MECOM.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
1 6
# MECOM
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -48,4 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
48 53
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
49 54
50 55
## 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.
56
+
MEF2C.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
5
+---
1 6
# MEF2C
2 7
3 8
## Overview
... ...
@@ -15,7 +20,7 @@ timeline
15 20
16 21
|Entity|Tier|Description |
17 22
|:------:|:----:|--------------------------|
18
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
23
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene[@arthurGenomewideDiscoverySomatic2018]|
19 24
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
MET.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
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+link-citations: true
5
+---
1 6
# MET
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -48,4 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
48 53
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
49 54
50 55
## 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.
56
+
MGA.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MGA
2 7
3 8
## Overview
... ...
@@ -16,8 +21,8 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------|
19
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
20
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
24
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@zhangGeneticHeterogeneityDiffuse2013]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
... ...
@@ -48,8 +53,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
48 53
![](images/gene_expression/MGA_by_pathology.svg)
49 54
50 55
## References
51
-1. *Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1398-403. doi: 10.1073/pnas.1205299110. Epub 2013 Jan 4. PMID: 23292937; PMCID: PMC3557051.*
52
-2. *Lee MJ, Koff JL, Switchenko JM, Jhaney CI, Harkins RA, Patel SP, Dave SS, Flowers CR. Genome-defined African ancestry is associated with distinct mutations and worse survival in patients with diffuse large B-cell lymphoma. Cancer. 2020 Aug 1;126(15):3493-3503. doi: 10.1002/cncr.32866. Epub 2020 May 29. PMID: 32469082; PMCID: PMC7494053.*
56
+
53 57
54 58
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
55 59
<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
MIR142.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
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+link-citations: true
5
+---
1 6
# MIR142
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|-----------------------------------------|
16
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established |
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
21
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established [@grandeGenomewideDiscoverySomatic2019]|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@kwanhianMicroRNA142Mutated202012b]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -40,5 +45,3 @@ timeline
40 45
<!-- DLBCL: kwanhianMicroRNA142Mutated202012b -->
41 46
42 47
## References
43
-1. Kwanhian W, Lenze D, Alles J, Motsch N, Barth S, Döll C, Imig J, Hummel M, Tinguely M, Trivedi P, Lulitanond V, Meister G, Renner C, Grässer FA. MicroRNA-142 is mutated in about 20% of diffuse large B-cell lymphoma. Cancer Med. 2012 Oct;1(2):141–155. PMCID: PMC3544448
44
-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.
MIR155HG.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MIR155HG
2 7
3 8
## Relevance tier by entity
MME.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MME
2 7
3 8
<<Warn("The variants reported in this gene failed QC")>>
... ...
@@ -16,7 +21,7 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------------------|
19
-|![BL](images/icons/BL_tier2.png) |2-F |Failed QC|
24
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@paneaWholeGenomeLandscape2019]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -51,4 +56,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
51 56
<!-- BL: paneaWholeGenomeLandscape2019 -->
52 57
53 58
## References
54
-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;
59
+
MPDZ.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
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+link-citations: true
5
+---
1 6
# MPDZ
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|-----------------------------------------|
16
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
21
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015a]|
22
+|![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
... ...
@@ -51,5 +56,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
51 56
<!-- PMBL: reichelFlowSortingExome2015a -->
52 57
53 58
## References
54
-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
55
-2. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972
MPEG1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MPEG1
2 7
3 8
## Overview
... ...
@@ -16,7 +21,7 @@ timeline
16 21
|Entity|Tier|Description |
17 22
|:------:|:----:|--------------------------|
18 23
|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
19
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene|
24
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene[@morinMutationalStructuralAnalysis2013]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -46,7 +51,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
46 51
![](images/gene_expression/MPEG1_by_pathology.svg)
47 52
48 53
## References
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):1256-65. doi: 10.1182/blood-2013-02-483727. Epub 2013 May 22. PMID: 23699601; PMCID: PMC3744992.*
50 54
51 55
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
52 56
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
MRGPRF.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MRGPRF
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|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]|
16 21
17 22
## 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/M
45 50
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
46 51
47 52
## 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.
MS4A1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MS4A1
2 7
3 8
## Overview
... ...
