HIST1H1B.md
... ...
@@ -1,3 +1,8 @@
1
+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
1 6
# HIST1H1B
2 7
3 8
## Overview
... ...
@@ -17,10 +22,10 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
25
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@sarkozyMutationalLandscapeGray2021a]|
21 26
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
22
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
23
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
27
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@chapuyMolecularSubtypesDiffuse2018b]|
28
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
24 29
25 30
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
26 31
... ...
@@ -61,6 +66,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
61 66
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
62 67
63 68
## References
64
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
65
-2. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
66
-3. Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765–1776. PMID: 32961552
HIST1H1C.md
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1
+---
2
+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H1C
2 7
3 8
## Overview
... ...
@@ -21,8 +26,8 @@ timeline
21 26
|Entity|Tier|Description |
22 27
|:------:|:----:|--------------------------------------|
23 28
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
24
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
25
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
29
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
30
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
26 31
|![BL](images/icons/BL_tier2.png) |2-F |Failed QC|
27 32
28 33
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -74,10 +79,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
74 79
75 80
## References
76 81
77
-1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
78
-2. *Li H, Kaminski MS, Li Y, Yildiz M, Ouillette P, Jones S, Fox H, Jacobi K, Saiya-Cork K, Bixby D, Lebovic D, Roulston D, Shedden K, Sabel M, Marentette L, Cimmino V, Chang AE, Malek SN. Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. Blood. 2014 Mar 6;123(10):1487-98. doi: 10.1182/blood-2013-05-500264. Epub 2014 Jan 16. PMID: 24435047; PMCID: PMC4729540.*
79
-3. *Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;*
80
-
81 82
82 83
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
83 84
<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
HIST1H1D.md
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@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H1D
2 7
3 8
## Overview
... ...
@@ -18,10 +23,10 @@ timeline
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20 25
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
21
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
26
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
22 27
|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
23
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
24
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
28
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@morinMutationalStructuralAnalysis2013]|
29
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
25 30
26 31
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27 32
... ...
@@ -63,6 +68,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
63 68
<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
64 69
65 70
## References
66
-1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992
67
-2. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
68
-3. Jallades L, Baseggio L, Sujobert P, Huet S, Chabane K, Callet-Bauchu E, Verney A, Hayette S, Desvignes JP, Salgado D, Levy N, Béroud C, Felman P, Berger F, Magaud JP, Genestier L, Salles G, Traverse-Glehen A. Exome sequencing identifies recurrent BCOR alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma. Haematologica. 2017 Oct;102(10):1758–1766. PMCID: PMC5622860
HIST1H1E.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H1E
2 7
3 8
## Overview
... ...
@@ -20,10 +25,10 @@ timeline
20 25
21 26
|Entity|Tier|Description |
22 27
|:------:|:----:|--------------------------------------|
23
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
24
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
25
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
26
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
28
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
29
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a]|
30
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
31
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@grandeGenomewideDiscoverySomatic2019]|
27 32
28 33
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
29 34
... ...
@@ -82,13 +87,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
82 87
![](images/gene_expression/HIST1H1E_by_pathology.svg)
83 88
84 89
## References
85
-1. *Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
86
-2. *Li H, Kaminski MS, Li Y, Yildiz M, Ouillette P, Jones S, Fox H, Jacobi K, Saiya-Cork K, Bixby D, Lebovic D, Roulston D, Shedden K, Sabel M, Marentette L, Cimmino V, Chang AE, Malek SN. Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. Blood. 2014 Mar 6;123(10):1487-98. doi: 10.1182/blood-2013-05-500264. Epub 2014 Jan 16. PMID: 24435047; PMCID: PMC4729540.*
87
-3. *Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992*
88
-4. *Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390*
89
-
90
-5. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
91
-
92 90
93 91
<!-- ORIGIN: 23699601 -->
94 92
<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
HIST1H2AC.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2AC
2 7
This gene encodes the H2A protein, one of the core proteins comprising nucleosomes. Although relatively common in DLBCL, little is known about the function of these mutations.
3 8
... ...
@@ -14,8 +19,8 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|--------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
18
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@morinMutationalStructuralAnalysis2013]|
23
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
19 24
20 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
21 26
... ...
@@ -75,5 +80,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
75 80
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
76 81
77 82
## References
78
-1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992
79
-2. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
HIST1H2AG.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2AG
2 7
3 8
## History
... ...
@@ -16,7 +21,7 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|-----------------------------------------|
19
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
24
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
20 25
|![BL](images/icons/BL_tier2.png) |2-F | Failed QC|
21 26
|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
22 27
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
HIST1H2AM.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2AM
2 7
3 8
<<Warn("The variants reported in this gene in BL failed QC")>>
... ...
@@ -21,7 +26,7 @@ timeline
21 26
|Entity|Tier|Description |
22 27
|:------:|:----:|--------------------------------------|
23 28
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
24
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
29
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
25 30
|![BL](images/icons/BL_tier2.png) |2-F |Failed QC|
26 31
27 32
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -103,5 +108,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
103 108
104 109
105 110
## References
106
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
107
-2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
HIST1H2BC.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2BC
2 7
3 8
## Overview
... ...
