Changes in 87f483b: more history

				ATP11C.md
			
          @@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A

           ## ATP11C Expression

           ![image](images/gene_expression/ATP11C_by_pathology.svg)

           <!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->

          +<!-- MCL: zhangGenomicLandscapeMantle2014 -->

				ATP6V1B2.md
			
          @@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A

           ## ATP6V1B2 Expression

           ![image](images/gene_expression/ATP6V1B2_by_pathology.svg)

           <!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->

          +<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->

				ATR.md
			
          @@ -1,10 +1,12 @@

           # ATR

          +## History

          +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. 

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

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

          -|DLBCL |2   |relevance in DLBCL not firmly established|

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

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

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

           |FL    |No  |No                   |0.000           |0.000           |

          -> [!NOTE]

          -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATR_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATR_protein_hg38.html)

           ![image](images/proteinpaint/ATR_NM_001184.svg)

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

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

           ## ATR Expression

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

          +

          +## References

          +1.  *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* 

          +

           <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

				B2M.md
			
          @@ -79,3 +79,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ## References

           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.*<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

          +<!-- PMBL: reichelFlowSortingExome2015a -->

          +<!-- FL: morinFrequentMutationHistonemodifying2011 -->

          +<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->

          +<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

				BACH2.md
			
          @@ -1,4 +1,6 @@

           # BACH2

          +## History

          +Mutations in this gene were first described in BL in 2019 by Grande et al.<sup>1</sup>

           ## Relevance tier by entity

          @@ -28,9 +30,6 @@

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

           |chr6    |90981034  |91016134|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134)|NA                |

          -> [!NOTE]

          -> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein_hg38.html)

          @@ -39,6 +38,13 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM

           View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BACH2.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BACH2_hg38.html)

           ![image](images/proteinpaint/BACH2.svg)

          +

           ## BACH2 Expression

           ![image](images/gene_expression/BACH2_by_pathology.svg)

          +

          +## References

          +1.  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: grandeGenomewideDiscoverySomatic2019 -->

          +<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

				BCL10.md
			
          @@ -6,22 +6,22 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an

           |Entity|Tier|Description                           |

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

          -|BL    |2   |relevance in BL not firmly established|

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

          -|FL    |2   |relevance in FL not firmly established|

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

          +|![FL](images/icons/FL_tier2.png)     |2   |relevance in FL not firmly established|

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

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

           |Entity|source               |frequency (%)|

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

          -|BL    |GAMBL genomes+capture|0.23         |

          -|BL    |Thomas cohort        |0.40         |

          -|BL    |Panea cohort         |  NA         |

           |DLBCL |GAMBL genomes        |3.82         |

           |DLBCL |Schmitz cohort       |7.66         |

           |DLBCL |Reddy cohort         |3.10         |

           |DLBCL |Chapuy cohort        |6.41         |

           |FL    |GAMBL genomes        |2.31         |

          +|BL    |GAMBL genomes+capture|0.23         |

          +|BL    |Thomas cohort        |0.40         |

          +|BL    |Panea cohort         |  NA         |

           ## Mutation pattern and selective pressure estimates

          @@ -59,3 +59,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           2. *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.*

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

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

          +<!-- MZL: spinaGeneticsNodalMarginal2016b -->

          +<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

				BCL11A.md
			
          @@ -62,4 +62,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           1. *Satterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B, Oscier DG, Siebert R, Tucker PW, Dyer MJ. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood. 2001 Dec 1;98(12):3413-20. doi: 10.1182/blood.v98.12.3413. PMID: 11719382.*

           ## BCL11A Expression

           ![image](images/gene_expression/BCL11A_by_pathology.svg)

          -<!-- ORIGIN: NA -->

          +<!-- ORIGIN: Unknown -->

				BCL2.md
			
          @@ -74,4 +74,8 @@ and BCL2 rearrangements-an LLMPP study. Blood. 2024. Epub May 3.*

           3. *Singh K, Briggs JM. Functional Implications of the spectrum of BCL2 mutations in Lymphoma. Mutat Res Rev Mutat Res. 2016 Jul-Sep;769:1-18. doi: 10.1016/j.mrrev.2016.06.001. Epub 2016 Jun 16. PMID: 27543313.*

           ## BCL2 Expression

           ![image](images/gene_expression/BCL2_by_pathology.svg)

          -<!-- ORIGIN: tanakaFrequentIncidenceSomatic1992 -->

          +<!-- ORIGIN: 1339299 -->

          +<!-- FL: morinFrequentMutationHistonemodifying2011 -->

          +<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->

          +<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->

          +<!-- DLBCL: tanakaFrequentIncidenceSomatic1992 -->

				BCL2L11.md
			
          @@ -38,4 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BCL2L11.svg)

           ## BCL2L11 Expression

           ![image](images/gene_expression/BCL2L11_by_pathology.svg)

          -<!-- ORIGIN: Unknown -->

          +<!-- ORIGIN:  -->

				BCL6.md
			
          @@ -76,4 +76,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           3. *Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407. doi: 10.1056/NEJMoa1801445. PMID: 29641966; PMCID: PMC6010183.*

           ## BCL6 Expression

           ![image](images/gene_expression/BCL6_by_pathology.svg)

          -<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

          +<!-- ORIGIN: 21796119 -->

          +<!-- BL: loveGeneticLandscapeMutations2012 -->

          +<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

				BCL7A.md
			
          @@ -1,15 +1,20 @@

           # BCL7A

           ## Overview

          -BCL7A protein interacts with components of the SWI/SNF chromatin remodeling complex, implicating it in chromatin remodeling processes essential for normal cellular function.<sup>1</sup> Mutations in the BCL7A gene have been identified in diffuse large B-cell lymphoma (DLBCL) and other B-cell lymphomas, implicating this gene in the pathogenesis of these cancers. Importantly, BCL7A 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. Due to the presence of some loss-of-function mutations, BCL7A has been described as a tumour-suppressor gene in DLBCL.<sup>3</sup> The rate of DLBCLs with biallelic loss of this locus remains unclear. 

