ARID1A.md
... ...
@@ -66,3 +66,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
66 66
3. 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;
67 67
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
68 68
5. Wienand K, Chapuy B, Stewart C, Dunford AJ, Wu D, Kim J, Kamburov A, Wood TR, Cader FZ, Ducar MD, Thorner AR, Nag A, Heubeck AT, Buonopane MJ, Redd RA, Bojarczuk K, Lawton LN, Armand P, Rodig SJ, Fromm JR, Getz G, Shipp MA. Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion. Blood Adv. 2019 Dec 10;3(23):4065–4080. PMCID: PMC6963251
69
+<!-- PMBL: wienandGenomicAnalysesFlowsorted2019b -->
BCL2.md
... ...
@@ -91,3 +91,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
91 91
2. 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 SJM, 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. PMCID: PMC3210554
92 92
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
93 93
4. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
94
+<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
BCL7A.md
... ...
@@ -67,7 +67,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
67 67
![image](images/gene_expression/BCL7A_by_pathology.svg)
68 68
69 69
70
-<!-- ORIGIN: 30275490 -->
70
+<!-- ORIGIN: reichelFlowSortingExome2015a -->
71 71
<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
72 72
<!-- FL: krysiakRecurrentSomaticMutations2017b -->
73 73
<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
... ...
@@ -83,3 +83,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
83 83
84 84
85 85
86
+<!-- PMBL: reichelFlowSortingExome2015a -->
BL_FL_DLBCL_sankey_methods.md
... ...
@@ -0,0 +1,141 @@
1
+
2
+
3
+```mermaid
4
+
5
+
6
+---
7
+config:
8
+ sankey:
9
+ showValues: false
10
+ linkColor: target
11
+ width: 800
12
+ height: 1000
13
+ nodeAlignment: right
14
+---
15
+sankey-beta
16
+
17
+Sanger, 2001, 4
18
+2001, Pasqualucci 2001, 4
19
+Pasqualucci 2001, DLBCL Tier 1, 3
20
+Pasqualucci 2001, DLBCL Tier 2, 1
21
+
22
+RNA-seq/WGS, 2011, 49
23
+2011, Morin 2011, 25
24
+Morin 2011, DLBCL Tier 1, 25
25
+2011, Morin 2011, 15
26
+Morin 2011, FL Tier 1, 14
27
+Morin 2011, FL Tier 2, 1
28
+2011, Pasqualucci 2011a, 7
29
+Pasqualucci 2011a, DLBCL Tier 1, 5
30
+Pasqualucci 2011a, DLBCL Tier 2, 2
31
+2011, Pasqualucci 2011b, 2
32
+Pasqualucci 2011b, FL Tier 1, 2
33
+Pasqualucci 2011b, DLBCL Tier 1, 2
34
+
35
+exome, 2012 exome studies, 68
36
+2012 exome studies, Richter 2012, 5
37
+2012 exome studies, Lohr 2012, 4
38
+2012 exome studies, Love 2012, 59
39
+
40
+Richter 2012, BL Tier 1, 5
41
+Lohr 2012, DLBCL Tier 1, 3
42
+Lohr 2012, DLBCL Tier 2, 1
43
+Love 2012, BL Tier 1, 3
44
+Love 2012, BL Tier 2, 56
45
+
46
+RNA-seq, 2012 RNA-seq studies, 19
47
+2012 RNA-seq studies, Schmitz 2012, 19
48
