EBF1.md
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@@ -79,7 +79,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
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1. *Györy I, Boller S, Nechanitzky R, Mandel E, Pott S, Liu E, Grosschedl R. Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev. 2012 Apr 1;26(7):668-82. doi: 10.1101/gad.187328.112. Epub 2012 Mar 19. PMID: 22431510; PMCID: PMC3323878.*
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## EBF1 Expression
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![](images/gene_expression/EBF1_by_pathology.svg)
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-<!-- ORIGIN: 23174882 -->
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-<!-- BL: 2 -->
82
+<!-- ORIGIN: bohleRoleEarlyBcell2013 -->
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+<!-- BL: thomasGeneticSubgroupsInform2023 -->
84 84
<!-- PMBL: reichelFlowSortingExome2015a -->
85 85
<!-- DLBCL: bohleRoleEarlyBcell2013 -->
EHD1.md
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@@ -35,6 +35,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
35 35
## EHD1 Expression
36 36
![](images/gene_expression/EHD1_by_pathology.svg)
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<!-- ORIGIN: Unknown -->
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-<!-- BL: 2 -->
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+<!-- BL: thomasGeneticSubgroupsInform2023 -->
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## References
EP300.md
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@@ -98,6 +98,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
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99 99
<!-- ORIGIN: 21390126 -->
100 100
<!-- FL: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
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-<!-- BL: 2 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
102 102
<!-- MZL: rossiCodingGenomeSplenic2012c -->
103 103
<!-- DLBCL: pasqualucciInactivatingMutationsAcetyltransferase2011a -->
EZH2.md
... ...
@@ -86,7 +86,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
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<!-- ORIGIN: morinSomaticMutationsAltering2010 -->
88 88
<!-- BL: loveGeneticLandscapeMutations2012 -->
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-<!-- FL: morinSomaticMutationsAltering2010 -->
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+<!-- FL: morinSomaticMutationsAltering2010a -->
90 90
<!-- BL: loveGeneticLandscapeMutations2012 -->
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<!-- DLBCL: morinSomaticMutationsAltering2010 -->
92 92
<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
KLHL6.md
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@@ -93,5 +93,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/K
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2. *Choi, J., Zhou, N., & Busino, L. (2019). KLHL6 is a tumor suppressor gene in diffuse large B-cell lymphoma. Cell Cycle, 18, 249 - 256. https://doi.org/10.1080/15384101.2019.1568765.*
94 94
<!-- MZL: ganapathiGeneticLandscapeDural2016 -->
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<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
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-<!-- BL: 2 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
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<!-- FL: morinFrequentMutationHistonemodifying2011 -->
LTB.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
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+link-citations: true
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+---
1 6
# LTB
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## Overview
... ...
@@ -15,10 +20,10 @@ timeline
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------------------|
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-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
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-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
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+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@deschGenotypingCirculatingTumor2020]|
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+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@chapuyMolecularSubtypesDiffuse2018b]|
20 25
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
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-|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
26
+|![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)
24 29
... ...
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## References
64 69
<!-- ORIGIN: 29713087 -->
65 70
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
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-<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
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-<!-- BL: 2 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
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+<!-- BL: paneaWholeGenomeLandscape2019 -->
PMAIP1.md
... ...
@@ -33,6 +33,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
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![image](images/proteinpaint/PMAIP1.svg)
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## PMAIP1 Expression
35 35
![image](images/gene_expression/PMAIP1_by_pathology.svg)
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-<!-- ORIGIN: Unknown -->
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+<!-- ORIGIN: -->
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<!-- BL: 2 -->
38 38
## References
PRDM1.md
... ...
@@ -61,7 +61,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
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## PRDM1 Expression
62 62
![](images/gene_expression/PRDM1_by_pathology.svg)
63 63
<!-- ORIGIN: pasqualucciInactivationPRDM1BLIMP12006 -->
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-<!-- DLBCL: pasqualucciInactivationPRDM1BLIMP12006 -->
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+<!-- DLBCL: pasqualucciInactivationPRDM1BLIMP12006a -->
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<!-- BL: 2 -->
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## References
RHOH.md
... ...
@@ -40,6 +40,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
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## RHOH Expression
42 42
![](images/gene_expression/RHOH_by_pathology.svg)
43
-<!-- ORIGIN: Unknown -->
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+<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
44 44
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## References
46
+<!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a -->
RPL22.md
... ...
@@ -33,6 +33,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
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![image](images/proteinpaint/RPL22.svg)
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## RPL22 Expression
35 35
![image](images/gene_expression/RPL22_by_pathology.svg)
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-<!-- ORIGIN: Unknown -->
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+<!-- ORIGIN: -->
37 37
<!-- BL: 2 -->
38 38
## References
SEPT10.md
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@@ -33,5 +33,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
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![image](images/proteinpaint/SEPT10.svg)
34 34
## SEPT10 Expression
35 35
![image](images/gene_expression/SEPT10_by_pathology.svg)
36
-<!-- ORIGIN: Unknown -->
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+<!-- ORIGIN: -->
37 37
<!-- BL: 2 -->
SESN1.md
... ...
@@ -33,6 +33,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
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34 34
## SESN1 Expression
35 35
![](images/gene_expression/SESN1_by_pathology.svg)
36
-<!-- ORIGIN: Unknown -->
36
+<!-- ORIGIN: oricchioGeneticEpigeneticInactivation2017b -->
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38 38
## References
39
+<!-- FL: oricchioGeneticEpigeneticInactivation2017b -->
SMARCA4.md
... ...
@@ -58,7 +58,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
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## SMARCA4 Expression
59 59
![](images/gene_expression/SMARCA4_by_pathology.svg)
60 60
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
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-<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
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+<!-- MCL: nadeuGenomicEpigenomicInsights2020b -->
62 62
<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
63 63
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
64 64
<!-- BL: richterRecurrentMutationID32012a -->
SMARCB1.md
... ...
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## SMARCB1 Expression
43 43
![](images/gene_expression/SMARCB1_by_pathology.svg)
44 44
<!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a -->
45
-<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
45
+<!-- MCL: nadeuGenomicEpigenomicInsights2020b -->
46 46
47 47
## References
48 48
1. Nadeu F, Martín-García 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, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020;
SYNE1.md
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## SYNE1 Expression
43 43
![](images/gene_expression/SYNE1_by_pathology.svg)
44 44
<!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a -->
45
-<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
45
+<!-- MCL: nadeuGenomicEpigenomicInsights2020b -->
46 46
47 47
## References
48 48
1. Nadeu F, Martín-García 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, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020;
TERT.md
... ...
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42 42
## TERT Expression
43 43
![](images/gene_expression/TERT_by_pathology.svg)
44 44
<!-- ORIGIN: nadeuGenomicEpigenomicInsights2020a -->
45
-<!-- MCL: nadeuGenomicEpigenomicInsights2020a -->
45
+<!-- MCL: nadeuGenomicEpigenomicInsights2020b -->
46 46
47 47
## References
48 48
1. Nadeu F, Martín-García 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, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020;
TNFRSF14.md
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<!-- ORIGIN: cheungAcquiredTNFRSF14Mutations2010a @cheungAcquiredTNFRSF14Mutations2010a -->
78 78
<!-- FL: cheungAcquiredTNFRSF14Mutations2010a -->
79 79
<!-- MZL: spinaGeneticsNodalMarginal2016b @spinaGeneticsNodalMarginal2016b -->
80
-<!-- DLBCL: cheungAcquiredTNFRSF14Mutations2010a -->
80
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
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# References
83 83