          +BCL7A protein interacts with components of the SWI/SNF chromatin remodeling complex, implicating it in chromatin remodeling processes essential for normal cellular function.<sup>1</sup> Mutations in the BCL7A gene have been identified in diffuse large B-cell lymphoma (DLBCL) and other B-cell lymphomas, implicating this gene in the pathogenesis of these cancers. Importantly, BCL7A 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. Due to the presence of some loss-of-function mutations, BCL7A has been described as a tumour-suppressor gene in DLBCL.<sup>2</sup> The rate of DLBCLs with biallelic loss of this locus remains unclear. 

          +

          +## History

          +Mutations in this gene were first described in FL in 2017 by Krysiak et al.<sup>3</sup>  Mutations were described in DLBCL in 2018 by Arthur et al<sup>4</sup> and in BL in 2019 by Grande et al.<sup>5</sup>

          +

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

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

          -|BL    |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |

          -|DLBCL |1-a | aSHM target and high-confidence DLBCL gene            |

          -|FL    |1-a | aSHM target and high-confidence FL gene               |

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

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

          +|![BL](images/icons/BL_tier2.png)    |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |

          +

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

          @@ -38,9 +43,6 @@ BCL7A protein interacts with components of the SWI/SNF chromatin remodeling comp

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

           |chr12   |122456912 |122464036|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A122456912%2D122464036)|poised_promoter   |

          -> [!NOTE]

          -> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL7A_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL7A_protein_hg38.html)

          @@ -50,10 +52,20 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BCL7A.svg)

          -## References

          -1. *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.*

          -2. *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. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.* 

          -3. *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.*

           ## BCL7A Expression

           ![image](images/gene_expression/BCL7A_by_pathology.svg)

          -<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->

          +

          +## References

          +1. *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.*

          +2. *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.*

          +3.  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

          +4.  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

          +

          +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. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.* 

          +

          +

          +<!-- ORIGIN: 30275490 -->

          +<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

          +<!-- FL: krysiakRecurrentSomaticMutations2017b -->

          +<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

          +<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

				BCOR.md
			
          @@ -52,4 +52,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           2. *Nadeu F, Martin-Garcia D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggros M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera-Cortada I, Siebert R, Colomer D, Torrents D, Gine E, López-Guillermo A, Küppers R, Martin-Subero JI, Puente XS, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020 Sep 17;136(12):1419-1432. doi: 10.1182/blood.2020005289. PMID: 32584970; PMCID: PMC7498364.*

           ## BCOR Expression

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

          -<!-- ORIGIN: NA -->

          +<!-- ORIGIN: jalladesExomeSequencingIdentifies2017 -->

          +<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->

          +<!-- MZL: jalladesExomeSequencingIdentifies2017 -->

				BIRC3.md
			
          @@ -44,4 +44,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BIRC3.svg)

           ## BIRC3 Expression

           ![image](images/gene_expression/BIRC3_by_pathology.svg)

          -<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->

          +<!-- ORIGIN: rossiAlterationBIRC3Multiple2011a -->

          +<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->

          +<!-- MZL: rossiAlterationBIRC3Multiple2011a -->

          +<!-- MCL: beaLandscapeSomaticMutations2013 -->

          +<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

				BIRC6.md
			
          @@ -1,15 +1,16 @@

           # BIRC6

           ## Overview

          -BIRC6, as a negative regulator of non-canonical NF-κB signaling, is implicated in lymphomagenesis. Mutations in the BIRC6 were identified in grey zone lymphoma (GZL), contributing to its distinct mutational profile compared to other related lymphomas.<sup>1</sup> These mutations are recurrent, albeit much less common, in DLBCL and FL.

          +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> 

          +

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

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

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

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

          -|BL    |2   |relevance in BL not firmly established|

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

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

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

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

          @@ -32,11 +33,6 @@ BIRC6, as a negative regulator of non-canonical NF-κB signaling, is implicated 

           |DLBCL |No  |No                   |1.795           |5.011           |

           |FL    |No  |No                   |2.997           |7.132           |

          -

          -> [!NOTE]

          -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)

          -

          -

            ## BIRC6 Hotspots

           | Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 

          @@ -52,8 +48,13 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BIRC6.svg)

           ## References

          +1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* 

          +

          +2. *Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765-1776. doi: 10.1182/blood.2020007507. PMID: 32961552.*

          +

          -1. *Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765-1776. doi: 10.1182/blood.2020007507. PMID: 32961552.*

           ## BIRC6 Expression

           ![image](images/gene_expression/BIRC6_by_pathology.svg)

           <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

          +<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->

				BLK.md
			
          @@ -39,4 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

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

           ## BLK Expression

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

          -<!-- ORIGIN: NA -->

          +<!-- ORIGIN: Unknown -->

				BRAF.md
			
          @@ -7,8 +7,8 @@ BRAF mutations, particularly the BRAF V600E hot spot mutation, are primarily ass

           |Entity|Tier|Description                           |

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

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

          -|BL    |2   |relevance in BL not firmly established|

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

          +|![BL](images/icons/Tier2_BL.png)    |2   |relevance in BL not firmly established|

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

          @@ -66,3 +66,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           2. *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: tiacciBRAFMutationsHairycell2011a -->

          +<!-- DLBCL: tiacciBRAFMutationsHairycell2011a -->

          +<!-- BL: loveGeneticLandscapeMutations2012 -->

				BRD4.md
			
          @@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ## BRD4 Expression

           ![image](images/gene_expression/BRD4_by_pathology.svg)

           <!-- ORIGIN: loveGeneticLandscapeMutations2012 -->

          +<!-- BL: loveGeneticLandscapeMutations2012 -->

				BRINP3.md
			
          @@ -1,10 +1,17 @@

           # BRINP3

          +## History

          +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. 