+Schmitz 2012, BL Tier 1, 3
49
+Schmitz 2012, BL Tier 2, 16
50
+
51
+WGS, 2013 WGS studies, 40
52
+2013 WGS studies, Morin 2013, 40
53
+Morin 2013, DLBCL Tier 1, 11
54
+Morin 2013, DLBCL Tier 2, 29
55
+
56
+
57
+exome, 2013 exome studies, 19
58
+2013 exome studies, Zhang 2013, 19
59
+Zhang 2013, DLBCL Tier 1, 11
60
+Zhang 2013, DLBCL Tier 2, 8
61
+
62
+exome, 2014 exome studies, 3
63
+2014 exome studies, Muppidi 2014, 3
64
+Muppidi 2014, BL Tier 1, 1
65
+Muppidi 2014, BL Tier 2, 2
66
+
67
+exome, 2016 exome studies, 2
68
+2016 exome studies, Mareschal 2016, 2
69
+Mareschal 2016, DLBCL Tier 1, 2
70
+
71
+WGS, 2016 WGS studies, 2
72
+2016 WGS studies, Okosun 2016, 2
73
+Okosun 2016, FL Tier 1, 2
74
+
75
+exome, 2016 exome studies, 2
76
+2016 exome studies, Morin 2016, 2
77
+Morin 2016, DLBCL Tier 1, 2
78
+
79
+exome, 2017 exome studies, 85
80
+2017 exome studies, Krysiak 2017, 22
81
+Krysiak 2017, FL Tier 1, 17
82
+Krysiak 2017, FL Tier 2, 5
83
+
84
+
85
+2017 exome studies, Albuquerque 2017, 3
86
+Albuquerque 2017, DLBCL Tier 1, 3
87
+
88
+2017 exome studies, Reddy 2017, 60
89
+Reddy 2017, DLBCL Tier 2, 50
90
+Reddy 2017, DLBCL Tier 1, 10
91
+
92
+exome, 2018 exome studies, 35
93
+2018 exome studies, Schmitz 2018, 16
94
+Schmitz 2018, DLBCL Tier 2, 7
95
+Schmitz 2018, DLBCL Tier 1, 9
96
+
97
+2018 exome studies, Chapuy 2018, 19
98
+Chapuy 2018, DLBCL Tier 2, 16
99
+Chapuy 2018, DLBCL Tier 1, 3
100
+
101
+WGS, 2018 WGS studies, 20
102
+2018 WGS studies, Arthur 2018, 20
103
+Arthur 2018, DLBCL Tier 2, 12
104
+Arthur 2018, DLBCL Tier 1, 8
105
+
106
+RNA-seq/exome,2019 RNA-seq/exome studies,47
107
+2019 RNA-seq/exome studies, Panea 2019, 47
108
+Panea 2019, BL Tier 2, 43
109
+Panea 2019, BL Tier 1, 4
110
+
111
+WGS,2019 WGS studies,13
112
+2019 WGS studies, Grande 2019, 13
113
+Grande 2019, BL Tier 1, 8
114
+Grande 2019, BL Tier 2, 5
115
+
116
+exome, 2020 exome studies, 2
117
+2020 exome studies, Pararajalingam 2020, 2
118
+Pararajalingam 2020, DLBCL Tier 1, 2
119
+
120
+WGS, 2021 WGS studies, 40
121
+2021 WGS studies, Hubschmann 2021, 17
122
+2021 WGS studies, Hubschmann 2021, 23
123
+Hubschmann 2021, FL Tier 2, 15
124
+Hubschmann 2021, FL Tier 1, 2
125
+Hubschmann 2021, DLBCL Tier 1, 4
126
+Hubschmann 2021, DLBCL Tier 2, 19
127
+
128
+exome, 2023 exome studies, 20
129
+2023 exome studies, Russler-Germain 2023, 20
130
+Russler-Germain 2023, FL Tier 1, 1
131
+Russler-Germain 2023, FL Tier 2, 19
132
+
133
+Panel, panel studies, 25
134
+panel studies, Burkhardt 2022, 25
135
+Burkhardt 2022, BL Tier 2, 25
136
+
137
+WGS, 2023 WGS studies, 3
138
+2023 WGS studies, Thomas 2023, 3
139
+Thomas 2023, BL Tier 2, 1
140
+Thomas 2023, BL Tier 1, 2
141
+```
... ...
\ No newline at end of file
BL_sankey.md
... ...
