Changes in abff706: move history

				ABCA3.md
			
          @@ -4,16 +4,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ABCA3

          +[[_TOC_]]

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2013-11-05 : Bea : MCL

          -```

           ## Relevance tier by entity

          @@ -35,6 +28,8 @@ timeline

           |MCL|GAMBL Genome |0.585 |

          +[[include:mermaid_ABCA3.md]]

          +

           ## References

				ABCB1.md
			
          @@ -4,16 +4,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ABCB1

          +[[_TOC_]]

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -       2020-07-01 : Fan : DLBCL

          -```

           ## Relevance tier by entity

          @@ -26,6 +19,8 @@ timeline

          +[[include:mermaid_ABCB1.md]]

          +

           ## References

				ABCC9.md
			
          @@ -4,16 +4,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ABCC9

          +[[_TOC_]]

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2013-11-05 : Be : MCL

          -```

           ## Relevance tier by entity

          @@ -34,6 +27,8 @@ timeline

           |FL|GAMBL Exome |0.573 |

          +[[include:mermaid_ABCC9.md]]

          +

           ## References

				ABI3BP.md
			
          @@ -3,18 +3,11 @@ bibliography: 'morinlab.bib'

           csl: 'NLM.csl'

           link-citations: true

           ---

          -# ABI3BP

          +[[_TOC_]]

          -## History

           Mutations were first described in DLBCL in 2013 by Morin et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation. 

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2013-08-15 : Morin : DLBCL

          -```

           ## Relevance tier by entity

          @@ -49,6 +42,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A

           [RG067](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Morin_2013/RG067.html)

           [RG081](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Morin_2013/RG081.html)

          +[[include:mermaid_ABI3BP.md]]

          +

           ## References

				ACAD9.md
			
          @@ -3,20 +3,13 @@ bibliography: 'morinlab.bib'

           csl: 'NLM.csl'

           link-citations: true

           ---

          -# ACAD9

          +[[_TOC_]]

           ## Overview

           Due to [minimal support](ACAD9#representative-mutation) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. 

           <<Warn("The variants reported in this gene in BL failed QC")>>

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2012-12-01 : Love : BL

          -```

           ## Relevance tier by entity

          @@ -66,6 +59,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A

           [851](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/851_reports.html)

          +[[include:mermaid_ACAD9.md]]

          +

           ## References

           <!-- ORIGIN: loveGeneticLandscapeMutations2012 -->

				ACE.md
			
          @@ -3,7 +3,7 @@ bibliography: 'morinlab.bib'

           csl: 'NLM.csl'

           link-citations: true

           ---

          -# ACE

          +[[_TOC_]]

           ## Overview

          @@ -11,14 +11,6 @@ Due to [minimal support](ACE#representative-mutation) in the original primary da

           <<Warn("The variants reported in this gene in BL failed QC")>>

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2012-12-01 : Love : BL

          -      2013-01-01 : Zhang : DLBCL

          -```

           ## Relevance tier by entity

          @@ -72,4 +64,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A

           [677](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/677_reports.html)

           [744](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/744_reports.html)

          +[[include:mermaid_ACE.md]]

          +

           ## References

				ACSM3.md
			
          @@ -4,16 +4,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ACSM3

          +[[_TOC_]]

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2013-01-01 : Zhang : DLBCL

          -```

           ## Relevance tier by entity

          @@ -26,6 +19,8 @@ timeline

          +[[include:mermaid_ACSM3.md]]

          +

           ## References

				ACSS2.md
			
          @@ -4,16 +4,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ACSS2

          +[[_TOC_]]

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2013-01-01 : Zhang : DLBCL

          -```

           ## Relevance tier by entity

          @@ -26,6 +19,8 @@ timeline

          +[[include:mermaid_ACSS2.md]]

          +

           ## References

				ACSS3.md
			
          @@ -4,16 +4,9 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ACSS3

          +[[_TOC_]]

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2013-01-01 : Zhang : DLBCL

          -```

           ## Relevance tier by entity

          @@ -26,6 +19,8 @@ timeline

          +[[include:mermaid_ACSS3.md]]

          +

           ## References

				ACTB.md
			
          @@ -4,26 +4,13 @@ csl: 'NLM.csl'

           link-citations: true

           ---

          -# ACTB

          +[[_TOC_]]

           ## Overview

           ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas. The function of mutations in ACTB and ACTG1 have not yet been determined.[@witjesPrevalenceCytoplasmicActin2020]

          -## History

          -

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2012-03-06 : Lohr : DLBCL

          -      2017-05-01 : Albuquerque : DLBCL

          -2017-10-10 : Reddy : DLBCL

          -2018-04-12 : Schmitz : DLBCL

          -2018-05-01 : Chapuy : DLBCL

          -      2019-12-10 : Wienand : PMBL

          -2021-05-05 : Hubschmann : DLBCL

          -```

          +

           ## Relevance tier by entity

          @@ -78,6 +65,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A

           ## ACTB Expression

           ![](images/gene_expression/ACTB_by_pathology.svg)