          +

          +

          +> [!WARNING]

          +> 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)

          +

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

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

          -|DLBCL |2   |relevance in DLBCL not firmly established|

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

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

          @@ -24,13 +31,6 @@

           |FL    |No  |No                   |1.586           |6.33            |

          -> [!NOTE]

          -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)

          -

          -> [!WARNING]

          -> 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)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_protein_hg38.html)

           ![image](images/proteinpaint/BRINP3_NM_199051.svg)

          @@ -40,4 +40,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BRINP3.svg)

           ## BRINP3 Expression

           ![image](images/gene_expression/BRINP3_by_pathology.svg)

          +

          +## References

          +1.  *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* 

          +

           <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

				BTBD3.md
			
          @@ -1,10 +1,12 @@

           # BTBD3

          +## History

          +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. 

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

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

          -|DLBCL |2   |relevance in DLBCL not firmly established|

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

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

          @@ -23,11 +25,6 @@

           |DLBCL |No  |No                   |0.722           |0               |

           |FL    |No  |No                   |2.655           |0               |

          -

          -> [!NOTE]

          -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_protein_hg38.html)

           ![image](images/proteinpaint/BTBD3_NM_014962.svg)

          @@ -37,4 +34,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B

           ![image](images/proteinpaint/BTBD3.svg)

           ## BTBD3 Expression

           ![image](images/gene_expression/BTBD3_by_pathology.svg)

          +

          +## References

          +1.  *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* 

          +

          +

           <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

				CASP8.md
			
          @@ -4,11 +4,14 @@

           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> 

          +## History

          +Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup>

          +

           ## Relevance tier by entity

           |Entity|Tier|Description               |

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

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

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

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

          @@ -40,10 +43,16 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CASP8.svg)

          +## CASP8 Expression

          +![image](images/gene_expression/CASP8_by_pathology.svg)

          +

           ## References

           1. *Yoo NJ, Soung YH, Lee SH, Kim KM, Lee SH. Absence of CASP7 and CASP8 mutation in gastrointestinal lymphomas. Eur J Haematol. 2007 Jul;79(1):86-7. doi: 10.1111/j.1600-0609.2007.00865.x. Epub 2007 May 28. PMID: 17532763.*

           2. *Hakem A, El Ghamrasni S, Maire G, Lemmers B, Karaskova J, Jurisicova A, Sanchez O, Squire J, Hakem R. Caspase-8 is essential for maintaining chromosomal stability and suppressing B-cell lymphomagenesis. Blood. 2012 Apr 12;119(15):3495-502. doi: 10.1182/blood-2011-07-367532. Epub 2012 Feb 16. PMID: 22343728.*

          -## CASP8 Expression

          -![image](images/gene_expression/CASP8_by_pathology.svg)

          +3. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* 

          +

          +

          +

           <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

				CD74.md
			
          @@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ## CD74 Expression

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

           <!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->

          +<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

				CD79B.md
			
          @@ -72,3 +72,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           3. *Wilson WH, Wright GW, Huang DW, Hodkinson B, Balasubramanian S, Fan Y, Vermeulen J, Shreeve M, Staudt LM. Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL. Cancer Cell. 2021 Dec 13;39(12):1643-1653.e3. doi: 10.1016/j.ccell.2021.10.006. Epub 2021 Nov 4. PMID: 34739844; PMCID: PMC8722194.*

           4. *Kim Y, Ju H, Kim DH, Yoo HY, Kim SJ, Kim WS, Ko YH. CD79B and MYD88 mutations in diffuse large B-cell lymphoma. Hum Pathol. 2014 Mar;45(3):556-64. doi: 10.1016/j.humpath.2013.10.023. Epub 2013 Oct 31. PMID: 24444466.*

           <!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->

          +<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

				CDH17.md
			
          @@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ## CDH17 Expression

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

           <!-- ORIGIN: loveGeneticLandscapeMutations2012 -->

          +<!-- BL: loveGeneticLandscapeMutations2012 -->

				CDH8.md
			
          @@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ## CDH8 Expression

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

           <!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->

          +<!-- MCL: zhangGenomicLandscapeMantle2014 -->

				CHD8.md
			
          @@ -1,11 +1,13 @@

           # CHD8

          +## 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>

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

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

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

          -|DLBCL |2   |relevance in DLBCL not firmly established|

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

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

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

          @@ -28,10 +30,6 @@

           |FL    |No  |No                   |1.344           |12.679          |

          -> [!NOTE]

          -> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD8_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD8_protein_hg38.html)

           ![image](images/proteinpaint/CHD8_NM_001170629.svg)

          @@ -39,6 +37,17 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM

           View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD8.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD8_hg38.html)

           ![image](images/proteinpaint/CHD8.svg)

          +

           ## CHD8 Expression

           ![image](images/gene_expression/CHD8_by_pathology.svg)

          +

          +## References

          +

          +1.  *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*

          +2.  *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: reddyGeneticFunctionalDrivers2017 -->

          +<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

				CHST2.md
			
          @@ -1,10 +1,12 @@

           # CHST2

          +## History

          +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. 

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

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

          -|DLBCL |2   |relevance in DLBCL not firmly established|

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

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

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

           |FL    |No  |No                   |0.000           |0               |

          -> [!NOTE]

          -> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)

          -

          -

           View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHST2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHST2_protein_hg38.html)

           ![image](images/proteinpaint/CHST2_NM_004267.svg)

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

           ![image](images/proteinpaint/CHST2.svg)

           ## CHST2 Expression

           ![image](images/gene_expression/CHST2_by_pathology.svg)

          +

          +## References

          +1.  *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.* 

          +

           <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->

          +<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

				CPNE8.md
			
          @@ -1,5 +1,8 @@

           # CPNE8

          +## 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                           |

          @@ -34,4 +37,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CPNE8.svg)

           ## CPNE8 Expression

           ![image](images/gene_expression/CPNE8_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 -->

				CXCR4.md
			
          @@ -3,6 +3,9 @@

           CXCR4 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. No notable hot spots have been described in this gene in the context of the cancers listed below. The mutation pattern in DLBCL implies the preferential accumulation of *inactivating mutations*.

