Changes in 09828c4: updates

				AICDA.md
			
          @@ -0,0 +1,41 @@

          +# [AICDA]

          +

          +## Mutation tier

          +

          +|Entity|Tier|Description                              |

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

          +|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |

          +## Mutation incidence

          +

          +|Entity|source        |frequency (%)|

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

          +|DLBCL |GAMBL genomes |0.38         |

          +|DLBCL |Schmitz cohort|0.43         |

          +|DLBCL |Reddy cohort  |0.30         |

          +|DLBCL |Chapuy cohort |0.43         |

          +

          +## Mutation pattern

          +

          +|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|

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

          +|BL    |Yes |No                   |2.589           |0               |

          +|DLBCL |Yes |No                   |2.652           |0               |

          +|FL    |Yes |No                   |4.955           |0               |

          +

          +## aSHM regions

          +

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

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

          +|chr12   |8762328   |8765099 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A8762328%2D8765099)|NA                |

          +

          +> [!NOTE]

          +> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)

          +

          +

          +View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA_protein.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA_protein_hg38.html)

          +

          +![image](images/proteinpaint/AICDA_NM_020661.svg)

          +

          +View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA_hg38.html)

          +

          +![image](images/proteinpaint/AICDA.svg)

				ANK2.md
			
          @@ -0,0 +1,33 @@

          +# [ANK2]

          +

          +## Mutation tier

          +

          +|Entity|Tier|Description                            |

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

          +|MCL   |2   |relevance in MCL not firmly established|

          +## Mutation incidence

          +

          +|Entity|source       |frequency (%)|

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

          +|MCL   |GAMBL genomes|1.9          |

          +

          +## Mutation pattern

          +

          +|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|

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

          +|BL    |No  |No                   |1.169           |1.1             |

          +|DLBCL |No  |No                   |0.393           |0.0             |

          +|FL    |No  |No                   |0.340           |0.0             |

          +

          +

          +> [!NOTE]

          +> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)

          +

          +

          +View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2_protein.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2_protein_hg38.html)

          +

          +![image](images/proteinpaint/ANK2_NM_001148.svg)

          +

          +View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2_hg38.html)

          +

          +![image](images/proteinpaint/ANK2.svg)

				ANKRD12.md
			
          @@ -10,9 +10,9 @@

           |Entity|source        |frequency (%)|

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

           |DLBCL |GAMBL genomes |2.29         |

          -|DLBCL |Schmitz cohort|  NA         |

          -|DLBCL |Reddy cohort  |  NA         |

          -|DLBCL |Chapuy cohort |  NA         |

          +|DLBCL |Schmitz cohort|6.17         |

          +|DLBCL |Reddy cohort  |2.10         |

          +|DLBCL |Chapuy cohort |5.13         |

           ## Mutation pattern

          @@ -24,6 +24,9 @@

           > [!NOTE]

          +> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)

          +

          +

           View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD12_protein.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD12_protein_hg38.html)

           ![image](images/proteinpaint/ANKRD12_NM_015208.svg)

				ANKRD17.md
			
          @@ -10,9 +10,9 @@

           |Entity|source        |frequency (%)|

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

           |DLBCL |GAMBL genomes |2.68         |

          -|DLBCL |Schmitz cohort|4.30         |

          +|DLBCL |Schmitz cohort|4.26         |

           |DLBCL |Reddy cohort  |3.80         |

          -|DLBCL |Chapuy cohort |2.10         |

          +|DLBCL |Chapuy cohort |2.14         |

           ## Mutation pattern

				ARID1A.md
			
          @@ -1,7 +1,5 @@

           # [ARID1A]

          -ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes a subunit of the SWI/SNF chromatin remodeling complex, which is involved in regulating DNA accessibility. Mutations in ARID1A are implicated in various cancers, including B-cell lymphomas. They are the most abundant in Burkitt lymphoma but also occur in FL and, to a lesser extent, DLBCL. 

