ABI3BP.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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# ABI3BP
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## History
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@morinMutationalStructuralAnalysis2013]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
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## References
48 53
49
-1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992
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<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
ABL2.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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# ABL2
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## History
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
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+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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41 46
![](images/gene_expression/ABL2_by_pathology.svg)
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## References
44
-1. *Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.*
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<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
ACAD9.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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# ACAD9
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## Overview
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
20 25
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
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## References
64
-1. *Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561*
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<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
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<!-- BL: loveGeneticLandscapeMutations2012 -->
ACE.md
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@@ -1,4 +1,10 @@
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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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# ACE
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+
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## Overview
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Due to [minimal support](ACE#representative-mutation) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL.
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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[744](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/744_reports.html)
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## References
66
-1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
ADAMTS1.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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# ADAMTS1
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## History
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
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+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
18 23
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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[SP193337](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193337.html)
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## References
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-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
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+
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<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
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ADAMTS5.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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# ADAMTS5
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## History
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
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... ...
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<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
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## References
48
-1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
ADNP.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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# ADNP
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## History
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
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+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
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<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
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## References
50
-1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
H1FOO.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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+
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+# H1FOO
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+
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+## History
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+
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+```mermaid
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+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2012-03-06 : Lohr : DLBCL
16
+```
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+
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+
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+## Relevance tier by entity
20
+
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+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012a]|
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+
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+
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+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |1.724 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |0.701 |
33
+
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+
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+## References
36
+
37
+