@@ -14,42 +14,38 @@ config:
14 14
---
15 15
sankey-beta
16 16
17
-exome, 2012-exome, 64
18
-2012-exome, richter 2012, 5
19
-2012-exome, love 2012, 59
17
+exome, 2012 exome studies, 64
18
+2012 exome studies, Richter 2012, 5
19
+2012 exome studies, Love 2012, 59
20 20
21
-richter 2012, BL Tier 1, 5
21
+Richter 2012, Tier 1 BL genes, 5
22 22
23
-love 2012, BL Tier 1, 3
24
-love 2012, BL Tier 2, 56
23
+Love 2012, Tier 1 BL genes, 3
24
+Love 2012, Tier 2 BL genes, 56
25 25
26
-RNA-seq, 2012-RNA-seq, 19
27
-2012-RNA-seq, schmitz 2012, 19
28
-schmitz 2012, BL Tier 1, 3
29
-schmitz 2012, BL Tier 2, 16
26
+RNA-seq, 2012 RNA-seq studies, 19
27
+2012 RNA-seq studies, Schmitz 2012, 19
28
+Schmitz 2012, BL Tier 1, 3
29
+Schmitz 2012, BL Tier 2, 16
30 30
31 31
32
+RNA-seq/exome, RNA-seq/exome studies,47
33
+RNA-seq/exome studies, Panea 2019, 47
34
+Panea 2019, Tier 2 BL genes, 43
35
+Panea 2019, Tier 1 BL genes, 4
32 36
37
+WGS,2019 WGS studies,13
38
+2019 WGS studies, Grande 2019, 13
39
+Grande 2019, Tier 1 BL genes, 8
40
+Grande 2019, Tier 2 BL genes, 5
33 41
34 42
43
+Panel, 2022 panel studies, 25
44
+2022 panel studies, Burkhardt 2022, 25
45
+Burkhardt 2022, Tier 2 BL genes, 25
35 46
36
-RNA-seq/exome,2019-RNA-seq/exome,47
37
-2019-RNA-seq/exome, panea 2019, 47
38
-panea 2019, BL Tier 2, 43
39
-panea 2019, BL Tier 1, 4
40
-
41
-WGS,2019-WGS,13
42
-2019-WGS, grande 2019, 13
43
-grande 2019, BL Tier 1, 8
44
-grande 2019, BL Tier 2, 5
45
-
46
-
47
-Panel, 2022-panel, 25
48
-2022-panel, burkhardt 2022, 25
49
-burkhardt 2022, BL Tier 2, 25
50
-
51
-WGS, 2023-WGS, 3
52
-2023-WGS, thomas 2023, 3
53
-thomas 2023, BL Tier 2, 1
54
-thomas 2023, BL Tier 1, 2
47
+WGS, 2023 WGS studies, 3
48
+2023 WGS studies, Thomas 2023, 3
49
+Thomas 2023, Tier 2 BL genes, 1
50
+Thomas 2023, Tier 1 BL genes, 2
55 51
```
... ...
\ No newline at end of file
BTG1.md
... ...
@@ -105,3 +105,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
105 105
5. 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
106 106
6. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
107 107
108
+<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
CARD11.md
... ...
@@ -88,3 +88,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
88 88
3. Yan Q, Huang Y, Watkins AJ, Kocialkowski S, Zeng N, Hamoudi RA, Isaacson PG, de Leval L, Wotherspoon A, Du MQ. BCR and TLR signaling pathways are recurrently targeted by genetic changes in splenic marginal zone lymphomas. Haematologica. 2012 Apr;97(4):595–598. PMCID: PMC3347666
89 89
4. Wu C, de Miranda NF, Chen L, Wasik AM, Mansouri L, Jurczak W, Galazka K, Dlugosz-Danecka M, Machaczka M, Zhang H, Peng R, Morin RD, Rosenquist R, Sander B, Pan-Hammarström Q. Genetic heterogeneity in primary and relapsed mantle cell lymphomas: Impact of recurrent CARD11 mutations. Oncotarget. 2016 Jun 21;7(25):38180–38190. PMCID: PMC5122381
90 90
5. 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;
91
+<!-- BL: paneaWholeGenomeLandscape2019 -->
CCND3.md
... ...
@@ -108,3 +108,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
108 108
<!-- BL: richterRecurrentMutationID32012a -->
109 109
<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
110 110
<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
111
+<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
CD58.md
... ...
