Changes in 4ceb594: Merge branch 'master' of github.com:morinlab/LLMPP.wiki

				BRINP3.md
			
          @@ -5,10 +5,10 @@ link-citations: true

           ---

           [[_TOC_]]

          -<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>>

          -Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>[@reddyGeneticFunctionalDrivers2017]</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. 

          +## Overview

          +Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>[@reddyGeneticFunctionalDrivers2017]</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. 

           ## Relevance tier by entity

          @@ -17,14 +17,18 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup

           |:------:|:----:|-----------------------------------------|

           |![DLBCL](images/icons/DLBCL_tier2.png) |2   |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|

          +## Warnings

          +

          +<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>> 

          +Details[@drevalRevisitingReddyDLBCL2023]

          +

           ## Mutation incidence in large patient cohorts (GAMBL reanalysis)

          -|Entity|source        |frequency (%)|

          -|:------:|:--------------:|:-------------:|

          -|DLBCL |GAMBL genomes |2.68         |

          -|DLBCL |Schmitz cohort|3.40         |

          -|DLBCL |Reddy cohort  |3.30         |

          -|DLBCL |Chapuy cohort |2.99         |

          +### DLBCL

          +[[include:DLBCL_BRINP3.md]]

          +

          +### BL

          +[[include:BL_BRINP3.md]]

           ## Mutation pattern and selective pressure estimates

          @@ -102,6 +106,9 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup

           [Reddy_3989T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3989T.html)

           [Reddy_695T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_695T.html)

          +Source[@reddyGeneticFunctionalDrivers2017]

          +

          +

           [[include:mermaid_BRINP3.md]]

           ## References

				CARD11.md
			
          @@ -5,6 +5,10 @@ link-citations: true

           ---

           [[_TOC_]]

          +## Overview

          +

          +Mutations in CARD11 were initially described as enriched in the ABC subgroup of DLBCL.[@lenzOncogenicCARD11Mutations2008]

          +More recent data contradicts this association and has implicated CARD11 in FL and additional B-cell lymphomas including FL and MCL.[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]

           ## Experimental Evidence

          @@ -65,7 +69,5 @@ The functional effect of CARD11 mutations in DLBCL was explored in the original 

           [[include:mermaid_CARD11.md]]

          -Mutations in CARD11 were initially described as enriched in the ABC subgroup of DLBCL.[@lenzOncogenicCARD11Mutations2008]

          -More recent data contradicts this association and has implicated CARD11 in FL and additional B-cell lymphomas including FL and MCL.[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]

           ## References

				CARD4.md
			
          @@ -5,11 +5,11 @@ link-citations: true

           ---

           [[_TOC_]]

          +## Overview

           *CARD4 is now known as NOD1.*

          -

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

				Template.md
			
          @@ -7,8 +7,9 @@ link-citations: true

           [[_TOC_]]

          +## Overview

          -## Gene lists

          +## Relevance tier by entity

           |Entity|Tier|Description                           |

           |:------:|:----:|--------------------------------------|

          @@ -17,10 +18,12 @@ link-citations: true

           |![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021]|

           |![BL](images/icons/BL_tier2.png)    |2   |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022]|

          -[[include:Template_Overview.md]]

          +## Warnings

          +*may not exist*

           ## Mutation incidence from meta-analysis

          +*sub headings per file here unless there is just one*

           ### DLBCL

           [[include:DLBCL_BCL2.md]]

          @@ -35,20 +38,26 @@ link-citations: true

           [[include:dnds_BCL2.md]]

          -[[include:Template_aSHM.md]]

          +## aSHM regions

          +*section will only exist for certain genes*

          -[[include:Template_Hotspots.md]]

          +|chr_name|hg19_start|hg19_end|region|regulatory_comment|

          +|:--------:|:----------:|:--------:|:--------:|:------------------:|

          +|chr6    |90981034  |91016134|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134)|NA|

          +

          +## Hotspots

          +

          +*section will only exist for certain genes*

           [[include:Template_Browser.md]]

          -[[include:Template_Expression.md]]

          +## Expression

          +

          +![](images/gene_expression/ZNF296_by_pathology.svg)

           [[include:Template_History.md]]

