AMOTL1.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# AMOTL1
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2013-12-13 : Parry : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@parryWholeExomeSequencing2013]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |2.874 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |1.725 |
33
+|DLBCL|GAMBL Genome |0.94 |
34
+|FL|GAMBL Exome |0.287 |
35
+
36
+
37
+## References
38
+
39
+
ANK2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ANK2
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/A
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.
ANKRD12.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ANKRD12
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
... ...
@@ -45,7 +50,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
45 50
![](images/gene_expression/ANKRD12_by_pathology.svg)
46 51
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
47 52
48
-## All Mutations
53
+## All Mutations[@hubschmannMutationalMechanismsShaping2021b]
49 54
50 55
[SP193744](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193744.html)
51 56
[SP116697](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP116697.html)
... ...
@@ -56,5 +61,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
56 61
[SP193375](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP193375.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
64
+
60 65
<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
ANKRD17.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ANKRD17
2 7
3 8
<<Warn("The variants reported in this gene in DLBCL failed QC")>>
... ...
@@ -16,7 +21,7 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|-----------------------------------------|
19
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
24
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -47,7 +52,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
47 52
## ANKRD17 Expression
48 53
![](images/gene_expression/ANKRD17_by_pathology.svg)
49 54
50
-## Representative Mutations
55
+## Representative Mutations[@reddyGeneticFunctionalDrivers2017]
51 56
52 57
![](/primary/Reddy_ANKRD17_1.svg)
53 58
&starf; &star; &star; &star; &star;
... ...
@@ -55,7 +60,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
55 60
![](/primary/Reddy_ANKRD17_2.svg)
56 61
&starf; &star; &star; &star; &star;
57 62
58
-## All Mutations
63
+## All Mutations[@reddyGeneticFunctionalDrivers2017]
59 64
60 65
[Reddy_1016T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_1016T.html)
61 66
[Reddy_2045T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2045T.html)
... ...
@@ -112,7 +117,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
112 117
[Reddy_705T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_705T.html)
113 118
114 119
## References
115
-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.*
116 120
117 121
118 122
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
ARHGEF1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ARHGEF1
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[@muppidiLossSignalingGa132014b]|
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/A
47 52
<!-- BL: muppidiLossSignalingGa132014b -->
48 53
49 54
## References
50
-1. Muppidi J, Schmitz R, Green JA, Green JA, Xiao W, Larsen AB, Braun S, An J, Xu Y, Rosenwald A, Ott G, Gascoyne R, Rimsza L, Campo E, Jaffe E, Delabie J, Smeland E, Braziel R, Tubbs R, Cook J, Weisenburger D, Chan W, Vaidehi N, Staudt L, Cyster J. Loss of signaling via Gα13 in germinal center B cell-derived lymphoma. Nature. 2014;516:254–258.
ARIH2.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ARIH2
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2015-02-12 : Reichel : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015a]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |1.149 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |0.755 |
33
+|DLBCL|GAMBL Genome |0.564 |
34
+|MCL|GAMBL Genome |0.585 |
35
+
36
+
37
+## References
38
+
39
+
ATM.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATM
2 7
3 8
## History
... ...
@@ -17,9 +22,9 @@ Mutations in this gene were first described in MZL by Braggio et al,<sup>1</sup>
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------|
20
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
22
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
25
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@braggioGenomicAnalysisMarginal2012]|
26
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@reddyGeneticFunctionalDrivers2017]|
27
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@beaLandscapeSomaticMutations2013]|
23 28
24 29
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 30
... ...
@@ -52,9 +57,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
52 57
![](images/gene_expression/ATM_by_pathology.svg)
53 58
54 59
## References
55
-1. *Braggio E, Dogan A, Keats JJ, Chng WJ, Huang G, Matthews JM, Maurer MJ, Law ME, Bosler DS, Barrett M, Lossos IS, Witzig TE, Fonseca R. Genomic analysis of marginal zone and lymphoplasmacytic lymphomas identified common and disease-specific abnormalities. Mod Pathol. 2012 May;25(5):651–660. PMCID: PMC3341516*
56
-2. *Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436*
57
-3. *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.*
58 60
59 61
60 62
<!-- ORIGIN: braggioGenomicAnalysisMarginal2012 -->
ATP11C.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATP11C
2 7
3 8
```mermaid
... ...