@@ -53,4 +53,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
53 53
54 54
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.*
55 55
2. *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.*
56
-<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
56
+<!-- ORIGIN: schneiderAlterationsCD58Gene2015a -->
57
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
58
+<!-- PMBL: schneiderAlterationsCD58Gene2015a -->
CD79B.md
... ...
@@ -80,3 +80,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
80 80
4. *Kim Y, Ju H, Kim DH, Yoo HY, Kim SJ, Kim WS, Ko YH. CD79B and MYD88 mutations in diffuse large B-cell lymphoma. Hum Pathol. 2014 Mar;45(3):556-64. doi: 10.1016/j.humpath.2013.10.023. Epub 2013 Oct 31. PMID: 24444466.*
81 81
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
82 82
<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
83
+<!-- BL: paneaWholeGenomeLandscape2019 -->
CD83.md
... ...
@@ -77,3 +77,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
77 77
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
78 78
<!-- BL: paneaWholeGenomeLandscape2019 -->
79 79
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
80
+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
CREBBP.md
... ...
@@ -96,3 +96,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
96 96
1. *Pasqualucci, L., Dominguez-Sola, D., Chiarenza, A., Fabbri, G., Grunn, A., Trifonov, V., Kasper, L., Lerach, S., Tang, H., Ma, J., Rossi, D., Chadburn, A., Murty, V., Mullighan, C., Gaidano, G., Rabadán, R., Brindle, P., & Dalla-Favera, R. (2010). Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature, 471, 189 - 195. https://doi.org/10.1038/nature09730.*
97 97
2. *Dreval K, Hilton LK, Cruz M, Shaalan H, Ben-Neriah S, Boyle M, Collinge B, Coyle KM, Duns G, Farinha P, Grande BM, Meissner B, Pararajalingam P, Rushton CK, Slack GW, Wong J, Mungall AJ, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns. Blood. 2023 Aug 10;142(6):561-573. doi: 10.1182/blood.2022018719. PMID: 37084389; PMCID: PMC10644066.*
98 98
99
+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
DDX3X.md
... ...
@@ -69,3 +69,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
69 69
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
70 70
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
71 71
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
72
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
DLBCL_sankey1.md
... ...
@@ -14,75 +14,72 @@ config:
14 14
---
15 15
sankey-beta
16 16
17
-RNA-seq/exome, 2011, 25
17
+RNA-seq/WGS, 2011, 25
18 18
2011, morin 2011, 25
19
-morin 2011,DLBCL Tier 1, 25
19
+morin 2011, Tier 1 DLBCL genes, 25
20 20
21
-exome, 2011, 7
21
+exome, 2011, 9
22 22
2011, pasqualucci 2011a, 7
23
-pasqualucci 2011a, DLBCL Tier 1, 5
24
-pasqualucci 2011a, DLBCL Tier 2, 2
23
+pasqualucci 2011a, Tier 1 DLBCL genes, 5
24
+pasqualucci 2011a, Tier 2 DLBCL genes, 2
25 25
2011, pasqualucci 2011b, 2
26
-pasqualucci 2011b, DLBCL Tier 1, 2
26