          +## History

          +Mutations in this gene were first described in DLBCL in 2012 by Khodabakhshi et al,<sup>1</sup> in FL in 2021 by Hübschmann et al<sup>2</sup> and in BL in 2019 by Panea et al.<sup>3</sup>

          +

           ## Relevance tier by entity

          @@ -52,4 +55,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           ![image](images/proteinpaint/CXCR4.svg)

           ## CXCR4 Expression

           ![image](images/gene_expression/CXCR4_by_pathology.svg)

          +

          +## References

          +1.  Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors JM, Gascoyne RD, Marra MA, Birol I, Jones SJM. Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget. 2012 Nov 12;3(11):1308–1319. PMCID: PMC3717795

          +2.  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

          +3.  Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; 

          +

           <!-- ORIGIN: khodabakhshiRecurrentTargetsAberrant2012 -->

          +

          +<!-- DLBCL: khodabakhshiRecurrentTargetsAberrant2012 -->

          +<!-- BL: paneaWholeGenomeLandscape2019 -->

          +<!-- FL: krysiakRecurrentSomaticMutations2017b -->

				FZR1.md
			
          @@ -1,4 +1,6 @@

           # FZR1

          +## 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

          @@ -20,11 +22,6 @@

           |DLBCL |No  |No                   | 4.444          |0               |

           |FL    |No  |No                   |12.412          |0               |

          -

          -> [!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/FZR1_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/FZR1_protein_hg38.html)

           ![image](images/proteinpaint/FZR1_NM_001136198.svg)

          @@ -32,6 +29,11 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM

           View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/FZR1.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/FZR1_hg38.html)

           ![image](images/proteinpaint/FZR1.svg)

          +

           ## FZR1 Expression

           ![image](images/gene_expression/FZR1_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 -->

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

           # GAK

          +## History

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

          +

           ## Relevance tier by entity

           |Entity|Tier|Description                              |

          @@ -23,11 +26,6 @@

           |DLBCL |No  |No                   |0.798           |9.151           |

           |FL    |No  |No                   |0.000           |0.000           |

          -

          -> [!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/GAK_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/GAK_protein_hg38.html)

           ![image](images/proteinpaint/GAK_NM_005255.svg)

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

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

           ## GAK Expression

           ![image](images/gene_expression/GAK_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 -->

...	...	@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
35	35	## ATP11C Expression
36	36	![image](images/gene_expression/ATP11C_by_pathology.svg)
37	37	<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
	38	+<!-- MCL: zhangGenomicLandscapeMantle2014 -->

...	...	@@ -39,3 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
39	39	## ATP6V1B2 Expression
40	40	![image](images/gene_expression/ATP6V1B2_by_pathology.svg)
41	41	<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
	42	+<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->

...	...	@@ -1,10 +1,12 @@
1	1	# ATR
	2	+## History
	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.
2	4
3	5	## Relevance tier by entity
4	6
5	7	\|Entity\|Tier\|Description \|
6	8	\|:------:\|:----:\|-----------------------------------------\|
7		-\|DLBCL \|2 \|relevance in DLBCL not firmly established\|
	9	+\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
8	10
9	11	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10	12
...	...	@@ -24,10 +26,6 @@
24	26	\|FL \|No \|No \|0.000 \|0.000 \|
25	27
26	28
27		-> [!NOTE]
28		-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29		-
30		-
31	29	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATR_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATR_protein_hg38.html)
32	30
33	31	![image](images/proteinpaint/ATR_NM_001184.svg)
...	...	@@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
37	35	![image](images/proteinpaint/ATR.svg)
38	36	## ATR Expression
39	37	![image](images/gene_expression/ATR_by_pathology.svg)
	38	+
	39	+## References
	40	+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	41	+
40	42	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	43	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

...	...	@@ -79,3 +79,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
79	79
80	80	## References
81	81	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.<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
	82	+<!-- PMBL: reichelFlowSortingExome2015a -->
	83	+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
	84	+<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
	85	+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -1,4 +1,6 @@
1	1	# BACH2
	2	+## History
	3	+Mutations in this gene were first described in BL in 2019 by Grande et al.<sup>1</sup>
2	4
3	5	## Relevance tier by entity
4	6
...	...	@@ -28,9 +30,6 @@
28	30	\|:--------:\|:----------:\|:--------:\|:-----------------------------------------------------------------------------------------:\|:------------------:\|
29	31	\|chr6 \|90981034 \|91016134\|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134)\|NA \|
30	32
31		-> [!NOTE]
32		-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
33		-
34	33
35	34	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein_hg38.html)
36	35
...	...	@@ -39,6 +38,13 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
39	38	View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BACH2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BACH2_hg38.html)
40	39
41	40	![image](images/proteinpaint/BACH2.svg)
	41	+
42	42	## BACH2 Expression
43	43	![image](images/gene_expression/BACH2_by_pathology.svg)
	44	+
	45	+## References
	46	+1. 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.
	47	+
	48	+
44	49	<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
	50	+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->