          +[[include:mermaid_ACTB.md]]

          +

           ## References

           <!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->

				mermaid_ABCA3.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-11-05 : Bea : MCL

          +```

				mermaid_ABCB1.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +       2020-07-01 : Fan : DLBCL

          +```

				mermaid_ABCC9.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-11-05 : Be : MCL

          +```

				mermaid_ABI3BP.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-08-15 : Morin : DLBCL

          +```

				mermaid_ACAD9.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2012-12-01 : Love : BL

          +```

				mermaid_ACE.md
			
          @@ -0,0 +1,8 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2012-12-01 : Love : BL

          +      2013-01-01 : Zhang : DLBCL

          +```

				mermaid_ACSM3.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-01-01 : Zhang : DLBCL

          +```

				mermaid_ACSS2.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-01-01 : Zhang : DLBCL

          +```

				mermaid_ACSS3.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2013-01-01 : Zhang : DLBCL

          +```

				mermaid_ACTB.md
			
          @@ -0,0 +1,13 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2012-03-06 : Lohr : DLBCL

          +      2017-05-01 : Albuquerque : DLBCL

          +2017-10-10 : Reddy : DLBCL

          +2018-04-12 : Schmitz : DLBCL

          +2018-05-01 : Chapuy : DLBCL

          +      2019-12-10 : Wienand : PMBL

          +2021-05-05 : Hubschmann : DLBCL

          +```

				mermaid_HLA-A.md
			
          @@ -0,0 +1,7 @@

          +## History

          +```mermaid

          +%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          +timeline

          +    title Publication timing

          +      2019-08-20 : Desch : PMBL

          +```

...	...	@@ -4,16 +4,9 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ABCA3
	7	+[[_TOC_]]
8	8
9		-## History
10	9
11		-```mermaid
12		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13		-timeline
14		- title Publication timing
15		- 2013-11-05 : Bea : MCL
16		-```
17	10
18	11
19	12	## Relevance tier by entity
...	...	@@ -35,6 +28,8 @@ timeline
35	28	\|MCL\|GAMBL Genome \|0.585 \|
36	29
37	30
	31	+[[include:mermaid_ABCA3.md]]
	32	+
38	33	## References
39	34
40	35

...	...	@@ -4,16 +4,9 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ABCB1
	7	+[[_TOC_]]
8	8
9		-## History
10	9
11		-```mermaid
12		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13		-timeline
14		- title Publication timing
15		- 2020-07-01 : Fan : DLBCL
16		-```
17	10
18	11
19	12	## Relevance tier by entity
...	...	@@ -26,6 +19,8 @@ timeline
26	19
27	20
28	21
	22	+[[include:mermaid_ABCB1.md]]
	23	+
29	24	## References
30	25
31	26

...	...	@@ -4,16 +4,9 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ABCC9
	7	+[[_TOC_]]
8	8
9		-## History
10	9
11		-```mermaid
12		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13		-timeline
14		- title Publication timing
15		- 2013-11-05 : Be : MCL
16		-```
17	10
18	11
19	12	## Relevance tier by entity
...	...	@@ -34,6 +27,8 @@ timeline
34	27	\|FL\|GAMBL Exome \|0.573 \|
35	28
36	29
	30	+[[include:mermaid_ABCC9.md]]
	31	+
37	32	## References
38	33
39	34

...	...	@@ -3,18 +3,11 @@ bibliography: 'morinlab.bib'
3	3	csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6		-# ABI3BP
	6	+[[_TOC_]]
7	7
8		-## History
9	8
10	9	Mutations were first described in DLBCL in 2013 by Morin et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
11	10
12		-```mermaid
13		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
14		-timeline
15		- title Publication timing
16		- 2013-08-15 : Morin : DLBCL
17		-```
18	11
19	12	## Relevance tier by entity
20	13
...	...	@@ -49,6 +42,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
49	42	[RG067](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Morin_2013/RG067.html)
50	43	[RG081](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Morin_2013/RG081.html)
51	44
	45	+[[include:mermaid_ABI3BP.md]]
	46	+
52	47	## References
53	48
54	49

...	...	@@ -3,20 +3,13 @@ bibliography: 'morinlab.bib'
3	3	csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6		-# ACAD9
	6	+[[_TOC_]]
7	7
8	8	## Overview
9	9	Due to [minimal support](ACAD9#representative-mutation) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL.
10	10
11	11	<<Warn("The variants reported in this gene in BL failed QC")>>
12	12
13		-## History
14		-```mermaid
15		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
16		-timeline
17		- title Publication timing
18		- 2012-12-01 : Love : BL
19		-```
20	13
21	14	## Relevance tier by entity
22	15
...	...	@@ -66,6 +59,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
66	59	[851](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/851_reports.html)
67	60
68	61
	62	+[[include:mermaid_ACAD9.md]]
	63	+
69	64	## References
70	65
71	66	<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->

