, Johnson NA, Morin RD. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv. 2020 Jul 14;4(13):2886-2898. doi: 10.1182/bloodadvances.2020001696. PMID: 32589730; PMCID: PMC7362366.
	55	+4. 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
	56	+5. 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.
	57	+
56	58
57	59	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
	60	+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
	61	+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
	62	+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
	63	+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
	64	+<!-- MCL: beaLandscapeSomaticMutations2013 -->
	65	+<!-- MZL: rossiCodingGenomeSplenic2012c -->

...	...	@@ -55,3 +55,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
55	55	1. Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernández-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17. PMID: 22343534; PMCID: PMC3309757.
56	56
57	57	<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->
	58	+<!-- DLBCL: lohrDiscoveryPrioritizationSomatic2012a -->

...	...	@@ -1,5 +1,8 @@
1	1	# MYCBP2
2	2
	3	+## History
	4	+Mutations in this gene were first described in FL in 2021 by Hübschmann et al.<sup>1</sup>
	5	+
3	6	## Relevance tier by entity
4	7
5	8	\|Entity\|Tier\|Description \|
...	...	@@ -21,10 +24,6 @@
21	24	\|FL \|No \|No \|0.850 \|7.277 \|
22	25
23	26
24		-> [!NOTE]
25		-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
26		-
27		-
28	27	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/MYCBP2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/MYCBP2_protein_hg38.html)
29	28
30	29	![image](images/proteinpaint/MYCBP2_NM_015057.svg)
...	...	@@ -34,4 +33,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
34	33	![image](images/proteinpaint/MYCBP2.svg)
35	34	## MYCBP2 Expression
36	35	![image](images/gene_expression/MYCBP2_by_pathology.svg)
	36	+
	37	+
	38	+## References
	39	+1. 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
	40	+
37	41	<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	42	+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -1,4 +1,6 @@
1	1	# PNPO
	2	+## History
	3	+Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
2	4
3	5	## Relevance tier by entity
4	6
...	...	@@ -24,10 +26,6 @@
24	26	\|FL \|No \|No \|0.000 \|0 \|
25	27
26	28
27		-> [!NOTE]
28		-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
29		-
30		-
31	29	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PNPO_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PNPO_protein_hg38.html)
32	30
33	31	![image](images/proteinpaint/PNPO_NM_018129.svg)
...	...	@@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37	35	![image](images/proteinpaint/PNPO.svg)
38	36	## PNPO Expression
39	37	![image](images/gene_expression/PNPO_by_pathology.svg)
	38	+
	39	+## References
	40	+1. 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
	41	+
40	42	<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	43	+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -37,4 +37,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
37	37	![image](images/proteinpaint/SIAH2.svg)
38	38	## SIAH2 Expression
39	39	![image](images/gene_expression/SIAH2_by_pathology.svg)
40		-<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	40	+<!-- ORIGIN: reichelFlowSortingExome2015a -->
	41	+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
	42	+<!-- PMBL: reichelFlowSortingExome2015a -->