          -

           ## Mutation tier

           |Entity|Tier|Description               |

          @@ -17,9 +15,9 @@ ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes

           |BL    |Thomas cohort        |36.00        |

           |BL    |Panea cohort         |19.80        |

           |DLBCL |GAMBL genomes        | 8.80        |

          -|DLBCL |Schmitz cohort       | 8.90        |

          +|DLBCL |Schmitz cohort       | 8.94        |

           |DLBCL |Reddy cohort         | 4.40        |

          -|DLBCL |Chapuy cohort        | 4.30        |

          +|DLBCL |Chapuy cohort        | 4.27        |

           |FL    |GAMBL genomes        |12.47        |

           ## Mutation pattern

          @@ -35,20 +33,6 @@ ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes

           > First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)

          - ## ARID1A Hotspots

          -

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

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

          -| chr1 | 27023114 | C>T | Q74* |

          -| chr1 | 27023420 | C>T | Q176* |

          -| chr1 | 27023423 | C>T | Q177* |

          -| chr1 | 27023429 | C>T | P179S |

          -| chr1 | 27023447 | C>T | Q185* |

          -| chr1 | 27100207 | C>T | R1335* |

          -| chr1 | 27100315 | T>C | F1343L |

          -| chr1 | 27106354 | C>T | R1989* |

          -| chr1 | 27106363 | T>C | S1992P |

          -

           View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein_hg38.html)

           ![image](images/proteinpaint/ARID1A_NM_006015.svg)

...	...	@@ -0,0 +1,41 @@
	1	+# [AICDA]
	2	+
	3	+## Mutation tier
	4	+
	5	+\|Entity\|Tier\|Description \|
	6	+\|:------:\|:----:\|-----------------------------------------\|
	7	+\|DLBCL \|2-a \| aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous \|
	8	+## Mutation incidence
	9	+
	10	+\|Entity\|source \|frequency (%)\|
	11	+\|:------:\|:--------------:\|:-------------:\|
	12	+\|DLBCL \|GAMBL genomes \|0.38 \|
	13	+\|DLBCL \|Schmitz cohort\|0.43 \|
	14	+\|DLBCL \|Reddy cohort \|0.30 \|
	15	+\|DLBCL \|Chapuy cohort \|0.43 \|
	16	+
	17	+## Mutation pattern
	18	+
	19	+\|Entity\|aSHM\|Significant selection\|dN/dS (missense)\|dN/dS (nonsense)\|
	20	+\|:------:\|:----:\|:---------------------:\|:----------------:\|:----------------:\|
	21	+\|BL \|Yes \|No \|2.589 \|0 \|
	22	+\|DLBCL \|Yes \|No \|2.652 \|0 \|
	23	+\|FL \|Yes \|No \|4.955 \|0 \|
	24	+
	25	+## aSHM regions
	26	+
	27	+\|chr_name\|hg19_start\|hg19_end\|region \|regulatory_comment\|
	28	+\|:--------:\|:----------:\|:--------:\|:----------------------------------------------------------------------------------------:\|:------------------:\|
	29	+\|chr12 \|8762328 \|8765099 \|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr12%3A8762328%2D8765099)\|NA \|
	30	+
	31	+> [!NOTE]
	32	+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
	33	+
	34	+
	35	+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA_protein_hg38.html)
	36	+
	37	+![image](images/proteinpaint/AICDA_NM_020661.svg)
	38	+
	39	+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/AICDA_hg38.html)
	40	+
	41	+![image](images/proteinpaint/AICDA.svg)