+pasqualucci 2011b, Tier 1 DLBCL genes, 2
27 27
28
-exome, 2012-exome, 4
29
-2012-exome, lohr 2012, 4
28
+exome, 2012 exome studies, 4
29
+2012 exome studies, lohr 2012, 4
30
+lohr 2012, Tier 2 DLBCL genes, 1
31
+lohr 2012, Tier 1 DLBCL genes, 3
30 32
31 33
34
+WGS, 2013 WGS studies, 40
35
+2013 WGS studies, morin 2013, 40
36
+morin 2013, Tier 2 DLBCL genes, 29
37
+morin 2013, Tier 1 DLBCL genes, 11
32 38
33
-lohr 2012, DLBCL Tier 2, 1
34
-lohr 2012, DLBCL Tier 1, 3
39
+exome, 2013 exome studies, 19
40
+2013 exome studies, zhang 2013, 19
41
+zhang 2013, Tier 1 DLBCL genes, 11
42
+zhang 2013, Tier 2 DLBCL genes, 8
35 43
36 44
37
-WGS, 2013-WGS, 40
38
-2013-WGS, morin 2013, 40
39
-morin 2013, DLBCL Tier 2, 29
40
-morin 2013, DLBCL Tier 1, 11
45
+exome, 2016 exome studies, 2
46
+2016 exome studies, mareschal 2016, 2
47
+mareschal 2016, Tier 1 DLBCL genes, 2
41 48
42
-exome, 2013-exome, 19
43
-2013-exome, zhang 2013, 19
44
-zhang 2013, DLBCL Tier 1, 11
45
-zhang 2013, DLBCL Tier 2, 8
49
+exome, 2016 exome studies, 2
50
+2016 exome studies, morin 2016, 2
51
+morin 2016, Tier 1 DLBCL genes, 2
46 52
53
+2017 exome studies, albuquerque 2017, 3
54
+albuquerque 2017, Tier 1 DLBCL genes, 3
47 55
48
-exome, 2016-exome, 2
49
-2016-exome, mareschal 2016, 2
50
-mareschal 2016, DLBCL Tier 1, 2
56
+exome, 2017 exome studies, 63
57
+2017 exome studies, reddy 2017, 60
58
+reddy 2017, Tier 2 DLBCL genes, 50
59
+reddy 2017, Tier 1 DLBCL genes, 10
51 60
52
-exome, 2016-exome, 2
53
-2016-exome, morin 2016, 2
54
-morin 2016, DLBCL Tier 1, 2
61
+exome, 2018 exome studies, 35
62
+2018 exome studies, schmitz 2018, 16
63
+schmitz 2018, Tier 2 DLBCL genes, 7
64
+schmitz 2018, Tier 1 DLBCL genes, 9
55 65
56
-2017-exome, albuquerque 2017, 3
57
-albuquerque 2017, DLBCL Tier 1, 3
66
+2018 exome studies, chapuy 2018, 19
67
+chapuy 2018, Tier 2 DLBCL genes, 16
68
+chapuy 2018, Tier 1 DLBCL genes, 3
58 69
59
-exome, 2017-exome, 63
60
-2017-exome, reddy 2017, 60
61
-reddy 2017, DLBCL Tier 2, 50
62
-reddy 2017, DLBCL Tier 1, 10
63
-
64
-exome, 2018-exome, 35
65
-2018-exome, schmitz 2018, 16
66
-schmitz 2018, DLBCL Tier 2, 7
67
-schmitz 2018, DLBCL Tier 1, 9
68
-
69
-2018-exome, chapuy 2018, 19
70
-chapuy 2018, DLBCL Tier 2, 16
71
-chapuy 2018, DLBCL Tier 1, 3
72
-
73
-WGS, 2018-WGS, 20
74
-2018-WGS, arthur 2018, 20
75
-arthur 2018, DLBCL Tier 2, 12
76
-arthur 2018, DLBCL Tier 1, 8
70
+WGS, 2018 WGS studies, 20
71
+2018 WGS studies, arthur 2018, 20
72
+arthur 2018, Tier 2 DLBCL genes, 12
73
+arthur 2018, Tier 1 DLBCL genes, 8
77 74
78 75
exome, 2020-exome, 2
79 76
2020-exome, pararajalingam 2020, 2
80
-pararajalingam 2020, DLBCL Tier 1, 2
77
+pararajalingam 2020, Tier 1 DLBCL genes, 2
81 78
82 79
WGS, 2021-WGS, 23
83 80
2021-WGS, hubschmann 2021, 23
84
-hubschmann 2021, DLBCL Tier 1, 4
85
-hubschmann 2021, DLBCL Tier 2, 19
81
+hubschmann 2021, Tier 1 DLBCL genes, 4
82
+hubschmann 2021, Tier 2 DLBCL genes, 19
86 83
87 84
88
-```
... ...
\ No newline at end of file
0
+```
DTX1.md
... ...