@@ -17,9 +22,9 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------|
20
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
22
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
25
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019b]|
26
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
27
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@krysiakRecurrentSomaticMutations2017b]|
23 28
24 29
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 30
... ...
@@ -82,7 +87,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
82 87
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
83 88
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
84 89
85
-## References
86
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
87
-2. Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.
88
-3. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115
90
+## References
... ...
\ No newline at end of file
HIST1H2BD.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2BD
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
20
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@krysiakRecurrentSomaticMutations2017b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -42,4 +47,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
42 47
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
43 48
44 49
## References
45
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
HIST1H2BG.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2BG
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
20
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@krysiakRecurrentSomaticMutations2017b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -42,4 +47,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
42 47
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
43 48
44 49
## References
45
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
HIST1H2BK.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2BK
2 7
3 8
## Overview
... ...
@@ -17,7 +22,7 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
25
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
21 26
|![BL](images/icons/BL_tier2.png) |2-F |Failed QC|
22 27
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
23 28
... ...
@@ -70,5 +75,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
70 75
71 76
72 77
## References
73
-1. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941
74
-2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
HIST1H2BM.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H2BM
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
20
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@krysiakRecurrentSomaticMutations2017b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -45,4 +50,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
45 50
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
46 51
47 52
## References
48
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
HIST1H3B.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H3B
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------|
16
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
17
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
21
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015a]|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
18 23
|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
19 24
20 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -62,5 +67,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
62 67
63 68
64 69
## References
65
-1. *Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan;*
66
-2. *Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972*
HIST1H3D.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H3D
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@paneaWholeGenomeLandscape2019]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -66,4 +71,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
66 71
67 72
68 73
## References
69
-1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
HIST1H3G.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H3G
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
20
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@krysiakRecurrentSomaticMutations2017b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -44,4 +49,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
44 49
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
45 50
46 51
## References
47
-1. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
HIST1H3H.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H3H
2 7
3 8
<<Warn("The variants reported in this gene failed QC")>>
... ...
@@ -59,4 +64,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
59 64
60 65
61 66
## References
62
-1. *Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;*
HIST1H3J.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H3J
2 7
3 8
<<Warn("The variants reported in this gene failed QC")>>
... ...
@@ -68,4 +73,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
68 73
69 74
70 75
## References
71
-1. *Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;*
HIST1H4J.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST1H4J
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------------------|
16
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
17
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
21
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019b]|
22
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@paneaWholeGenomeLandscape2019]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -52,8 +57,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
52 57
&starf; &starf; &starf; &star; &star;
53 58
54 59
## References
55
-1. Mottok A, Hung SS, Chavez EA, Woolcock B, Telenius A, Chong LC, Meissner B, Nakamura H, Rushton C, Viganò E, Sarkozy C, Gascoyne RD, Connors JM, Ben-Neriah S, Mungall A, Marra MA, Siebert R, Scott DW, Savage KJ, Steidl C. Integrative genomic analysis identifies key pathogenic mechanisms in primary mediastinal large B-cell lymphoma. Blood. 2019 Sep 5;134(10):802–813. PMID: 31292115
56
-2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
60
+
57 61
<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
58 62
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
59 63
<!-- BL: paneaWholeGenomeLandscape2019 -->
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+
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+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
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+</head>
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+ mermaid.initialize({
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+ ? 'dark'
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+ : 'default'
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+ });
