COL11A1.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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# COL11A1
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## History
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13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|---------------------------------------|
16
-|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
21
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -46,4 +51,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
46 51
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
47 52
48 53
## References
49
-1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
COL16A1.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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# COL16A1
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## History
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|Entity|Tier|Description |
15 20
|:------:|:----:|---------------------------------------|
16
-|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
21
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -46,4 +51,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
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<!-- MCL: zhangGenomicLandscapeMantle2014 -->
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## References
49
-1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
COL4A2.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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# COL4A2
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+
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## Overview
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Due to [minimal support](COL4A2#representative-mutations) 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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|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
26
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
21 27
22 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 29
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@@ -63,5 +69,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
63 69
[747](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html)
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65 71
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-## References
67
-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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+## References
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\ No newline at end of file
COQ7.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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# COQ7
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## History
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|Entity|Tier|Description |
15 20
|:------:|:----:|-----------------------------------------|
16
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
21
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
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49 54
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
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## References
52
-1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
CPNE8.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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# CPNE8
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## History
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|Entity|Tier|Description |
16 21
|:------:|:----:|--------------------------------------|
17
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
22
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -53,7 +58,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
53 58
[SP116720](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP116720.html)
54 59
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## References
56
-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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<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
59 63
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
CPXM2.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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# CPXM2
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## History
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|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------------------|
16
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
21
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
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48 53
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
49 54
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## References
51
-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
CRIP1.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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# CRIP1
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## History
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
16
-|![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[@chapuyMolecularSubtypesDiffuse2018b]|
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18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -49,4 +54,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
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<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
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## References
52
-1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
CTCF.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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# CTCF
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<<Warn("The variants reported in this gene in BL failed QC")>>
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|Entity|Tier|Description |
17 22
|:------:|:----:|--------------------------------------|
18
-|![BL](images/icons/BL_tier2.png) |2-F |Failed QC|
23
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@paneaWholeGenomeLandscape2019]|
19 24
20 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
21 26
... ...
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62 67
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## References
65
-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;
CTNNA2.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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# CTNNA2
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## History
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|Entity|Tier|Description |
15 20
|:------:|:----:|---------------------------------------|
16
-|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
21
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -46,4 +51,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
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<!-- MCL: zhangGenomicLandscapeMantle2014 -->
47 52
48 53
## References
49
-1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
DLC1.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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# DLC1
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## History
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12 17
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|Entity|Tier|Description |
14 19
|:------:|:----:|---------------------------------------|
15
-|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
20
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]|
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## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -45,4 +50,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
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<!-- MCL: zhangGenomicLandscapeMantle2014 -->
46 51
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## References
48
-1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.