Changes in cc46f1e: add incidence

				Template.md
			
          @@ -7,11 +7,17 @@ link-citations: true

           [[_TOC_]]

          -[[include:Template_Overview.md]]

          +## Relevance tier by entity

          -[[include:Template_History.md]]

          +|Entity|Tier|Description                           |

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

          +|![DLBCL](images/icons/DLBCL_tier1.png) |1[@balSuperenhancerHypermutationAlters2022]   |high-confidence DLBCL gene            [@tanakaFrequentIncidenceSomatic1992]|

          +|![FL](images/icons/FL_tier1.png)    |1   |high-confidence FL gene| 

          +|![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]]

          -[[include:Template_Relevance.md]]

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

          @@ -23,37 +29,15 @@ link-citations: true

           [[include:Pattern.md]]

          -## aSHM regions

          -

          -|chr_name|hg19_start|hg19_end|region                                                                                       |regulatory_comment|

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

          -|chr18   |60796984  |60814103|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60796984%2D60814103)|strong_enhancer   |

          -|chr18   |60982728  |60988342|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342)   |active_promoter   |

          +[[include:Template_aSHM.md]]

          +[[include:Template_History.md]]

          +[[include:Template_Hotspots.md]]

          -## Hotspots

          -

          -| Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 

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

          -| chr18 | 60985854 | T>C | M16V |

          -| chr18 | 60985854 | T>A | M16L |

          -| chr18 | 60985853 | A>T | M16K |

          -| chr18 | 60985852 | C>T | M16I |

          -| chr18 | 60985849 | C>G | K17N |

          -| chr18 | 60985842 | G>A | H20Y |

          -| chr18 | 60985840 | A>C | H20Q |

          -| chr18 | 60985838 | T>G | Y21S |

          -| chr18 | 60985835 | T>C | K22R |

          -| chr18 | 60985834 | CT>TC | K22R |

          -

          -View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein_hg38.html)

          -

          -![](images/proteinpaint/BCL2_NM_000633.svg)

          -View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_hg38.html)

          +[[include:Template_Browser.md]]

          -![](images/proteinpaint/BCL2.svg)

           ## Expression

				Template_Browser.md
			
          @@ -0,0 +1,9 @@

          +## Browse mutations

          +

          +View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein_hg38.html)

          +

          +![](images/proteinpaint/BCL2_NM_000633.svg)

          +

          +View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_hg38.html)

          +

          +![](images/proteinpaint/BCL2.svg)

				Template_Hotspots.md
			
          @@ -0,0 +1,14 @@

          +## Hotspots

          +

          +| Chromosome |Coordinate (hg19) | ref>alt | HGVSp | 

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

          +| chr18 | 60985854 | T>C | M16V |

          +| chr18 | 60985854 | T>A | M16L |

          +| chr18 | 60985853 | A>T | M16K |

          +| chr18 | 60985852 | C>T | M16I |

          +| chr18 | 60985849 | C>G | K17N |

          +| chr18 | 60985842 | G>A | H20Y |

          +| chr18 | 60985840 | A>C | H20Q |

          +| chr18 | 60985838 | T>G | Y21S |

          +| chr18 | 60985835 | T>C | K22R |

          +| chr18 | 60985834 | CT>TC | K22R |

				Template_aSHM.md
			
          @@ -0,0 +1,6 @@

          +## aSHM regions

          +

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

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

          +|chr18   |60796984  |60814103|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60796984%2D60814103)|strong_enhancer   |

          +|chr18   |60982728  |60988342|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342)   |active_promoter   |