@@ -11,7 +16,7 @@ timeline
11 16
12 17
|Entity|Tier|Description |
13 18
|:------:|:----:|---------------------------------------|
14
-|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
19
+|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]|
15 20
16 21
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
17 22
... ...
@@ -44,4 +49,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
44 49
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
45 50
46 51
## References
47
-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.
ATP2C2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATP2C2
2 7
3 8
... ...
@@ -17,7 +22,7 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
25
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
... ...
@@ -65,4 +70,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
65 70
[677](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/677_reports.html)
66 71
67 72
## References
68
-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
ATP6AP1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATP6AP1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
20
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@okosunRecurrentMTORC1activatingRRAGC2016a]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -44,4 +49,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
44 49
<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->
45 50
46 51
## References
47
-1. Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016 Feb;48(2):183–188. PMCID: PMC4731318
ATP6V1A.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATP6V1A
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
... ...
@@ -56,7 +61,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
56 61
[SP194216](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP194216.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
60 64
61 65
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
62 66
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
ATP6V1B2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATP6V1B2
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
20
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@okosunRecurrentMTORC1activatingRRAGC2016a]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -51,4 +56,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
51 56
<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->
52 57
53 58
## References
54
-1. Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, Escudero-Ibarz L, Al Seraihi AF, Richter J, Bernhart SH, Efeyan A, Iqbal S, Matthews J, Clear A, Guerra-Assunção JA, Bödör C, Quentmeier H, Mansbridge C, Johnson P, Davies A, Strefford JC, Packham G, Barrans S, Jack A, Du MQ, Calaminici M, Lister TA, Auer R, Montoto S, Gribben JG, Siebert R, Chelala C, Zoncu R, Sabatini DM, Fitzgibbon J. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016 Feb;48(2):183–188. PMCID: PMC4731318
ATR_tmp.html
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+ </script>
368
+<h1 id="atr">ATR</h1>
369
+<h2 id="history">History</h2>
370
+<p>Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.</p>
371
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
372
+timeline
373
+ title Publication timing
374
+ 2017-10-10 : Reddy : DLBCL
375
+</div></code></pre>
376
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
377
+<table>
378
+<thead>
379
+<tr>
380
+<th style="text-align:center">Entity</th>
381
+<th style="text-align:center">Tier</th>
382
+<th>Description</th>
383
+</tr>
384
+</thead>
385
+<tbody>
386
+<tr>
387
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
388
+<td style="text-align:center">2</td>
389
+<td>relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]</td>
390
+</tr>
391
+</tbody>
392
+</table>
393
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
394
+<table>
395
+<thead>
396
+<tr>
397
+<th style="text-align:center">Entity</th>
398
+<th style="text-align:center">source</th>
399
+<th style="text-align:center">frequency (%)</th>
400
+</tr>
401
+</thead>
402
+<tbody>
403
+<tr>
404
+<td style="text-align:center">DLBCL</td>
405
+<td style="text-align:center">GAMBL genomes</td>
406
+<td style="text-align:center">2.68</td>
407
+</tr>
408
+<tr>
409
+<td style="text-align:center">DLBCL</td>
410
+<td style="text-align:center">Schmitz cohort</td>
411
+<td style="text-align:center">4.89</td>
412
+</tr>
413
+<tr>
414
+<td style="text-align:center">DLBCL</td>
415
+<td style="text-align:center">Reddy cohort</td>
416
+<td style="text-align:center">2.80</td>
417
+</tr>
418
+<tr>
419
+<td style="text-align:center">DLBCL</td>
420
+<td style="text-align:center">Chapuy cohort</td>
421
+<td style="text-align:center">3.85</td>
422
+</tr>
423
+</tbody>
424
+</table>
425
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
426
+<table>
427
+<thead>
428
+<tr>
429
+<th style="text-align:center">Entity</th>
430
+<th style="text-align:center">aSHM</th>
431
+<th style="text-align:center">Significant selection</th>
432
+<th style="text-align:center">dN/dS (missense)</th>
433
+<th style="text-align:center">dN/dS (nonsense)</th>
434
+</tr>
435
+</thead>
436
+<tbody>
437
+<tr>
438
+<td style="text-align:center">BL</td>
439
+<td style="text-align:center">No</td>
440
+<td style="text-align:center">No</td>
441
+<td style="text-align:center">0.459</td>
442
+<td style="text-align:center">0.000</td>
443
+</tr>
444
+<tr>
445
+<td style="text-align:center">DLBCL</td>
446
+<td style="text-align:center">No</td>
447
