ACAD9.md
... ...
@@ -8,6 +8,7 @@ link-citations: true
8 8
## Overview
9 9
Due to [minimal support](ACAD9#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.
10 10
11
+<<Warn("The variants reported in this gene in BL failed QC")>>
11 12
12 13
## History
13 14
```mermaid
... ...
@@ -21,7 +22,7 @@ timeline
21 22
22 23
|Entity|Tier|Description |
23 24
|:------:|:----:|--------------------------------------|
24
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
25
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
25 26
26 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27 28
ACE.md
... ...
@@ -9,6 +9,8 @@ link-citations: true
9 9
10 10
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.
11 11
12
+<<Warn("The variants reported in this gene in BL failed QC")>>
13
+
12 14
## History
13 15
```mermaid
14 16
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -21,7 +23,7 @@ timeline
21 23
22 24
|Entity|Tier|Description |
23 25
|:------:|:----:|--------------------------------------|
24
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
26
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
25 27
26 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27 29
ATP2C2.md
... ...
@@ -9,6 +9,7 @@ link-citations: true
9 9
## Overview
10 10
Due to [minimal support](ATP2C2#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.
11 11
12
+<<Warn("The variants reported in this gene in BL failed QC")>>
12 13
13 14
## History
14 15
```mermaid
... ...
@@ -22,7 +23,7 @@ timeline
22 23
23 24
|Entity|Tier|Description |
24 25
|:------:|:----:|--------------------------------------|
25
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
26
+|![BL](images/icons/BL_tier2.png) |2-F |Failed QC[@loveGeneticLandscapeMutations2012]|
26 27
27 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
28 29
FUBP1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# FUBP1
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
... ...
@@ -54,4 +59,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
54 59
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
55 60
56 61
## References
57
-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.
FUT5.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# FUT5
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/F
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
+
FZD3.md
... ...
@@ -1,6 +1,11 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# FZD3
2 7
3
-<<Warn("The variants reported in this gene failed QC")>>
8
+<<Warn("The variants reported in BL in this gene failed QC")>>
4 9
5 10
**[See below ](#representative-mutations) or [the study page ](papers/paneaWholeGenomeLandscape2019.md#tier-2) for more information**
6 11
... ...
@@ -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
FZR1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# FZR1
2 7
3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|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
... ...
@@ -47,7 +52,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
47 52
[SP193650](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193650.html)
48 53
49 54
## References
50
-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
55
+
51 56
52 57
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
53 58
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
GABRA2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GABRA2
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/G
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
+
GAK.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GAK
2 7
3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -51,7 +56,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
51 56
[SP192870](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP192870.html)
52 57
53 58
## References
54
-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
59
+
55 60
56 61
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
57 62
<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
GBP7.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GBP7
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[@russler-germainMutationsAssociatedProgression2023b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -45,4 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
45 50
<!-- FL: russler-germainMutationsAssociatedProgression2023b -->
46 51
47 52
## References
48
-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.
53
+
GGTLA4.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GGTLA4
2 7
3 8
## History
... ...
@@ -13,7 +18,7 @@ timeline
13 18
14 19
|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[@loveGeneticLandscapeMutations2012]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -45,4 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
45 50
[698](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/698_reports.html)
46 51
47 52
## References
48
-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
53
+
GNAI2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GNAI2
2 7
3 8
## Overview
... ...
@@ -18,8 +23,8 @@ timeline
18 23
19 24
|Entity|Tier|Description |
20 25
|:------:|:----:|--------------------------|
21
-|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
22
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
26
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene [@grandeGenomewideDiscoverySomatic2019]|
27
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@morinMutationalStructuralAnalysis2013]|
23 28
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
24 29
25 30
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -72,9 +77,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
72 77
![](images/gene_expression/GNAI2_by_pathology.svg)
73 78
74 79
## References
75
-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*
76
-
77
-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.*
78 80
79 81
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
80 82
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
GNAS.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GNAS
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
... ...
@@ -98,4 +103,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
98 103
[Reddy_816T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_816T.html)
99 104
100 105
## References
101
-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.
106
+
GOLGA5.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# GOLGA5
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 +53,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/G
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.