...	...	@@ -6,22 +6,22 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an
6	6
7	7	\|Entity\|Tier\|Description \|
8	8	\|:------:\|:----:\|--------------------------------------\|
9		-\|BL \|2 \|relevance in BL not firmly established\|
10		-\|DLBCL \|1 \|high-confidence DLBCL gene \|
11		-\|FL \|2 \|relevance in FL not firmly established\|
	9	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene \|
	10	+\|![FL](images/icons/FL_tier2.png) \|2 \|relevance in FL not firmly established\|
	11	+\|![BL](images/icons/BL_tier2.png) \|2 \|relevance in BL not firmly established\|
12	12
13	13	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14	14
15	15	\|Entity\|source \|frequency (%)\|
16	16	\|:------:\|:---------------------:\|:-------------:\|
17		-\|BL \|GAMBL genomes+capture\|0.23 \|
18		-\|BL \|Thomas cohort \|0.40 \|
19		-\|BL \|Panea cohort \| NA \|
20	17	\|DLBCL \|GAMBL genomes \|3.82 \|
21	18	\|DLBCL \|Schmitz cohort \|7.66 \|
22	19	\|DLBCL \|Reddy cohort \|3.10 \|
23	20	\|DLBCL \|Chapuy cohort \|6.41 \|
24	21	\|FL \|GAMBL genomes \|2.31 \|
	22	+\|BL \|GAMBL genomes+capture\|0.23 \|
	23	+\|BL \|Thomas cohort \|0.40 \|
	24	+\|BL \|Panea cohort \| NA \|
25	25
26	26	## Mutation pattern and selective pressure estimates
27	27
...	...	@@ -59,3 +59,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
59	59	2. 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.
60	60
61	61	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
	62	+<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
	63	+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
	64	+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -62,4 +62,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
62	62	1. Satterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B, Oscier DG, Siebert R, Tucker PW, Dyer MJ. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood. 2001 Dec 1;98(12):3413-20. doi: 10.1182/blood.v98.12.3413. PMID: 11719382.
63	63	## BCL11A Expression
64	64	![image](images/gene_expression/BCL11A_by_pathology.svg)
65		-<!-- ORIGIN: NA -->
	65	+<!-- ORIGIN: Unknown -->

...	...	@@ -74,4 +74,8 @@ and BCL2 rearrangements-an LLMPP study. Blood. 2024. Epub May 3.*
74	74	3. Singh K, Briggs JM. Functional Implications of the spectrum of BCL2 mutations in Lymphoma. Mutat Res Rev Mutat Res. 2016 Jul-Sep;769:1-18. doi: 10.1016/j.mrrev.2016.06.001. Epub 2016 Jun 16. PMID: 27543313.
75	75	## BCL2 Expression
76	76	![image](images/gene_expression/BCL2_by_pathology.svg)
77		-<!-- ORIGIN: tanakaFrequentIncidenceSomatic1992 -->
	77	+<!-- ORIGIN: 1339299 -->
	78	+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
	79	+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
	80	+<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
	81	+<!-- DLBCL: tanakaFrequentIncidenceSomatic1992 -->

...	...	@@ -38,4 +38,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
38	38	![image](images/proteinpaint/BCL2L11.svg)
39	39	## BCL2L11 Expression
40	40	![image](images/gene_expression/BCL2L11_by_pathology.svg)
41		-<!-- ORIGIN: Unknown -->
	41	+<!-- ORIGIN: -->

...	...	@@ -76,4 +76,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
76	76	3. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396-1407. doi: 10.1056/NEJMoa1801445. PMID: 29641966; PMCID: PMC6010183.
77	77	## BCL6 Expression
78	78	![image](images/gene_expression/BCL6_by_pathology.svg)
79		-<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
	79	+<!-- ORIGIN: 21796119 -->
	80	+<!-- BL: loveGeneticLandscapeMutations2012 -->
	81	+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -1,15 +1,20 @@
1	1	# BCL7A
2	2	## Overview
3	3
4		-BCL7A protein interacts with components of the SWI/SNF chromatin remodeling complex, implicating it in chromatin remodeling processes essential for normal cellular function.<sup>1</sup> Mutations in the BCL7A gene have been identified in diffuse large B-cell lymphoma (DLBCL) and other B-cell lymphomas, implicating this gene in the pathogenesis of these cancers. Importantly, BCL7A 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. Due to the presence of some loss-of-function mutations, BCL7A has been described as a tumour-suppressor gene in DLBCL.<sup>3</sup> The rate of DLBCLs with biallelic loss of this locus remains unclear.
	4	+BCL7A protein interacts with components of the SWI/SNF chromatin remodeling complex, implicating it in chromatin remodeling processes essential for normal cellular function.<sup>1</sup> Mutations in the BCL7A gene have been identified in diffuse large B-cell lymphoma (DLBCL) and other B-cell lymphomas, implicating this gene in the pathogenesis of these cancers. Importantly, BCL7A 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. Due to the presence of some loss-of-function mutations, BCL7A has been described as a tumour-suppressor gene in DLBCL.<sup>2</sup> The rate of DLBCLs with biallelic loss of this locus remains unclear.
	5	+
	6	+## History
	7	+Mutations in this gene were first described in FL in 2017 by Krysiak et al.<sup>3</sup> Mutations were described in DLBCL in 2018 by Arthur et al<sup>4</sup> and in BL in 2019 by Grande et al.<sup>5</sup>
	8	+
5	9
6	10	## Relevance tier by entity
7	11
8	12	\|Entity\|Tier\|Description \|
9	13	\|:------:\|:----:\|--------------------------------------\|
10		-\|BL \|2-a \| aSHM target; Although recurrent, the relevance of mutations in BL is tenuous \|
11		-\|DLBCL \|1-a \| aSHM target and high-confidence DLBCL gene \|
12		-\|FL \|1-a \| aSHM target and high-confidence FL gene \|
	14	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1-a \| aSHM target and high-confidence DLBCL gene \|
	15	+\|![FL](images/icons/FL_tier1.png) \|1-a \| aSHM target and high-confidence FL gene \|
	16	+\|![BL](images/icons/BL_tier2.png) \|2-a \| aSHM target; Although recurrent, the relevance of mutations in BL is tenuous \|
	17	+
13	18
14	19	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
15	20
...	...	@@ -38,9 +43,6 @@ BCL7A protein interacts with components of the SWI/SNF chromatin remodeling comp
38	43	\|:--------:\|:----------:\|:---------:\|:--------------------------------------------------------------------------------------------:\|:------------------:\|
39	44	\|chr12 \|122456912 \|122464036\|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A122456912%2D122464036)\|poised_promoter \|
40	45
41		-> [!NOTE]
42		-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
43		-
44	46
45	47	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL7A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL7A_protein_hg38.html)
46	48
...	...	@@ -50,10 +52,20 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
50	52
51	53	![image](images/proteinpaint/BCL7A.svg)
52	54
53		-## References
54		-1. 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.
55		-2. 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. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.
56		-3. 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.
57	55	## BCL7A Expression
58	56	![image](images/gene_expression/BCL7A_by_pathology.svg)
59		-<!-- ORIGIN: krysiakRecurrentSomaticMutations2017b -->
	57	+
	58	+## References
	59	+1. 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.
	60	+2. 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.
	61	+3. 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
	62	+4. 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
	63	+
	64	+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. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.
	65	+
	66	+
	67	+<!-- ORIGIN: 30275490 -->
	68	+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
	69	+<!-- FL: krysiakRecurrentSomaticMutations2017b -->
	70	+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
	71	+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