@@ -119,3 +119,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
119 119
<!-- BL: paneaWholeGenomeLandscape2019 -->
120 120
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
121 121
<!-- MZL: rossiCodingGenomeSplenic2012c -->
122
+<!-- PMBL: gomezUltraDeepSequencingReveals2023 -->
EZH2.md
... ...
@@ -89,3 +89,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
89 89
<!-- FL: morinSomaticMutationsAltering2010 -->
90 90
<!-- BL: loveGeneticLandscapeMutations2012 -->
91 91
<!-- DLBCL: morinSomaticMutationsAltering2010 -->
92
+<!-- PMBL: mottokIntegrativeGenomicAnalysis2019b -->
NRXN2.md
... ...
@@ -1,5 +1,11 @@
1 1
# NRXN2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/NRXN2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/NRXN2_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N
38 42
![image](images/gene_expression/NRXN2_by_pathology.svg)
39 43
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 44
<!-- BL: loveGeneticLandscapeMutations2012 -->
45
+## References
46
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
OGDHL.md
... ...
@@ -1,5 +1,11 @@
1 1
# OGDHL
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |0.000 |0 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
26
-
27 30
28 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OGDHL_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OGDHL_protein_hg38.html)
29 32
... ...
@@ -36,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
36 39
![image](images/gene_expression/OGDHL_by_pathology.svg)
37 40
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 41
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
42
+## References
43
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
OR8H2.md
... ...
@@ -1,5 +1,11 @@
1 1
# OR8H2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2023-07-26 : Russler-Germain : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |7.647 |0 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
26
-
27 30
28 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/OR8H2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/OR8H2_protein_hg38.html)
29 32
... ...
@@ -36,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
36 39
![image](images/gene_expression/OR8H2_by_pathology.svg)
37 40
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38 41
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
42
+## References
43
+1. 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.
OSBPL10.md
... ...
@@ -1,7 +1,13 @@
1 1
# OSBPL10
2 2
## Overview
3 3
OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
4
-
4
+## History
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2018-10-01 : Arthur : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
... ...
@@ -44,3 +50,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/O
44 50
![image](images/gene_expression/OSBPL10_by_pathology.svg)
45 51
<!-- ORIGIN: arthurGenomewideDiscoverySomatic2018 -->
46 52
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
53
+## References
54
+1. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379
PCDHA11.md
... ...
@@ -1,5 +1,11 @@
1 1
# PCDHA11
2 2
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 44
![image](images/gene_expression/PCDHA11_by_pathology.svg)
39 45
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40 46
<!-- BL: paneaWholeGenomeLandscape2019 -->
47
+## References
48
+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;
PCDHB11.md
... ...
@@ -1,5 +1,11 @@
1 1
# PCDHB11
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,10 +30,6 @@
24 30
|FL |No |No |1.816 | 0.000 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29
-
30
-
31 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHB11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHB11_protein_hg38.html)
32 34
33 35
![image](images/proteinpaint/PCDHB11_NM_018931.svg)
... ...
@@ -39,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 41
![image](images/gene_expression/PCDHB11_by_pathology.svg)
40 42
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 43
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
44
+## References
45
+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
PCDHB2.md
... ...
@@ -1,5 +1,11 @@
1 1
# PCDHB2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |0.000 |0 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
26
-
27 30
28 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PCDHB2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PCDHB2_protein_hg38.html)
29 32
... ...
@@ -36,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
36 39
![image](images/gene_expression/PCDHB2_by_pathology.svg)
37 40
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 41
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
42
+## References
43
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
PDCD11.md
... ...
@@ -1,5 +1,11 @@
1 1
# PDCD11
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-10-04 : Schmitz : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDCD11_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDCD11_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 41
![image](images/gene_expression/PDCD11_by_pathology.svg)
39 42
<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
40 43
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
44
+## References
45
+1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867
PDE4DIP.md
... ...
@@ -1,5 +1,11 @@
1 1
# PDE4DIP
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2018-05-01 : Chapuy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,10 +30,6 @@
24 30
|FL |No |No |2.010 |7.866 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
29
-
30
-
31 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PDE4DIP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PDE4DIP_protein_hg38.html)
32 34
33 35
![image](images/proteinpaint/PDE4DIP_NM_014644.svg)
... ...