...	...	@@ -3,7 +3,7 @@ bibliography: 'morinlab.bib'
3	3	csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6		-# ACE
	6	+[[_TOC_]]
7	7
8	8	## Overview
9	9
...	...	@@ -11,14 +11,6 @@ Due to [minimal support](ACE#representative-mutation) in the original primary da
11	11
12	12	<<Warn("The variants reported in this gene in BL failed QC")>>
13	13
14		-## History
15		-```mermaid
16		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
17		-timeline
18		- title Publication timing
19		- 2012-12-01 : Love : BL
20		- 2013-01-01 : Zhang : DLBCL
21		-```
22	14
23	15	## Relevance tier by entity
24	16
...	...	@@ -72,4 +64,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
72	64	[677](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/677_reports.html)
73	65	[744](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/744_reports.html)
74	66
	67	+[[include:mermaid_ACE.md]]
	68	+
75	69	## References

...	...	@@ -4,16 +4,9 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ACSM3
	7	+[[_TOC_]]
8	8
9		-## History
10	9
11		-```mermaid
12		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13		-timeline
14		- title Publication timing
15		- 2013-01-01 : Zhang : DLBCL
16		-```
17	10
18	11
19	12	## Relevance tier by entity
...	...	@@ -26,6 +19,8 @@ timeline
26	19
27	20
28	21
	22	+[[include:mermaid_ACSM3.md]]
	23	+
29	24	## References
30	25
31	26

...	...	@@ -4,16 +4,9 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ACSS2
	7	+[[_TOC_]]
8	8
9		-## History
10	9
11		-```mermaid
12		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13		-timeline
14		- title Publication timing
15		- 2013-01-01 : Zhang : DLBCL
16		-```
17	10
18	11
19	12	## Relevance tier by entity
...	...	@@ -26,6 +19,8 @@ timeline
26	19
27	20
28	21
	22	+[[include:mermaid_ACSS2.md]]
	23	+
29	24	## References
30	25
31	26

...	...	@@ -4,16 +4,9 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ACSS3
	7	+[[_TOC_]]
8	8
9		-## History
10	9
11		-```mermaid
12		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13		-timeline
14		- title Publication timing
15		- 2013-01-01 : Zhang : DLBCL
16		-```
17	10
18	11
19	12	## Relevance tier by entity
...	...	@@ -26,6 +19,8 @@ timeline
26	19
27	20
28	21
	22	+[[include:mermaid_ACSS3.md]]
	23	+
29	24	## References
30	25
31	26

...	...	@@ -4,26 +4,13 @@ csl: 'NLM.csl'
4	4	link-citations: true
5	5	---
6	6
7		-# ACTB
	7	+[[_TOC_]]
8	8
9	9	## Overview
10	10
11	11	ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas. The function of mutations in ACTB and ACTG1 have not yet been determined.[@witjesPrevalenceCytoplasmicActin2020]
12	12
13		-## History
14		-
15		-```mermaid
16		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
17		-timeline
18		- title Publication timing
19		- 2012-03-06 : Lohr : DLBCL
20		- 2017-05-01 : Albuquerque : DLBCL
21		-2017-10-10 : Reddy : DLBCL
22		-2018-04-12 : Schmitz : DLBCL
23		-2018-05-01 : Chapuy : DLBCL
24		- 2019-12-10 : Wienand : PMBL
25		-2021-05-05 : Hubschmann : DLBCL
26		-```
	13	+
27	14
28	15	## Relevance tier by entity
29	16
...	...	@@ -78,6 +65,8 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
78	65	## ACTB Expression
79	66	![](images/gene_expression/ACTB_by_pathology.svg)
80	67
	68	+[[include:mermaid_ACTB.md]]
	69	+
81	70	## References
82	71
83	72	<!-- ORIGIN: lohrDiscoveryPrioritizationSomatic2012a -->

...	...	@@ -0,0 +1,7 @@
	1	+## History
	2	+```mermaid
	3	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	4	+timeline
	5	+ title Publication timing
	6	+ 2013-11-05 : Bea : MCL
	7	+```

...	...	@@ -0,0 +1,8 @@
	1	+## History
	2	+```mermaid
	3	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	4	+timeline
	5	+ title Publication timing
	6	+ 2012-12-01 : Love : BL
	7	+ 2013-01-01 : Zhang : DLBCL
	8	+```

...	...	@@ -0,0 +1,13 @@
	1	+## History
	2	+```mermaid
	3	+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
	4	+timeline
	5	+ title Publication timing
	6	+ 2012-03-06 : Lohr : DLBCL
	7	+ 2017-05-01 : Albuquerque : DLBCL
	8	+2017-10-10 : Reddy : DLBCL
	9	+2018-04-12 : Schmitz : DLBCL
	10	+2018-05-01 : Chapuy : DLBCL
	11	+ 2019-12-10 : Wienand : PMBL
	12	+2021-05-05 : Hubschmann : DLBCL
	13	+```