+<td style="text-align:center">No</td>
448
+<td style="text-align:center">1.146</td>
449
+<td style="text-align:center">3.261</td>
450
+</tr>
451
+<tr>
452
+<td style="text-align:center">FL</td>
453
+<td style="text-align:center">No</td>
454
+<td style="text-align:center">No</td>
455
+<td style="text-align:center">0.000</td>
456
+<td style="text-align:center">0.000</td>
457
+</tr>
458
+</tbody>
459
+</table>
460
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR_protein_hg38.html">hg38</a></p>
461
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ATR_NM_001184.svg" alt=""></p>
462
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/ATR_hg38.html">hg38</a></p>
463
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ATR.svg" alt=""></p>
464
+<h2 id="atr-expression">ATR Expression</h2>
465
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/ATR_by_pathology.svg" alt=""></p>
466
+<h2 id="representative-mutations">Representative Mutations</h2>
467
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Reddy_ATR_1.svg" alt="">
468
+<strong>Rating</strong>
469
+★ ★ ★ ★ ★</p>
470
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Reddy_ATR_2.svg" alt="">
471
+<strong>Rating</strong>
472
+★ ★ ☆ ☆ ☆</p>
473
+<h2 id="all-mutations">All Mutations</h2>
474
+<p><a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2121T.html">Reddy_2121T</a>
475
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2150T.html">Reddy_2150T</a>
476
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2163T.html">Reddy_2163T</a>
477
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2192T.html">Reddy_2192T</a>
478
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2195T.html">Reddy_2195T</a>
479
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2206T.html">Reddy_2206T</a>
480
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2236T.html">Reddy_2236T</a>
481
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2475T.html">Reddy_2475T</a>
482
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2476T.html">Reddy_2476T</a>
483
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2585T.html">Reddy_2585T</a>
484
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2594T.html">Reddy_2594T</a>
485
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2758T.html">Reddy_2758T</a>
486
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2768T.html">Reddy_2768T</a>
487
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2775T.html">Reddy_2775T</a>
488
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2779T.html">Reddy_2779T</a>
489
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2805T.html">Reddy_2805T</a>
490
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2828T.html">Reddy_2828T</a>
491
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2838T.html">Reddy_2838T</a>
492
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2898T.html">Reddy_2898T</a>
493
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2933T.html">Reddy_2933T</a>
494
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_2947T.html">Reddy_2947T</a>
495
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3384T.html">Reddy_3384T</a>
496
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3385T.html">Reddy_3385T</a>
497
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3405T.html">Reddy_3405T</a>
498
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3489T.html">Reddy_3489T</a>
499
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3502T.html">Reddy_3502T</a>
500
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3520T.html">Reddy_3520T</a>
501
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3548T.html">Reddy_3548T</a>
502
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3549T.html">Reddy_3549T</a>
503
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3557T.html">Reddy_3557T</a>
504
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3561T.html">Reddy_3561T</a>
505
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3562T.html">Reddy_3562T</a>
506
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3594T.html">Reddy_3594T</a>
507
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3622T.html">Reddy_3622T</a>
508
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3653T.html">Reddy_3653T</a>
509
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3662T.html">Reddy_3662T</a>
510
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3779T.html">Reddy_3779T</a>
511
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3810T.html">Reddy_3810T</a>
512
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3812T.html">Reddy_3812T</a>
513
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3820T.html">Reddy_3820T</a>
514
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3822T.html">Reddy_3822T</a>
515
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3843T.html">Reddy_3843T</a>
516
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3856T.html">Reddy_3856T</a>
517
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3879T.html">Reddy_3879T</a>
518
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3992T.html">Reddy_3992T</a>
519
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_705T.html">Reddy_705T</a></p>
520
+<h2 id="references">References</h2>
521
+<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
522
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
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+
524
+</body>
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+</html>