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+ </script>
368
+<h1 id="hist1h4j">HIST1H4J</h1>
369
+<h2 id="history">History</h2>
370
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
+timeline
372
+ title Publication timing
373
+ 2019-09-05 : Mottok : PMBL
374
+ 2019-09-26 : Panea : BL
375
+</div></code></pre>
376
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
377
+<table>
378
+<thead>
379
+<tr>
380
+<th style="text-align:center">Entity</th>
381
+<th style="text-align:center">Tier</th>
382
+<th>Description</th>
383
+</tr>
384
+</thead>
385
+<tbody>
386
+<tr>
387
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/PMBL_tier2.png" alt="PMBL"></td>
388
+<td style="text-align:center">2</td>
389
+<td>relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019b]</td>
390
+</tr>
391
+<tr>
392
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
393
+<td style="text-align:center">2</td>
394
+<td>relevance in BL not firmly established[@paneaWholeGenomeLandscape2019]</td>
395
+</tr>
396
+</tbody>
397
+</table>
398
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
399
+<table>
400
+<thead>
401
+<tr>
402
+<th style="text-align:center">Entity</th>
403
+<th style="text-align:center">source</th>
404
+<th style="text-align:center">frequency (%)</th>
405
+</tr>
406
+</thead>
407
+<tbody>
408
+<tr>
409
+<td style="text-align:center">BL</td>
410
+<td style="text-align:center">GAMBL genomes+capture</td>
411
+<td style="text-align:center">0.46</td>
412
+</tr>
413
+<tr>
414
+<td style="text-align:center">BL</td>
415
+<td style="text-align:center">Thomas cohort</td>
416
+<td style="text-align:center">0.40</td>
417
+</tr>
418
+<tr>
419
+<td style="text-align:center">BL</td>
420
+<td style="text-align:center">Panea cohort</td>
421
+<td style="text-align:center">NA</td>
422
+</tr>
423
+</tbody>
424
+</table>
425
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
426
+<table>
427
+<thead>
428
+<tr>
429
+<th style="text-align:center">Entity</th>
430
+<th style="text-align:center">aSHM</th>
431
+<th style="text-align:center">Significant selection</th>
432
+<th style="text-align:center">dN/dS (missense)</th>
433
+<th style="text-align:center">dN/dS (nonsense)</th>
434
+</tr>
435
+</thead>
436
+<tbody>
437
+<tr>
438
+<td style="text-align:center">BL</td>
439
+<td style="text-align:center">No</td>
440
+<td style="text-align:center">No</td>
441
+<td style="text-align:center">0.955</td>
442
+<td style="text-align:center">0</td>
443
+</tr>
444
+<tr>
445
+<td style="text-align:center">DLBCL</td>
446
+<td style="text-align:center">No</td>
447
+<td style="text-align:center">No</td>
448
+<td style="text-align:center">1.504</td>
449
+<td style="text-align:center">0</td>
450
+</tr>
451
+<tr>
452
+<td style="text-align:center">FL</td>
453
+<td style="text-align:center">No</td>
454
+<td style="text-align:center">No</td>
455
+<td style="text-align:center">0.000</td>
456
+<td style="text-align:center">0</td>
457
+</tr>
458
+</tbody>
459
+</table>
460
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J_protein_hg38.html">hg38</a></p>
461
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/HIST1H4J_NM_021968.svg" alt=""></p>
462
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/HIST1H4J_hg38.html">hg38</a></p>
463
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/HIST1H4J.svg" alt=""></p>
464
+<h2 id="representative-mutations">Representative Mutations</h2>
465
+<h3 id="blsup2sup">BL<sup>2</sup></h3>
466
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Panea_HIST1H4J.svg" alt="">
467
+<strong>Rating</strong>
468
+★ ★ ★ ☆ ☆</p>
469
+<h2 id="references">References</h2>
470
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
471
+<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
472
+<!-- BL: paneaWholeGenomeLandscape2019 -->
473
+<!-- BL: paneaWholeGenomeLandscape2019 -->
474
+
475
+</body>
476
+</html>
HIST2H2BE.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# HIST2H2BE
2 7
3 8
## Overview
... ...
@@ -15,7 +20,7 @@ timeline
15 20
16 21
|Entity|Tier|Description |
17 22
|:------:|:----:|--------------------------|
18
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
23
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@schmitzGeneticsPathogenesisDiffuse2018a]|
19 24
20 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
21 26
... ...
@@ -48,4 +53,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/H
48 53
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
49 54
50 55
## References
51
-1. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183
IGLL5.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# IGLL5
2 7
3 8
## History
... ...
@@ -14,10 +19,10 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
18
-|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
22
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]|
23
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@paneaWholeGenomeLandscape2019]|
19 24
|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
20
-|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
25
+|![FL](images/icons/FL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous [@russler-germainMutationsAssociatedProgression2023b]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
... ...
@@ -60,9 +65,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
60 65
![](images/gene_expression/IGLL5_by_pathology.svg)
61 66
62 67
## References
63
-1. Desch AK, Hartung K, Botzen A, Brobeil A, Rummel M, Kurch L, Georgi T, Jox T, Bielack S, Burdach S, Classen CF, Claviez A, Debatin KM, Ebinger M, Eggert A, Faber J, Flotho C, Frühwald M, Graf N, Jorch N, Kontny U, Kramm C, Kulozik A, Kühr J, Sykora KW, Metzler M, Müller HL, Nathrath M, Nüßlein T, Paulussen M, Pekrun A, Reinhardt D, Reinhard H, Rössig C, Sauerbrey A, Schlegel PG, Schneider DT, Scheurlen W, Schweigerer L, Simon T, Suttorp M, Vorwerk P, Schmitz R, Kluge R, Mauz-Körholz C, Körholz D, Gattenlöhner S, Bräuninger A. Genotyping circulating tumor DNA of pediatric Hodgkin lymphoma. Leukemia. 2020 Jan;34(1):151–166. PMID: 31431735
64
-2. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
65
-3. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.
66 68
<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
67 69
<!-- ORIGIN: deschGenotypingCirculatingTumor2020 -->
68 70
<!-- BL: paneaWholeGenomeLandscape2019 -->
PLCG2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PLCG2
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@paneaWholeGenomeLandscape2019]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -53,4 +58,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
53 58
<!-- BL: paneaWholeGenomeLandscape2019 -->
54 59
55 60
## References
56
-1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;