Changes in 0db93e1: tracking

				CRIP1.md
			
          @@ -53,4 +53,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_361-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_361-Tumor.html)

          +[DLBCL-RICOVER_950-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_950-Tumor.html)

          +

           ## References

				DOCK1.md
			
          @@ -53,5 +53,15 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_107-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_107-Tumor.html)

          +[DLBCL-RICOVER_253-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_253-Tumor.html)

          +[DLBCL-RICOVER_299-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_299-Tumor.html)

          +[DLBCL-RICOVER_338-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_338-Tumor.html)

          +[DLBCL-RICOVER_522-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_522-Tumor.html)

          +[DLBCL-RICOVER_773-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_773-Tumor.html)

          +[DLBCL-RICOVER_977-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_977-Tumor.html)

          +

           ## References

				FUT5.md
			
          @@ -52,5 +52,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_173-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_173-Tumor.html)

          +

           ## References

				IL6.md
			
          @@ -52,5 +52,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_253-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_253-Tumor.html)

          +[DLBCL-RICOVER_623-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_623-Tumor.html)

          +[DLBCL-RICOVER_704-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_704-Tumor.html)

          +

           ## References

				LYN.md
			
          @@ -19,7 +19,7 @@ timeline

           |Entity|Tier|Description               |

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

          -|![DLBCL](images/icons/DLBCL_tier1.png) |1   |high-confidence DLBCL gene[@chapuyMolecularSubtypesDiffuse2018b]|

          +|![DLBCL](images/icons/DLBCL_tier1.png) |2   |low-confidence DLBCL gene[@chapuyMolecularSubtypesDiffuse2018b]|

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

          @@ -55,5 +55,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_1081-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_1081-Tumor.html)

          +[DLBCL-RICOVER_181-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_181-Tumor.html)

          +[DLBCL-RICOVER_773-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_773-Tumor.html)

          +

           ## References

				NAV1.md
			
          @@ -51,4 +51,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_839-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_839-Tumor.html)

          +

           ## References

				NLRP8.md
			
          @@ -51,5 +51,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_1235-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_1235-Tumor.html)

          +[DLBCL-RICOVER_325-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_325-Tumor.html)

          +[DLBCL-RICOVER_720-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_720-Tumor.html)

          +

           ## References

				PDE4DIP.md
			
          @@ -50,5 +50,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_107-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_107-Tumor.html)

          +[DLBCL-RICOVER_288-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_288-Tumor.html)

          +[DLBCL-RICOVER_384-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_384-Tumor.html)

          +[DLBCL-RICOVER_496-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_496-Tumor.html)

          +

           ## References

				PRPS1.md
			
          @@ -52,5 +52,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_288-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_288-Tumor.html)

          +[DLBCL-RICOVER_449-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_449-Tumor.html)

          +

           ## References

				TLR2.md
			
          @@ -60,5 +60,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- MCL: beaLandscapeSomaticMutations2013 -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_1269-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_1269-Tumor.html)

          +[DLBCL-RICOVER_174-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_174-Tumor.html)

          +

           ## References

				ZNF423.md
			
          @@ -52,4 +52,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z

           <!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->

           <!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->

          +## All Mutations

          +

          +[DLBCL-RICOVER_181-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_181-Tumor.html)

          +

           ## References

				papers/chapuyMolecularSubtypesDiffuse2018b.md
			
          @@ -47,7 +47,7 @@ All other DLBCL studies, DLBCL Tier 2, 181

           ### Tier 2

           |Novel Gene|BL tier|Average variant quality|QC outcome|

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

          -|[CCL4](../CCL4)|2 |

          +|[CCL4](../CCL4)|2 |*No variants reported*|**Fail**|

           |[COQ7](../COQ7)|2 |

           |[CRIP1](../CRIP1)|2 |

           |[DOCK1](../DOCK1)|2 |

          @@ -55,12 +55,12 @@ All other DLBCL studies, DLBCL Tier 2, 181

           |[GABRA2](../GABRA2)|2 |

           |[IL6](../IL6)|2 |

           |[LYN](../LYN)|2 |

          -|[NANOG](../NANOG)|2 |

          +|[NANOG](../NANOG)|2 |*No variants reported*|**Fail**|

           |[NAV1](../NAV1)|2 |

           |[NLRP8](../NLRP8)|2 |

           |[PDE4DIP](../PDE4DIP)|2 |

           |[PRPS1](../PRPS1)|2 |

          -|[RAD9A](../RAD9A)|2 |

          +|[RAD9A](../RAD9A)|2 |*No variants reported*|**Fail**|

           |[SMEK1](../SMEK1)|2 |

           |[TLR2](../TLR2)|2 |

           |[ZNF423](../ZNF423)|2 |

...	...	@@ -53,4 +53,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
53	53	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
54	54	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
55	55
	56	+## All Mutations
	57	+
	58	+[DLBCL-RICOVER_361-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_361-Tumor.html)
	59	+[DLBCL-RICOVER_950-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_950-Tumor.html)
	60	+
56	61	## References

...	...	@@ -53,5 +53,15 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
53	53	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
54	54	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
55	55
	56	+## All Mutations
	57	+
	58	+[DLBCL-RICOVER_107-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_107-Tumor.html)
	59	+[DLBCL-RICOVER_253-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_253-Tumor.html)
	60	+[DLBCL-RICOVER_299-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_299-Tumor.html)
	61	+[DLBCL-RICOVER_338-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_338-Tumor.html)
	62	+[DLBCL-RICOVER_522-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_522-Tumor.html)
	63	+[DLBCL-RICOVER_773-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_773-Tumor.html)
	64	+[DLBCL-RICOVER_977-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_977-Tumor.html)
	65	+
56	66	## References
57	67