@@ -16,8 +21,8 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------|
19
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
20
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
24
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@mottokIntegrativeGenomicAnalysis2019b]|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene[@rushtonGeneticEvolutionaryPatterns2020]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
MSH2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MSH2
2 7
3 8
<<Warn("The variants reported in this gene in DLBCL failed QC")>>
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC[@reddyGeneticFunctionalDrivers2017]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -89,4 +94,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
89 94
[Reddy_799T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_799T.html)
90 95
91 96
## References
92
-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.
97
+
MSH6.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# MSH6
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -48,4 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
48 53
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
49 54
50 55
## 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.
56
+
NANOG.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NANOG
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -47,4 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
47 52
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
48 53
49 54
## References
50
-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
55
+
NAV1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NAV1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -47,4 +52,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
47 52
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
48 53
49 54
## References
50
-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
NBEAL1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NBEAL1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -57,4 +62,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
57 62
[849](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/849_reports.html)
58 63
59 64
## References
60
-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
NCOA3.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NCOA3
2 7
3 8
## Relevance tier by entity
NCOR1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NCOR1
2 7
3 8
<<Warn("The variants reported in this gene in DLBCL failed QC")>>
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC[@reddyGeneticFunctionalDrivers2017]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -88,4 +93,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
88 93
[Reddy_3931T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3931T.html)
89 94
90 95
## References
91
-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.
96
+
NCOR2.md
... ...
@@ -1,7 +1,12 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NCOR2
2 7
3 8
## Overview
4
-Mutations in this gene are relatively rare in DLBCL overall but show a pattern of inactivation. *Without further support, this gene may be migrated to Tier 2.*
9
+Mutations in this gene are relatively rare in DLBCL overall but show a pattern of inactivation.
5 10
6 11
## History
7 12
```mermaid
... ...
@@ -17,10 +22,10 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
21
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
22
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
23
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
25
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021a]|
26
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@spinaGeneticsNodalMarginal2016b]|
27
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@schmitzBurkittLymphomaPathogenesis2012]|
28
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established |
24 29
25 30
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
26 31
... ...
@@ -68,7 +73,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
68 73
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
69 74
70 75
## References
71
-1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867
72
-2. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373.
73
-3. 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. PMID: 32961552
74 76
<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
NF1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NF1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -48,4 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
48 53
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
49 54
50 55
## 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.
56
+
NFKB1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NFKB1
2 7
3 8
## Overview
NFKB2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NFKB2
2 7
3 8
<<Warn("The variants reported in this gene in DLBCL failed QC")>>
... ...
@@ -15,8 +20,8 @@ timeline
15 20
16 21
|Entity|Tier|Description |
17 22
|:------:|:----:|-----------------------------------------|
18
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
19
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019b]|
24
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC[@reddyGeneticFunctionalDrivers2017]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -78,5 +83,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
78 83
[Reddy_695T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_695T.html)
79 84
80 85
## References
81
-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.
82
-2. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115
86
+
NFKBIA.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# NFKBIA
2 7
3 8
## Overview
... ...
@@ -17,9 +22,9 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
22
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
25
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@wienandGenomicAnalysesFlowsorted2019b]|
26
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@lakeMutationsNFKBIAEncoding2009]|
27
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023b]|
23 28
24 29
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 30
... ...
@@ -60,7 +65,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
60 65
<!-- PMBL: wienandGenomicAnalysesFlowsorted2019b -->
61 66
62 67
## References
63
-1. Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.