...	...	@@ -52,4 +52,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
52	52	2. Nadeu F, Martin-Garcia D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggros M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera-Cortada I, Siebert R, Colomer D, Torrents D, Gine E, López-Guillermo A, Küppers R, Martin-Subero JI, Puente XS, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis, and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020 Sep 17;136(12):1419-1432. doi: 10.1182/blood.2020005289. PMID: 32584970; PMCID: PMC7498364.
53	53	## BCOR Expression
54	54	![image](images/gene_expression/BCOR_by_pathology.svg)
55		-<!-- ORIGIN: NA -->
	55	+<!-- ORIGIN: jalladesExomeSequencingIdentifies2017 -->
	56	+<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
	57	+<!-- MZL: jalladesExomeSequencingIdentifies2017 -->

...	...	@@ -44,4 +44,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
44	44	![image](images/proteinpaint/BIRC3.svg)
45	45	## BIRC3 Expression
46	46	![image](images/gene_expression/BIRC3_by_pathology.svg)
47		-<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
	47	+<!-- ORIGIN: rossiAlterationBIRC3Multiple2011a -->
	48	+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
	49	+<!-- MZL: rossiAlterationBIRC3Multiple2011a -->
	50	+<!-- MCL: beaLandscapeSomaticMutations2013 -->
	51	+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

...	...	@@ -1,15 +1,16 @@
1	1	# BIRC6
2	2
3	3	## Overview
4		-BIRC6, as a negative regulator of non-canonical NF-κB signaling, is implicated in lymphomagenesis. Mutations in the BIRC6 were identified in grey zone lymphoma (GZL), contributing to its distinct mutational profile compared to other related lymphomas.<sup>1</sup> These mutations are recurrent, albeit much less common, in DLBCL and FL.
	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	+
5	6
6	7	## Relevance tier by entity
7	8
8	9	\|Entity\|Tier\|Description \|
9	10	\|:------:\|:----:\|--------------------------------------\|
10		-\|DLBCL \|1 \|high-confidence DLBCL gene \|
11		-\|FL \|1 \|high-confidence FL gene \|
12		-\|BL \|2 \|relevance in BL not firmly established\|
	11	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene \|
	12	+\|![FL](images/icons/FL_tier1.png) \|1 \|high-confidence FL gene \|
	13	+\|![BL](images/icons/BL_tier2.png) \|2 \|relevance in BL not firmly established\|
13	14
14	15	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
15	16
...	...	@@ -32,11 +33,6 @@ BIRC6, as a negative regulator of non-canonical NF-κB signaling, is implicated
32	33	\|DLBCL \|No \|No \|1.795 \|5.011 \|
33	34	\|FL \|No \|No \|2.997 \|7.132 \|
34	35
35		-
36		-> [!NOTE]
37		-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
38		-
39		-
40	36	## BIRC6 Hotspots
41	37
42	38	\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
...	...	@@ -52,8 +48,13 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
52	48	![image](images/proteinpaint/BIRC6.svg)
53	49
54	50	## References
	51	+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	52	+
	53	+2. Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765-1776. doi: 10.1182/blood.2020007507. PMID: 32961552.
	54	+
55	55
56		-1. Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765-1776. doi: 10.1182/blood.2020007507. PMID: 32961552.
57	56	## BIRC6 Expression
58	57	![image](images/gene_expression/BIRC6_by_pathology.svg)
59	58	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	59	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
	60	+<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->

...	...	@@ -39,4 +39,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
39	39	![image](images/proteinpaint/BLK.svg)
40	40	## BLK Expression
41	41	![image](images/gene_expression/BLK_by_pathology.svg)
42		-<!-- ORIGIN: NA -->
	42	+<!-- ORIGIN: Unknown -->

...	...	@@ -7,8 +7,8 @@ BRAF mutations, particularly the BRAF V600E hot spot mutation, are primarily ass
7	7
8	8	\|Entity\|Tier\|Description \|
9	9	\|:------:\|:----:\|--------------------------------------\|
10		-\|DLBCL \|1 \|high-confidence DLBCL gene \|
11		-\|BL \|2 \|relevance in BL not firmly established\|
	10	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene \|
	11	+\|![BL](images/icons/Tier2_BL.png) \|2 \|relevance in BL not firmly established\|
12	12
13	13	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14	14
...	...	@@ -66,3 +66,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
66	66	2. 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.
67	67
68	68	<!-- ORIGIN: tiacciBRAFMutationsHairycell2011a -->
	69	+<!-- DLBCL: tiacciBRAFMutationsHairycell2011a -->
	70	+<!-- BL: loveGeneticLandscapeMutations2012 -->