...	...	@@ -0,0 +1,33 @@
	1	+# [ANK2]
	2	+
	3	+## Mutation tier
	4	+
	5	+\|Entity\|Tier\|Description \|
	6	+\|:------:\|:----:\|---------------------------------------\|
	7	+\|MCL \|2 \|relevance in MCL not firmly established\|
	8	+## Mutation incidence
	9	+
	10	+\|Entity\|source \|frequency (%)\|
	11	+\|:------:\|:-------------:\|:-------------:\|
	12	+\|MCL \|GAMBL genomes\|1.9 \|
	13	+
	14	+## Mutation pattern
	15	+
	16	+\|Entity\|aSHM\|Significant selection\|dN/dS (missense)\|dN/dS (nonsense)\|
	17	+\|:------:\|:----:\|:---------------------:\|:----------------:\|:----------------:\|
	18	+\|BL \|No \|No \|1.169 \|1.1 \|
	19	+\|DLBCL \|No \|No \|0.393 \|0.0 \|
	20	+\|FL \|No \|No \|0.340 \|0.0 \|
	21	+
	22	+
	23	+> [!NOTE]
	24	+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
	25	+
	26	+
	27	+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2_protein_hg38.html)
	28	+
	29	+![image](images/proteinpaint/ANK2_NM_001148.svg)
	30	+
	31	+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANK2_hg38.html)
	32	+
	33	+![image](images/proteinpaint/ANK2.svg)

...	...	@@ -10,9 +10,9 @@
10	10	\|Entity\|source \|frequency (%)\|
11	11	\|:------:\|:--------------:\|:-------------:\|
12	12	\|DLBCL \|GAMBL genomes \|2.29 \|
13		-\|DLBCL \|Schmitz cohort\| NA \|
14		-\|DLBCL \|Reddy cohort \| NA \|
15		-\|DLBCL \|Chapuy cohort \| NA \|
	13	+\|DLBCL \|Schmitz cohort\|6.17 \|
	14	+\|DLBCL \|Reddy cohort \|2.10 \|
	15	+\|DLBCL \|Chapuy cohort \|5.13 \|
16	16
17	17	## Mutation pattern
18	18
...	...	@@ -24,6 +24,9 @@
24	24
25	25
26	26	> [!NOTE]
	27	+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
	28	+
	29	+
27	30	View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ANKRD12_protein_hg38.html)
28	31
29	32	![image](images/proteinpaint/ANKRD12_NM_015208.svg)

...	...	@@ -1,7 +1,5 @@
1	1	# [ARID1A]
2	2
3		-ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes a subunit of the SWI/SNF chromatin remodeling complex, which is involved in regulating DNA accessibility. Mutations in ARID1A are implicated in various cancers, including B-cell lymphomas. They are the most abundant in Burkitt lymphoma but also occur in FL and, to a lesser extent, DLBCL.
4		-
5	3	## Mutation tier
6	4
7	5	\|Entity\|Tier\|Description \|
...	...	@@ -17,9 +15,9 @@ ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes
17	15	\|BL \|Thomas cohort \|36.00 \|
18	16	\|BL \|Panea cohort \|19.80 \|
19	17	\|DLBCL \|GAMBL genomes \| 8.80 \|
20		-\|DLBCL \|Schmitz cohort \| 8.90 \|
	18	+\|DLBCL \|Schmitz cohort \| 8.94 \|
21	19	\|DLBCL \|Reddy cohort \| 4.40 \|
22		-\|DLBCL \|Chapuy cohort \| 4.30 \|
	20	+\|DLBCL \|Chapuy cohort \| 4.27 \|
23	21	\|FL \|GAMBL genomes \|12.47 \|
24	22
25	23	## Mutation pattern
...	...	@@ -35,20 +33,6 @@ ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes
35	33	> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
36	34
37	35
38		- ## ARID1A Hotspots
39		-
40		-\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
41		- \| :---:\| :---: \| :--: \| :---: \|
42		-\| chr1 \| 27023114 \| C>T \| Q74* \|
43		-\| chr1 \| 27023420 \| C>T \| Q176* \|
44		-\| chr1 \| 27023423 \| C>T \| Q177* \|
45		-\| chr1 \| 27023429 \| C>T \| P179S \|
46		-\| chr1 \| 27023447 \| C>T \| Q185* \|
47		-\| chr1 \| 27100207 \| C>T \| R1335* \|
48		-\| chr1 \| 27100315 \| T>C \| F1343L \|
49		-\| chr1 \| 27106354 \| C>T \| R1989* \|
50		-\| chr1 \| 27106363 \| T>C \| S1992P \|
51		-
52	36	View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein_hg38.html)
53	37
54	38	![image](images/proteinpaint/ARID1A_NM_006015.svg)