          +## References

          +

          -<!-- ORIGIN: 1339299 -->

          -<!-- FL: morinFrequentMutationHistonemodifying2011 -->

          -<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->

          -<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->

          -<!-- DLBCL: tanakaFrequentIncidenceSomatic1992 -->

...	...	@@ -5,10 +5,10 @@ link-citations: true
5	5	---
6	6	[[_TOC_]]
7	7
8		-<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>>
9	8
10		-Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>[@reddyGeneticFunctionalDrivers2017]</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
	9	+## Overview
11	10
	11	+Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>[@reddyGeneticFunctionalDrivers2017]</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
12	12
13	13
14	14	## Relevance tier by entity
...	...	@@ -17,14 +17,18 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup
17	17	\|:------:\|:----:\|-----------------------------------------\|
18	18	\|![DLBCL](images/icons/DLBCL_tier2.png) \|2 \|relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]\|
19	19
	20	+## Warnings
	21	+
	22	+<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>>
	23	+Details[@drevalRevisitingReddyDLBCL2023]
	24	+
20	25	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
21	26
22		-\|Entity\|source \|frequency (%)\|
23		-\|:------:\|:--------------:\|:-------------:\|
24		-\|DLBCL \|GAMBL genomes \|2.68 \|
25		-\|DLBCL \|Schmitz cohort\|3.40 \|
26		-\|DLBCL \|Reddy cohort \|3.30 \|
27		-\|DLBCL \|Chapuy cohort \|2.99 \|
	27	+### DLBCL
	28	+[[include:DLBCL_BRINP3.md]]
	29	+
	30	+### BL
	31	+[[include:BL_BRINP3.md]]
28	32
29	33	## Mutation pattern and selective pressure estimates
30	34
...	...	@@ -102,6 +106,9 @@ Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup
102	106	[Reddy_3989T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3989T.html)
103	107	[Reddy_695T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_695T.html)
104	108
	109	+Source[@reddyGeneticFunctionalDrivers2017]
	110	+
	111	+
105	112	[[include:mermaid_BRINP3.md]]
106	113
107	114	## References

...	...	@@ -5,6 +5,10 @@ link-citations: true
5	5	---
6	6	[[_TOC_]]
7	7
	8	+## Overview
	9	+
	10	+Mutations in CARD11 were initially described as enriched in the ABC subgroup of DLBCL.[@lenzOncogenicCARD11Mutations2008]
	11	+More recent data contradicts this association and has implicated CARD11 in FL and additional B-cell lymphomas including FL and MCL.[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]
8	12
9	13	## Experimental Evidence
10	14
...	...	@@ -65,7 +69,5 @@ The functional effect of CARD11 mutations in DLBCL was explored in the original
65	69
66	70	[[include:mermaid_CARD11.md]]
67	71
68		-Mutations in CARD11 were initially described as enriched in the ABC subgroup of DLBCL.[@lenzOncogenicCARD11Mutations2008]
69		-More recent data contradicts this association and has implicated CARD11 in FL and additional B-cell lymphomas including FL and MCL.[@morinFrequentMutationHistonemodifying2011; @wuGeneticHeterogeneityPrimary2016]
70	72
71	73	## References

...	...	@@ -5,11 +5,11 @@ link-citations: true
5	5	---
6	6	[[_TOC_]]
7	7
	8	+## Overview
8	9
9	10	CARD4 is now known as NOD1.
10	11
11	12
12		-
13	13	## Relevance tier by entity
14	14
15	15	\|Entity\|Tier\|Description \|

...	...	@@ -7,8 +7,9 @@ link-citations: true
7	7
8	8	[[_TOC_]]
9	9
	10	+## Overview
10	11
11		-## Gene lists
	12	+## Relevance tier by entity
12	13
13	14	\|Entity\|Tier\|Description \|
14	15	\|:------:\|:----:\|--------------------------------------\|
...	...	@@ -17,10 +18,12 @@ link-citations: true
17	18	\|![PMBL](images/icons/PMBL_tier2.png)\|2\|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021]\|
18	19	\|![BL](images/icons/BL_tier2.png) \|2 \|relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022]\|
19	20
20		-[[include:Template_Overview.md]]
	21	+## Warnings
21	22
	23	+may not exist
22	24
23	25	## Mutation incidence from meta-analysis
	26	+sub headings per file here unless there is just one
24	27
25	28	### DLBCL
26	29	[[include:DLBCL_BCL2.md]]
...	...	@@ -35,20 +38,26 @@ link-citations: true
35	38
36	39	[[include:dnds_BCL2.md]]
37	40
38		-[[include:Template_aSHM.md]]
	41	+## aSHM regions
39	42
	43	+section will only exist for certain genes
40	44
41		-[[include:Template_Hotspots.md]]
	45	+\|chr_name\|hg19_start\|hg19_end\|region\|regulatory_comment\|
	46	+\|:--------:\|:----------:\|:--------:\|:--------:\|:------------------:\|
	47	+\|chr6 \|90981034 \|91016134\|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134)\|NA\|
	48	+
	49	+## Hotspots
	50	+
	51	+section will only exist for certain genes
42	52
43	53	[[include:Template_Browser.md]]
44	54
45		-[[include:Template_Expression.md]]
	55	+## Expression
	56	+
	57	+![](images/gene_expression/ZNF296_by_pathology.svg)
46	58
47	59	[[include:Template_History.md]]
48	60
	61	+## References
	62	+
49	63
50		-<!-- ORIGIN: 1339299 -->
51		-<!-- FL: morinFrequentMutationHistonemodifying2011 -->
52		-<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
53		-<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
54		-<!-- DLBCL: tanakaFrequentIncidenceSomatic1992 -->