...	...	@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
37	37	## BRD4 Expression
38	38	![image](images/gene_expression/BRD4_by_pathology.svg)
39	39	<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
	40	+<!-- BL: loveGeneticLandscapeMutations2012 -->

...	...	@@ -1,10 +1,17 @@
1	1	# BRINP3
	2	+## History
	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	+
	5	+
	6	+> [!WARNING]
	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	+
2	9
3	10	## Relevance tier by entity
4	11
5	12	\|Entity\|Tier\|Description \|
6	13	\|:------:\|:----:\|-----------------------------------------\|
7		-\|DLBCL \|2 \|relevance in DLBCL not firmly established\|
	14	+\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
8	15
9	16	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10	17
...	...	@@ -24,13 +31,6 @@
24	31	\|FL \|No \|No \|1.586 \|6.33 \|
25	32
26	33
27		-> [!NOTE]
28		-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29		-
30		-> [!WARNING]
31		-> 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)
32		-
33		-
34	34	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BRINP3_protein_hg38.html)
35	35
36	36	![image](images/proteinpaint/BRINP3_NM_199051.svg)
...	...	@@ -40,4 +40,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
40	40	![image](images/proteinpaint/BRINP3.svg)
41	41	## BRINP3 Expression
42	42	![image](images/gene_expression/BRINP3_by_pathology.svg)
	43	+
	44	+## References
	45	+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	46	+
43	47	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	48	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

...	...	@@ -1,10 +1,12 @@
1	1	# BTBD3
	2	+## History
	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.
2	4
3	5	## Relevance tier by entity
4	6
5	7	\|Entity\|Tier\|Description \|
6	8	\|:------:\|:----:\|-----------------------------------------\|
7		-\|DLBCL \|2 \|relevance in DLBCL not firmly established\|
	9	+\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
8	10
9	11	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10	12
...	...	@@ -23,11 +25,6 @@
23	25	\|DLBCL \|No \|No \|0.722 \|0 \|
24	26	\|FL \|No \|No \|2.655 \|0 \|
25	27
26		-
27		-> [!NOTE]
28		-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29		-
30		-
31	28	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BTBD3_protein_hg38.html)
32	29
33	30	![image](images/proteinpaint/BTBD3_NM_014962.svg)
...	...	@@ -37,4 +34,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
37	34	![image](images/proteinpaint/BTBD3.svg)
38	35	## BTBD3 Expression
39	36	![image](images/gene_expression/BTBD3_by_pathology.svg)
	37	+
	38	+## References
	39	+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	40	+
	41	+
40	42	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	43	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

...	...	@@ -4,11 +4,14 @@
4	4
5	5	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>
6	6
	7	+## History
	8	+Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup>
	9	+
7	10	## Relevance tier by entity
8	11
9	12	\|Entity\|Tier\|Description \|
10	13	\|:------:\|:----:\|--------------------------\|
11		-\|DLBCL \|1 \|high-confidence DLBCL gene\|
	14	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene\|
12	15
13	16	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14	17
...	...	@@ -40,10 +43,16 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
40	43
41	44	![image](images/proteinpaint/CASP8.svg)
42	45
	46	+## CASP8 Expression
	47	+![image](images/gene_expression/CASP8_by_pathology.svg)
	48	+
43	49	## References
44	50
45	51	1. Yoo NJ, Soung YH, Lee SH, Kim KM, Lee SH. Absence of CASP7 and CASP8 mutation in gastrointestinal lymphomas. Eur J Haematol. 2007 Jul;79(1):86-7. doi: 10.1111/j.1600-0609.2007.00865.x. Epub 2007 May 28. PMID: 17532763.
46	52	2. Hakem A, El Ghamrasni S, Maire G, Lemmers B, Karaskova J, Jurisicova A, Sanchez O, Squire J, Hakem R. Caspase-8 is essential for maintaining chromosomal stability and suppressing B-cell lymphomagenesis. Blood. 2012 Apr 12;119(15):3495-502. doi: 10.1182/blood-2011-07-367532. Epub 2012 Feb 16. PMID: 22343728.
47		-## CASP8 Expression
48		-![image](images/gene_expression/CASP8_by_pathology.svg)
	53	+3. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	54	+
	55	+
	56	+
49	57	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	58	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

...	...	@@ -43,3 +43,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
43	43	## CD74 Expression
44	44	![image](images/gene_expression/CD74_by_pathology.svg)
45	45	<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
	46	+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->

...	...	@@ -72,3 +72,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
72	72	3. Wilson WH, Wright GW, Huang DW, Hodkinson B, Balasubramanian S, Fan Y, Vermeulen J, Shreeve M, Staudt LM. Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL. Cancer Cell. 2021 Dec 13;39(12):1643-1653.e3. doi: 10.1016/j.ccell.2021.10.006. Epub 2021 Nov 4. PMID: 34739844; PMCID: PMC8722194.
73	73	4. Kim Y, Ju H, Kim DH, Yoo HY, Kim SJ, Kim WS, Ko YH. CD79B and MYD88 mutations in diffuse large B-cell lymphoma. Hum Pathol. 2014 Mar;45(3):556-64. doi: 10.1016/j.humpath.2013.10.023. Epub 2013 Oct 31. PMID: 24444466.
74	74	<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
	75	+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->

...	...	@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37	37	## CDH17 Expression
38	38	![image](images/gene_expression/CDH17_by_pathology.svg)
39	39	<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
	40	+<!-- BL: loveGeneticLandscapeMutations2012 -->

...	...	@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
35	35	## CDH8 Expression
36	36	![image](images/gene_expression/CDH8_by_pathology.svg)
37	37	<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
	38	+<!-- MCL: zhangGenomicLandscapeMantle2014 -->

