Changes in 7257be1: Updated CD70 (markdown)

				CD70.md
			
          @@ -1,25 +1,27 @@

           # CD70

          +## Overview

          +CD70 genetic aberrations are relatively common in DLBCL and appear more frequent in certain DLBCL patient populations. For instance, in a Chinese DLBCL cohort, 24% of cases exhibited CD70 genetic changes, compared to 10.8% in a Swedish cohort.<sup>1</sup> CD70 mutations are associated with the BN2 genetic subtype of DLBCL. 

           ## Relevance tier by entity

           |Entity|Tier|Description                           |

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

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

           |DLBCL |1   |high-confidence DLBCL gene            |

           |FL    |2   |relevance in FL not firmly established|

          +|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        |0.40         |

          -|BL    |Panea cohort         |3.00         |

           |DLBCL |GAMBL genomes        |5.54         |

           |DLBCL |Schmitz cohort       |9.36         |

           |DLBCL |Reddy cohort         |6.91         |

           |DLBCL |Chapuy cohort        |7.69         |

           |FL    |GAMBL genomes        |1.15         |

          +|BL    |GAMBL genomes+capture|0.92         |

          +|BL    |Thomas cohort        |0.40         |

          +|BL    |Panea cohort         |3.00         |

           ## Mutation pattern and selective pressure estimates

          @@ -30,8 +32,6 @@

           |FL    |No  |No                   | 0.000          |106.251         |

          -

          -

            ## CD70 Hotspots

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

          @@ -49,3 +49,7 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM

           View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD70.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD70_hg38.html)

           ![image](images/proteinpaint/CD70.svg)

          +

          +# References

          +1. *Nie M, Ren W, Ye X, Berglund M, Wang X, Fjordén K, Du L, Giannoula Y, Lei D, Su W, Li W, Liu D, Linderoth J, Jiang C, Bao H, Jiang W, Huang H, Hou Y, Zhu S, Enblad G, Jerkeman M, Wu K, Zhang H, Amini RM, Li ZM, Pan-Hammarström Q. The dual role of CD70 in B-cell lymphomagenesis. Clin Transl Med. 2022 Dec;12(12):e1118. doi: 10.1002/ctm2.1118. PMID: 36471481; PMCID: PMC9722974.*

          +2. **Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.**

...	...	@@ -1,25 +1,27 @@
1	1	# CD70
	2	+## Overview
	3	+CD70 genetic aberrations are relatively common in DLBCL and appear more frequent in certain DLBCL patient populations. For instance, in a Chinese DLBCL cohort, 24% of cases exhibited CD70 genetic changes, compared to 10.8% in a Swedish cohort.<sup>1</sup> CD70 mutations are associated with the BN2 genetic subtype of DLBCL.
2	4
3	5	## Relevance tier by entity
4	6
5	7	\|Entity\|Tier\|Description \|
6	8	\|:------:\|:----:\|--------------------------------------\|
7		-\|BL \|2 \|relevance in BL not firmly established\|
8	9	\|DLBCL \|1 \|high-confidence DLBCL gene \|
9	10	\|FL \|2 \|relevance in FL not firmly established\|
	11	+\|BL \|2 \|relevance in BL not firmly established\|
10	12
11	13	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12	14
13	15	\|Entity\|source \|frequency (%)\|
14	16	\|:------:\|:---------------------:\|:-------------:\|
15		-\|BL \|GAMBL genomes+capture\|0.92 \|
16		-\|BL \|Thomas cohort \|0.40 \|
17		-\|BL \|Panea cohort \|3.00 \|
18	17	\|DLBCL \|GAMBL genomes \|5.54 \|
19	18	\|DLBCL \|Schmitz cohort \|9.36 \|
20	19	\|DLBCL \|Reddy cohort \|6.91 \|
21	20	\|DLBCL \|Chapuy cohort \|7.69 \|
22	21	\|FL \|GAMBL genomes \|1.15 \|
	22	+\|BL \|GAMBL genomes+capture\|0.92 \|
	23	+\|BL \|Thomas cohort \|0.40 \|
	24	+\|BL \|Panea cohort \|3.00 \|
23	25
24	26	## Mutation pattern and selective pressure estimates
25	27
...	...	@@ -30,8 +32,6 @@
30	32	\|FL \|No \|No \| 0.000 \|106.251 \|
31	33
32	34
33		-
34		-
35	35	## CD70 Hotspots
36	36
37	37	\| Chromosome \|Coordinate (hg19) \| ref>alt \| HGVSp \|
...	...	@@ -49,3 +49,7 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
49	49	View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/CD70.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/CD70_hg38.html)
50	50
51	51	![image](images/proteinpaint/CD70.svg)
	52	+
	53	+# References
	54	+1. Nie M, Ren W, Ye X, Berglund M, Wang X, Fjordén K, Du L, Giannoula Y, Lei D, Su W, Li W, Liu D, Linderoth J, Jiang C, Bao H, Jiang W, Huang H, Hou Y, Zhu S, Enblad G, Jerkeman M, Wu K, Zhang H, Amini RM, Li ZM, Pan-Hammarström Q. The dual role of CD70 in B-cell lymphomagenesis. Clin Transl Med. 2022 Dec;12(12):e1118. doi: 10.1002/ctm2.1118. PMID: 36471481; PMCID: PMC9722974.
	55	+2. Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell. 2020 Apr 13;37(4):551-568.e14. doi: 10.1016/j.ccell.2020.03.015. PMID: 32289277; PMCID: PMC8459709.