...	...	@@ -52,5 +52,9 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
52	52	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
53	53	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
54	54
	55	+## All Mutations
	56	+
	57	+[DLBCL-RICOVER_173-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_173-Tumor.html)
	58	+
55	59	## References
56	60

...	...	@@ -52,5 +52,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
52	52	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
53	53	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
54	54
	55	+## All Mutations
	56	+
	57	+[DLBCL-RICOVER_253-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_253-Tumor.html)
	58	+[DLBCL-RICOVER_623-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_623-Tumor.html)
	59	+[DLBCL-RICOVER_704-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_704-Tumor.html)
	60	+
55	61	## References
56	62

...	...	@@ -19,7 +19,7 @@ timeline
19	19
20	20	\|Entity\|Tier\|Description \|
21	21	\|:------:\|:----:\|--------------------------\|
22		-\|![DLBCL](images/icons/DLBCL_tier1.png) \|1 \|high-confidence DLBCL gene[@chapuyMolecularSubtypesDiffuse2018b]\|
	22	+\|![DLBCL](images/icons/DLBCL_tier1.png) \|2 \|low-confidence DLBCL gene[@chapuyMolecularSubtypesDiffuse2018b]\|
23	23
24	24	## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25	25
...	...	@@ -55,5 +55,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/L
55	55	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
56	56	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
57	57
	58	+## All Mutations
	59	+
	60	+[DLBCL-RICOVER_1081-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_1081-Tumor.html)
	61	+[DLBCL-RICOVER_181-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_181-Tumor.html)
	62	+[DLBCL-RICOVER_773-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_773-Tumor.html)
	63	+
58	64	## References
59	65

...	...	@@ -51,4 +51,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
51	51	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
52	52	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
53	53
	54	+## All Mutations
	55	+
	56	+[DLBCL-RICOVER_839-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_839-Tumor.html)
	57	+
54	58	## References

...	...	@@ -51,5 +51,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
51	51	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
52	52	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
53	53
	54	+## All Mutations
	55	+
	56	+[DLBCL-RICOVER_1235-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_1235-Tumor.html)
	57	+[DLBCL-RICOVER_325-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_325-Tumor.html)
	58	+[DLBCL-RICOVER_720-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_720-Tumor.html)
	59	+
54	60	## References
55	61

...	...	@@ -50,5 +50,12 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
50	50	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
51	51	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
52	52
	53	+## All Mutations
	54	+
	55	+[DLBCL-RICOVER_107-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_107-Tumor.html)
	56	+[DLBCL-RICOVER_288-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_288-Tumor.html)
	57	+[DLBCL-RICOVER_384-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_384-Tumor.html)
	58	+[DLBCL-RICOVER_496-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_496-Tumor.html)
	59	+
53	60	## References
54	61

...	...	@@ -52,5 +52,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
52	52	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
53	53	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
54	54
	55	+## All Mutations
	56	+
	57	+[DLBCL-RICOVER_288-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_288-Tumor.html)
	58	+[DLBCL-RICOVER_449-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_449-Tumor.html)
	59	+
55	60	## References
56	61

...	...	@@ -60,5 +60,10 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
60	60	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
61	61	<!-- MCL: beaLandscapeSomaticMutations2013 -->
62	62
	63	+## All Mutations
	64	+
	65	+[DLBCL-RICOVER_1269-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_1269-Tumor.html)
	66	+[DLBCL-RICOVER_174-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_174-Tumor.html)
	67	+
63	68	## References
64	69

...	...	@@ -52,4 +52,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z
52	52	<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
53	53	<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
54	54
	55	+## All Mutations
	56	+
	57	+[DLBCL-RICOVER_181-Tumor](https://bcgsc.ca/downloads/morinlab/GAMBL/Chapuy_2018/DLBCL-RICOVER_181-Tumor.html)
	58	+
55	59	## References

...	...	@@ -47,7 +47,7 @@ All other DLBCL studies, DLBCL Tier 2, 181
47	47	### Tier 2
48	48	\|Novel Gene\|BL tier\|Average variant quality\|QC outcome\|
49	49	\|:-\|:-:\|:-:\|:-:\|
50		-\|[CCL4](../CCL4)\|2 \|
	50	+\|[CCL4](../CCL4)\|2 \|No variants reported\|Fail\|
51	51	\|[COQ7](../COQ7)\|2 \|
52	52	\|[CRIP1](../CRIP1)\|2 \|
53	53	\|[DOCK1](../DOCK1)\|2 \|
...	...	@@ -55,12 +55,12 @@ All other DLBCL studies, DLBCL Tier 2, 181
55	55	\|[GABRA2](../GABRA2)\|2 \|
56	56	\|[IL6](../IL6)\|2 \|
57	57	\|[LYN](../LYN)\|2 \|
58		-\|[NANOG](../NANOG)\|2 \|
	58	+\|[NANOG](../NANOG)\|2 \|No variants reported\|Fail\|
59	59	\|[NAV1](../NAV1)\|2 \|
60	60	\|[NLRP8](../NLRP8)\|2 \|
61	61	\|[PDE4DIP](../PDE4DIP)\|2 \|
62	62	\|[PRPS1](../PRPS1)\|2 \|
63		-\|[RAD9A](../RAD9A)\|2 \|
	63	+\|[RAD9A](../RAD9A)\|2 \|No variants reported\|Fail\|
64	64	\|[SMEK1](../SMEK1)\|2 \|
65	65	\|[TLR2](../TLR2)\|2 \|
66	66	\|[ZNF423](../ZNF423)\|2 \|