Changes in 083fcc0: Updated CD58 (markdown)

				CD58.md
			
          @@ -1,23 +1,26 @@

           # CD58

          +## Overview

          +

          +CD58, also known as lymphocyte function-associated antigen 3 (LFA-3), is crucial for immune recognition, facilitating interactions between tumor cells and cytotoxic T cells and natural killer (NK) cells. In DLBCL, mutations prevent the expression of CD58 on the cell surface, impairing the ability of T and NK cells to recognize and attack the tumor cells. This is often accompanied by mutations in the β2-Microglobulin gene, which further aids in immune evasion.<sup>1</sup>

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

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

          -|BL    |2   |relevance in BL not firmly established|

           |DLBCL |1   |high-confidence DLBCL gene            |

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

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

           |Entity|source               |frequency (%)|

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

          -|BL    |GAMBL genomes+capture| 0.92        |

          -|BL    |Thomas cohort        | 0.80        |

          -|BL    |Panea cohort         | 2.00        |

           |DLBCL |GAMBL genomes        | 7.84        |

           |DLBCL |Schmitz cohort       |10.00        |

           |DLBCL |Reddy cohort         | 2.80        |

           |DLBCL |Chapuy cohort        | 6.84        |

          +|BL    |GAMBL genomes+capture| 0.92        |

          +|BL    |Thomas cohort        | 0.80        |

          +|BL    |Panea cohort         | 2.00        |

           ## Mutation pattern and selective pressure estimates

          @@ -39,3 +42,7 @@ View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morin

           View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58.html)  or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58_hg38.html)

           ![image](images/proteinpaint/CD58.svg)

          +

          +## References

          +

          +1. *Challa-Malladi M, Lieu YK, Califano O, Holmes AB, Bhagat G, Murty VV, Dominguez-Sola D, Pasqualucci L, Dalla-Favera R. Combined genetic inactivation of β2-Microglobulin and CD58 reveals frequent escape from immune recognition in diffuse large B cell lymphoma. Cancer Cell. 2011 Dec 13;20(6):728-40. doi: 10.1016/j.ccr.2011.11.006. Epub 2011 Dec 1. PMID: 22137796; PMCID: PMC3660995.*

...	...	@@ -1,23 +1,26 @@
1	1	# CD58
	2	+## Overview
	3	+
	4	+CD58, also known as lymphocyte function-associated antigen 3 (LFA-3), is crucial for immune recognition, facilitating interactions between tumor cells and cytotoxic T cells and natural killer (NK) cells. In DLBCL, mutations prevent the expression of CD58 on the cell surface, impairing the ability of T and NK cells to recognize and attack the tumor cells. This is often accompanied by mutations in the β2-Microglobulin gene, which further aids in immune evasion.<sup>1</sup>
2	5
3	6	## Relevance tier by entity
4	7
5	8	\|Entity\|Tier\|Description \|
6	9	\|:------:\|:----:\|--------------------------------------\|
7		-\|BL \|2 \|relevance in BL not firmly established\|
8	10	\|DLBCL \|1 \|high-confidence DLBCL gene \|
	11	+\|BL \|2 \|relevance in BL not firmly established\|
9	12
10	13	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11	14
12	15	\|Entity\|source \|frequency (%)\|
13	16	\|:------:\|:---------------------:\|:-------------:\|
14		-\|BL \|GAMBL genomes+capture\| 0.92 \|
15		-\|BL \|Thomas cohort \| 0.80 \|
16		-\|BL \|Panea cohort \| 2.00 \|
17	17	\|DLBCL \|GAMBL genomes \| 7.84 \|
18	18	\|DLBCL \|Schmitz cohort \|10.00 \|
19	19	\|DLBCL \|Reddy cohort \| 2.80 \|
20	20	\|DLBCL \|Chapuy cohort \| 6.84 \|
	21	+\|BL \|GAMBL genomes+capture\| 0.92 \|
	22	+\|BL \|Thomas cohort \| 0.80 \|
	23	+\|BL \|Panea cohort \| 2.00 \|
21	24
22	25	## Mutation pattern and selective pressure estimates
23	26
...	...	@@ -39,3 +42,7 @@ View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morin
39	42	View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58_hg38.html)
40	43
41	44	![image](images/proteinpaint/CD58.svg)
	45	+
	46	+## References
	47	+
	48	+1. Challa-Malladi M, Lieu YK, Califano O, Holmes AB, Bhagat G, Murty VV, Dominguez-Sola D, Pasqualucci L, Dalla-Favera R. Combined genetic inactivation of β2-Microglobulin and CD58 reveals frequent escape from immune recognition in diffuse large B cell lymphoma. Cancer Cell. 2011 Dec 13;20(6):728-40. doi: 10.1016/j.ccr.2011.11.006. Epub 2011 Dec 1. PMID: 22137796; PMCID: PMC3660995.