@@ -39,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 41
![image](images/gene_expression/PDE4DIP_by_pathology.svg)
40 42
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 43
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
44
+## References
45
+1. 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
PDS5B.md
... ...
@@ -2,6 +2,13 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL in 2013 by Morin et al<sup>1</sup> and in FL in 2021 by Hübschmann et al.<sup>2</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2013-08-15 : Morin : DLBCL
10
+ 2021-05-05 : H : FL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
... ...
@@ -44,3 +51,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
44 51
45 52
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
46 53
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
54
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
PDZRN3.md
... ...
@@ -1,5 +1,11 @@
1 1
# PDZRN3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -38,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 44
![image](images/gene_expression/PDZRN3_by_pathology.svg)
39 45
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40 46
<!-- BL: paneaWholeGenomeLandscape2019 -->
47
+## References
48
+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;
PIM1.md
... ...
@@ -92,3 +92,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
92 92
1. Pasqualucci L, Neumeister P, Goossens T, Nanjangud G, Chaganti RS, Küppers R, Dalla-Favera R. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature. 2001 Jul 19;412(6844):341–346. PMID: 11460166
93 93
2. Duns G, Viganò E, Ennishi D, Sarkozy C, Hung SS, Chavez E, Takata K, Rushton C, Jiang A, Ben-Neriah S, Woolcock BW, Slack GW, Hsi ED, Craig JW, Hilton LK, Shah SP, Farinha P, Mottok A, Gascoyne RD, Morin RD, Savage KJ, Scott DW, Steidl C. Characterization of DLBCL with a PMBL gene expression signature. Blood. 2021 Jul 15;138(2):136–148. PMID: 33684939
94 94
3. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
95
+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
PKD1.md
... ...
@@ -1,5 +1,12 @@
1 1
# PKD1
2 2
3
+## History
4
+```mermaid
5
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6
+timeline
7
+ title Publication timing
8
+ 2013-08-15 : Morin : DLBCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -24,9 +31,6 @@
24 31
|FL |No |No |1.705 |0.000 |
25 32
26 33
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29
-
30 34
31 35
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PKD1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PKD1_protein_hg38.html)
32 36
... ...
@@ -39,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 43
![image](images/gene_expression/PKD1_by_pathology.svg)
40 44
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 45
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
46
+## References
47
+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
PLCG2.md
... ...
@@ -1,5 +1,11 @@
1 1
# PLCG2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |1.491 | 0.000 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
28 32
29 33
30 34
## PLCG2 Hotspots
... ...
@@ -44,3 +48,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
44 48
![image](images/gene_expression/PLCG2_by_pathology.svg)
45 49
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
46 50
<!-- BL: paneaWholeGenomeLandscape2019 -->
51
+## References
52
+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;
PLXNB3.md
... ...
@@ -1,9 +1,17 @@
1 1
# PLXNB3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
8
+ 2016-09-08 : Spina : MZL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
6 13
|:------:|:----:|---------------------------------------|
14
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
7 15
|![MCL](images/icons/MCL_tier2.png) |2 |relevance in MCL not firmly established|
8 16
9 17
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -21,9 +29,6 @@
21 29
|FL |No |No |0.000 |0 |
22 30
23 31
24
-> [!NOTE]
25
-> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
26
-
27 32
28 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PLXNB3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PLXNB3_protein_hg38.html)
29 34
... ...
@@ -37,3 +42,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 42
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 43
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
39 44
<!-- MZL: spinaGeneticsNodalMarginal2016b -->
45
+## References
46
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
47
+2. Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373.
PMAIP1.md
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
35 35
![image](images/gene_expression/PMAIP1_by_pathology.svg)
36 36
<!-- ORIGIN: Unknown -->
37 37
<!-- BL: 2 -->
38
+## References
PNPO.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2021-05-05 : Hübschmann : DLBCL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
POGZ.md
... ...