GPC5_tmp.html
... ...
@@ -0,0 +1,470 @@
1
+<!DOCTYPE html>
2
+<html>
3
+<head>
4
+<title>GPC5.md</title>
5
+<meta http-equiv="Content-type" content="text/html;charset=UTF-8">
6
+
7
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+
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+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
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+<body>
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+ mermaid.initialize({
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+ </script>
368
+<h1 id="gpc5">GPC5</h1>
369
+<h2 id="history">History</h2>
370
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
+timeline
372
+ title Publication timing
373
+ 2018-04-12 : Schmitz : DLBCL
374
+</div></code></pre>
375
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
376
+<table>
377
+<thead>
378
+<tr>
379
+<th style="text-align:center">Entity</th>
380
+<th style="text-align:center">Tier</th>
381
+<th>Description</th>
382
+</tr>
383
+</thead>
384
+<tbody>
385
+<tr>
386
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
387
+<td style="text-align:center">2</td>
388
+<td>relevance in DLBCL not firmly established[@schmitzGeneticsPathogenesisDiffuse2018a]</td>
389
+</tr>
390
+</tbody>
391
+</table>
392
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
393
+<table>
394
+<thead>
395
+<tr>
396
+<th style="text-align:center">Entity</th>
397
+<th style="text-align:center">source</th>
398
+<th style="text-align:center">frequency (%)</th>
399
+</tr>
400
+</thead>
401
+<tbody>
402
+<tr>
403
+<td style="text-align:center">DLBCL</td>
404
+<td style="text-align:center">GAMBL genomes</td>
405
+<td style="text-align:center">1.34</td>
406
+</tr>
407
+<tr>
408
+<td style="text-align:center">DLBCL</td>
409
+<td style="text-align:center">Schmitz cohort</td>
410
+<td style="text-align:center">1.91</td>
411
+</tr>
412
+<tr>
413
+<td style="text-align:center">DLBCL</td>
414
+<td style="text-align:center">Reddy cohort</td>
415
+<td style="text-align:center">2.20</td>
416
+</tr>
417
+<tr>
418
+<td style="text-align:center">DLBCL</td>
419
+<td style="text-align:center">Chapuy cohort</td>
420
+<td style="text-align:center">0.85</td>
421
+</tr>
422
+</tbody>
423
+</table>
424
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
425
+<table>
426
+<thead>
427
+<tr>
428
+<th style="text-align:center">Entity</th>
429
+<th style="text-align:center">aSHM</th>
430
+<th style="text-align:center">Significant selection</th>
431
+<th style="text-align:center">dN/dS (missense)</th>
432
+<th style="text-align:center">dN/dS (nonsense)</th>
433
+</tr>
434
+</thead>
435
+<tbody>
436
+<tr>
437
+<td style="text-align:center">BL</td>
438
+<td style="text-align:center">No</td>
439
+<td style="text-align:center">No</td>
440
+<td style="text-align:center">1.380</td>
441
+<td style="text-align:center">0</td>
442
+</tr>
443
+<tr>
444
+<td style="text-align:center">DLBCL</td>
445
+<td style="text-align:center">No</td>
446
+<td style="text-align:center">No</td>
447
+<td style="text-align:center">0.000</td>
448
+<td style="text-align:center">0</td>
449
+</tr>
450
+<tr>
451
+<td style="text-align:center">FL</td>
452
+<td style="text-align:center">No</td>
453
+<td style="text-align:center">No</td>
454
+<td style="text-align:center">1.144</td>
455
+<td style="text-align:center">0</td>
456
+</tr>
457
+</tbody>
458
+</table>
459
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5_protein_hg38.html">hg38</a></p>
460
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/GPC5_NM_004466.svg" alt=""></p>
461
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/GPC5_hg38.html">hg38</a></p>
462
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/GPC5.svg" alt=""></p>
463
+<h2 id="gpc5-expression">GPC5 Expression</h2>
464
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/GPC5_by_pathology.svg" alt=""></p>
465
+<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
466
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
467
+<h2 id="references">References</h2>
468
+
469
+</body>
470
+</html>