CTSS.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# CTSS
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## History
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------|
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-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
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+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@barariaCathepsinAlterationsInduce2020c]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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<!-- FL: barariaCathepsinAlterationsInduce2020c -->
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## References
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-1. Bararia D, Hildebrand JA, Stolz S, Haebe S, Alig S, Trevisani CP, Osorio-Barrios F, Bartoschek MD, Mentz M, Pastore A, Gaitzsch E, Heide M, Jurinovic V, Rautter K, Gunawardana J, Sabdia MB, Szczepanowski M, Richter J, Klapper W, Louissaint A, Ludwig C, Bultmann S, Leonhardt H, Eustermann S, Hopfner KP, Hiddemann W, von Bergwelt-Baildon M, Steidl C, Kridel R, Tobin JWD, Gandhi MK, Weinstock DM, Schmidt-Supprian M, Sárosi MB, Rudelius M, Passerini V, Mautner J, Weigert O. Cathepsin S Alterations Induce a Tumor-Promoting Immune Microenvironment in Follicular Lymphoma. Cell Rep. 2020 May 5;31(5):107522. PMID: 32330423
CXCR4.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# CXCR4
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## Overview
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
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-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
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-|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
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-|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
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+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@khodabakhshiRecurrentTargetsAberrant2012]|
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+|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous [@krysiakRecurrentSomaticMutations2017b]|
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+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@paneaWholeGenomeLandscape2019]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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## References
80
-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
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-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
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-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;
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<!-- ORIGIN: khodabakhshiRecurrentTargetsAberrant2012 -->
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EIF4A1.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# EIF4A1
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## History
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------|
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-|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene|
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+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene[@paneaWholeGenomeLandscape2019]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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<!-- BL: paneaWholeGenomeLandscape2019 -->
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## References
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-1. 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;
EPPK1.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# EPPK1
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## History
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------|
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-|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene|
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+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene[@paneaWholeGenomeLandscape2019]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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<!-- BL: paneaWholeGenomeLandscape2019 -->
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## References
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-1. 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;