...	...	@@ -1,11 +1,13 @@
1	1	# CHD8
	2	+## History
	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>
2	4
3	5	## Relevance tier by entity
4	6
5	7	\|Entity\|Tier\|Description \|
6	8	\|:------:\|:----:\|-----------------------------------------\|
7		-\|BL \|1 \|high-confidence BL gene \|
8		-\|DLBCL \|2 \|relevance in DLBCL not firmly established\|
	9	+\|![BL](images/icons/BL_tier1.png) \|1 \|high-confidence BL gene \|
	10	+\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
9	11
10	12	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11	13
...	...	@@ -28,10 +30,6 @@
28	30	\|FL \|No \|No \|1.344 \|12.679 \|
29	31
30	32
31		-> [!NOTE]
32		-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
33		-
34		-
35	33	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD8_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD8_protein_hg38.html)
36	34
37	35	![image](images/proteinpaint/CHD8_NM_001170629.svg)
...	...	@@ -39,6 +37,17 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
39	37	View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHD8.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHD8_hg38.html)
40	38
41	39	![image](images/proteinpaint/CHD8.svg)
	40	+
42	41	## CHD8 Expression
43	42	![image](images/gene_expression/CHD8_by_pathology.svg)
	43	+
	44	+## References
	45	+
	46	+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	47	+2. 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.
	48	+
	49	+
	50	+
44	51	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	52	+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
	53	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

...	...	@@ -1,10 +1,12 @@
1	1	# CHST2
	2	+## History
	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.
2	4
3	5	## Relevance tier by entity
4	6
5	7	\|Entity\|Tier\|Description \|
6	8	\|:------:\|:----:\|-----------------------------------------\|
7		-\|DLBCL \|2 \|relevance in DLBCL not firmly established\|
	9	+\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established\|
8	10
9	11	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10	12
...	...	@@ -24,10 +26,6 @@
24	26	\|FL \|No \|No \|0.000 \|0 \|
25	27
26	28
27		-> [!NOTE]
28		-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29		-
30		-
31	29	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CHST2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CHST2_protein_hg38.html)
32	30
33	31	![image](images/proteinpaint/CHST2_NM_004267.svg)
...	...	@@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
37	35	![image](images/proteinpaint/CHST2.svg)
38	36	## CHST2 Expression
39	37	![image](images/gene_expression/CHST2_by_pathology.svg)
	38	+
	39	+## References
	40	+1. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
	41	+
40	42	<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
	43	+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->

...	...	@@ -1,5 +1,8 @@
1	1	# CPNE8
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 \|
...	...	@@ -34,4 +37,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
34	37	![image](images/proteinpaint/CPNE8.svg)
35	38	## CPNE8 Expression
36	39	![image](images/gene_expression/CPNE8_by_pathology.svg)
	40	+
	41	+## References
	42	+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
	43	+
37	44	<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	45	+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -3,6 +3,9 @@
3	3
4	4	CXCR4 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. No notable hot spots have been described in this gene in the context of the cancers listed below. The mutation pattern in DLBCL implies the preferential accumulation of inactivating mutations.
5	5
	6	+## History
	7	+Mutations in this gene were first described in DLBCL in 2012 by Khodabakhshi et al,<sup>1</sup> in FL in 2021 by Hübschmann et al<sup>2</sup> and in BL in 2019 by Panea et al.<sup>3</sup>
	8	+
6	9
7	10	## Relevance tier by entity
8	11
...	...	@@ -52,4 +55,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
52	55	![image](images/proteinpaint/CXCR4.svg)
53	56	## CXCR4 Expression
54	57	![image](images/gene_expression/CXCR4_by_pathology.svg)
	58	+
	59	+## References
	60	+1. Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors JM, Gascoyne RD, Marra MA, Birol I, Jones SJM. Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget. 2012 Nov 12;3(11):1308–1319. PMCID: PMC3717795
	61	+2. 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
	62	+3. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
	63	+
55	64	<!-- ORIGIN: khodabakhshiRecurrentTargetsAberrant2012 -->
	65	+
	66	+<!-- DLBCL: khodabakhshiRecurrentTargetsAberrant2012 -->
	67	+<!-- BL: paneaWholeGenomeLandscape2019 -->
	68	+<!-- FL: krysiakRecurrentSomaticMutations2017b -->

...	...	@@ -1,4 +1,6 @@
1	1	# FZR1
	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
...	...	@@ -20,11 +22,6 @@
20	22	\|DLBCL \|No \|No \| 4.444 \|0 \|
21	23	\|FL \|No \|No \|12.412 \|0 \|
22	24
23		-
24		-> [!NOTE]
25		-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
26		-
27		-
28	25	View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/FZR1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/FZR1_protein_hg38.html)
29	26
30	27	![image](images/proteinpaint/FZR1_NM_001136198.svg)
...	...	@@ -32,6 +29,11 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
32	29	View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/FZR1.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/FZR1_hg38.html)
33	30
34	31	![image](images/proteinpaint/FZR1.svg)
	32	+
35	33	## FZR1 Expression
36	34	![image](images/gene_expression/FZR1_by_pathology.svg)
	35	+## References
	36	+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
	37	+
37	38	<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
	39	+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->

...	...	@@ -1,5 +1,8 @@
1	1	# GAK
2	2
	3	+## History
	4	+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
	5	+
3	6	## Relevance tier by entity
4	7
5	8	\|Entity\|Tier\|Description \|
...	...	@@ -23,11 +26,6 @@
23	26	\|DLBCL \|No \|No \|0.798 \|9.151 \|
24	27	\|FL \|No \|No \|0.000 \|0.000 \|
25	28
26		-
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/GAK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/GAK_protein_hg38.html)
32	30
33	31	![image](images/proteinpaint/GAK_NM_005255.svg)
...	...	@@ -37,4 +35,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
37	35	![image](images/proteinpaint/GAK.svg)
38	36	## GAK Expression
39	37	![image](images/gene_expression/GAK_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 -->