64
-2. Lake A, Shield LA, Cordano P, Chui DTY, Osborne J, Crae S, Wilson KS, Tosi S, Knight SJL, Gesk S, Siebert R, Hay RT, Jarrett RF. Mutations of NFKBIA, encoding IkappaB alpha, are a recurrent finding in classical Hodgkin lymphoma but are not a unifying feature of non-EBV-associated cases. Int J Cancer. 2009 Sep 15;125(6):1334–1342. PMID: 19507254
65
-3. Wienand K, Chapuy B, Stewart C, Dunford AJ, Wu D, Kim J, Kamburov A, Wood TR, Cader FZ, Ducar MD, Thorner AR, Nag A, Heubeck AT, Buonopane MJ, Redd RA, Bojarczuk K, Lawton LN, Armand P, Rodig SJ, Fromm JR, Getz G, Shipp MA. Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion. Blood Adv. 2019 Dec 10;3(23):4065–4080. PMCID: PMC6963251
66
-4. 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.
POR.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# POR
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -53,4 +58,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
53 58
54 59
55 60
## References
56
-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
61
+
POT1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# POT1
2 7
3 8
## History
... ...
@@ -13,7 +18,7 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|------------------------|
16
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
21
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene[@zhangGenomicLandscapeMantle2014]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -46,4 +51,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
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.
54
+
POU2AF1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# POU2AF1
2 7
3 8
## Overview
... ...
@@ -17,7 +22,7 @@ timeline
17 22
|:------:|:----:|--------------------------|
18 23
|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
19 24
|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated|
20
-|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated |
25
+|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated [@krysiakRecurrentSomaticMutations2017b]|
21 26
22 27
23 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -69,4 +74,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
69 74
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
70 75
71 76
## References
72
-1. 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
77
+
POU2F2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# POU2F2
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------|
16
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
17
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
21
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
22
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -61,5 +66,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
61 66
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
62 67
63 68
## References
64
-1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan;
65
-2. 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
69
+
PPP1R9B.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PPP1R9B
2 7
3 8
## Relevance tier by entity
PPP4C.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PPP4C
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
20
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -56,4 +61,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
56 61
[SP59320](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP59320.html)
57 62
58 63
## References
59
-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
PPP6R2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PPP6R2
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -47,4 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 52
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
48 53
49 54
## 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
55
+
PRDM1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PRDM1
2 7
3 8
## History
... ...
@@ -13,7 +18,7 @@ timeline
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15 20
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
16
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
21
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@pasqualucciInactivationPRDM1BLIMP12006a]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -65,4 +70,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
65 70
<!-- BL: 2 -->
66 71
67 72
## References
68
-1. Pasqualucci L, Compagno M, Houldsworth J, Monti S, Grunn A, Nandula SV, Aster JC, Murty VV, Shipp MA, Dalla-Favera R. Inactivation of the PRDM1/BLIMP1 gene in diffuse large B cell lymphoma. J Exp Med. 2006 Feb;203(2):311–317.
73
+
PREX1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PREX1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -47,4 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 52
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
48 53
49 54
## 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
55
+
PRKCB.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PRKCB
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@morinMutationalStructuralAnalysis2013]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -47,4 +52,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
47 52
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
48 53
49 54
## References
50
-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
55
+
PRKDC.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PRKDC
2 7
3 8
## History
... ...
@@ -14,8 +19,8 @@ timeline
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------------------|
16 21
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
17
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
18
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@schmitzGeneticsPathogenesisDiffuse2018a]|
23
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
19 24
20 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
21 26
... ...
@@ -62,5 +67,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
62 67
[SP116720](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP116720.html)
63 68
64 69
## References
65
-1. 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. PMCID: PMC6010183
66
-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
PRPS1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PRPS1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -48,4 +53,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
48 53
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
49 54
50 55
## References
51
-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
56
+
PRSS22.md
... ...
@@ -1,9 +1,16 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PRSS22
2 7
3 8
## Overview
4 9
5 10
Due to [minimal support](PRSS22#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.
6 11
12
+<<Warn("The variants reported in this gene in BL failed QC")>>
13
+
7 14
## History
8 15
```mermaid
9 16
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -16,7 +23,7 @@ timeline
16 23
17 24
|Entity|Tier|Description |
18 25
|:------:|:----:|--------------------------------------|
19
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
26
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
20 27
21 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 29
... ...
@@ -56,4 +63,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
56 63
&starf; &star; &star; &star; &star;
57 64
58 65
## References
59
-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
66
+