...	...	@@ -7,11 +7,17 @@ link-citations: true
7	7
8	8	[[_TOC_]]
9	9
10		-[[include:Template_Overview.md]]
	10	+## Relevance tier by entity
11	11
12		-[[include:Template_History.md]]
	12	+\|Entity\|Tier\|Description \|
	13	+\|:------:\|:----:\|--------------------------------------\|
	14	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|1[@balSuperenhancerHypermutationAlters2022] \|high-confidence DLBCL gene [@tanakaFrequentIncidenceSomatic1992]\|
	15	+\|![FL](images/icons/FL_tier1.png) \|1 \|high-confidence FL gene\|
	16	+\|![PMBL](images/icons/PMBL_tier2.png)\|2\|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021]\|
	17	+\|![BL](images/icons/BL_tier2.png) \|2 \|relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022]\|
	18	+
	19	+[[include:Template_Overview.md]]
13	20
14		-[[include:Template_Relevance.md]]
15	21
16	22	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
17	23
...	...	@@ -23,37 +29,15 @@ link-citations: true
23	29
24	30	[[include:Pattern.md]]
25	31
26		-## aSHM regions
27		-
28		-\|chr_name\|hg19_start\|hg19_end\|region \|regulatory_comment\|
29		-\|:--------:\|:----------:\|:--------:\|:---------------------------------------------------------------------------------------------:\|:------------------:\|
30		-\|chr18 \|60796984 \|60814103\|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60796984%2D60814103)\|strong_enhancer \|
31		-\|chr18 \|60982728 \|60988342\|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342) \|active_promoter \|
	32	+[[include:Template_aSHM.md]]
32	33
	34	+[[include:Template_History.md]]
33	35
	36	+[[include:Template_Hotspots.md]]
34	37
35		-## Hotspots
36		-
37		-\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
38		- \| :---:\| :---: \| :--: \| :---: \|
39		-\| chr18 \| 60985854 \| T>C \| M16V \|
40		-\| chr18 \| 60985854 \| T>A \| M16L \|
41		-\| chr18 \| 60985853 \| A>T \| M16K \|
42		-\| chr18 \| 60985852 \| C>T \| M16I \|
43		-\| chr18 \| 60985849 \| C>G \| K17N \|
44		-\| chr18 \| 60985842 \| G>A \| H20Y \|
45		-\| chr18 \| 60985840 \| A>C \| H20Q \|
46		-\| chr18 \| 60985838 \| T>G \| Y21S \|
47		-\| chr18 \| 60985835 \| T>C \| K22R \|
48		-\| chr18 \| 60985834 \| CT>TC \| K22R \|
49		-
50		-View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein_hg38.html)
51		-
52		-![](images/proteinpaint/BCL2_NM_000633.svg)
53	38
54		-View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_hg38.html)
	39	+[[include:Template_Browser.md]]
55	40
56		-![](images/proteinpaint/BCL2.svg)
57	41
58	42
59	43	## Expression

...	...	@@ -0,0 +1,9 @@
	1	+## Browse mutations
	2	+
	3	+View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_protein_hg38.html)
	4	+
	5	+![](images/proteinpaint/BCL2_NM_000633.svg)
	6	+
	7	+View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/BCL2.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/BCL2_hg38.html)
	8	+
	9	+![](images/proteinpaint/BCL2.svg)

...	...	@@ -0,0 +1,14 @@
	1	+## Hotspots
	2	+
	3	+\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
	4	+ \| :---:\| :---: \| :--: \| :---: \|
	5	+\| chr18 \| 60985854 \| T>C \| M16V \|
	6	+\| chr18 \| 60985854 \| T>A \| M16L \|
	7	+\| chr18 \| 60985853 \| A>T \| M16K \|
	8	+\| chr18 \| 60985852 \| C>T \| M16I \|
	9	+\| chr18 \| 60985849 \| C>G \| K17N \|
	10	+\| chr18 \| 60985842 \| G>A \| H20Y \|
	11	+\| chr18 \| 60985840 \| A>C \| H20Q \|
	12	+\| chr18 \| 60985838 \| T>G \| Y21S \|
	13	+\| chr18 \| 60985835 \| T>C \| K22R \|
	14	+\| chr18 \| 60985834 \| CT>TC \| K22R \|

...	...	@@ -0,0 +1,6 @@
	1	+## aSHM regions
	2	+
	3	+\|chr_name\|hg19_start\|hg19_end\|region \|regulatory_comment\|
	4	+\|:--------:\|:----------:\|:--------:\|:---------------------------------------------------------------------------------------------:\|:------------------:\|
	5	+\|chr18 \|60796984 \|60814103\|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60796984%2D60814103)\|strong_enhancer \|
	6	+\|chr18 \|60982728 \|60988342\|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342) \|active_promoter \|