@@ -1,5 +1,11 @@
1 1
# POGZ
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,9 +30,6 @@
24 30
|FL |No |No |0 |0 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29
-
30 33
31 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POGZ_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POGZ_protein_hg38.html)
32 35
... ...
@@ -39,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 42
![image](images/gene_expression/POGZ_by_pathology.svg)
40 43
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 44
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
45
+## References
46
+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
POLRMT.md
... ...
@@ -1,5 +1,11 @@
1 1
# POLRMT
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,10 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
-
29
-
30 32
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POLRMT_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POLRMT_protein_hg38.html)
31 33
32 34
![image](images/proteinpaint/POLRMT_NM_005035.svg)
... ...
@@ -38,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 40
![image](images/gene_expression/POLRMT_by_pathology.svg)
39 41
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 42
<!-- BL: loveGeneticLandscapeMutations2012 -->
43
+## References
44
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
POR.md
... ...
@@ -1,5 +1,11 @@
1 1
# POR
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/POR_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/POR_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 41
![image](images/gene_expression/POR_by_pathology.svg)
39 42
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 43
<!-- BL: loveGeneticLandscapeMutations2012 -->
44
+## References
45
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
PPP1R9B.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
37 37
<!-- FLAGGED FOR TIER 2 -->
38 38
39 39
<!-- ORIGIN: Unknown -->
40
+## References
PPP4C.md
... ...
@@ -1,5 +1,11 @@
1 1
# PPP4C
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2021-05-05 : H : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |43.394 | 0.000 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
26
-
27 30
## PPP4C Hotspots
28 31
29 32
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -41,3 +44,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
41 44
![image](images/gene_expression/PPP4C_by_pathology.svg)
42 45
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
43 46
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
47
+## References
48
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
PPP6R2.md
... ...
@@ -1,5 +1,11 @@
1 1
# PPP6R2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2022-07-06 : Burkhardt : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PPP6R2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PPP6R2_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 42
![image](images/gene_expression/PPP6R2_by_pathology.svg)
39 43
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40 44
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
45
+## References
46
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
PREX1.md
... ...
@@ -1,5 +1,11 @@
1 1
# PREX1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2022-07-06 : Burkhardt : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |1.695 |10.067 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PREX1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PREX1_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 42
![image](images/gene_expression/PREX1_by_pathology.svg)
39 43
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40 44
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
45
+## References
46
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
PRKCB.md
... ...
@@ -1,5 +1,11 @@
1 1
# PRKCB
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,9 +30,6 @@
24 30
|FL |No |No |1.828 |0 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29
-
30 33
31 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRKCB_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRKCB_protein_hg38.html)
32 35
... ...
@@ -39,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 42
![image](images/gene_expression/PRKCB_by_pathology.svg)
40 43
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 44
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
45
+## References
46
+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
PRPS1.md
... ...
@@ -1,5 +1,11 @@
1 1
# PRPS1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2018-05-01 : Chapuy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,8 +30,6 @@
24 30
|FL |No |No |0.000 |0 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
29 33
30 34
31 35
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRPS1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRPS1_protein_hg38.html)
... ...
@@ -39,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 43
![image](images/gene_expression/PRPS1_by_pathology.svg)
40 44
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 45
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
46
+## References
47
+1. 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
PRSS22.md
... ...
@@ -1,5 +1,11 @@
1 1
# PRSS22
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PRSS22_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PRSS22_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 42
![image](images/gene_expression/PRSS22_by_pathology.svg)
39 43
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 44
<!-- BL: loveGeneticLandscapeMutations2012 -->
45
+## References
46
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
PTMA.md
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
40 40
## PTMA Expression
41 41
![image](images/gene_expression/PTMA_by_pathology.svg)
42 42
<!-- ORIGIN: Unknown -->
43
+## References
PTPN23.md
... ...
@@ -1,5 +1,11 @@
1 1
# PTPN23
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -39,3 +45,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 45
![image](images/gene_expression/PTPN23_by_pathology.svg)
40 46
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 47
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
48
+## References
49
+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
PTPN6.md
... ...
@@ -1,5 +1,11 @@
1 1
# PTPN6
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-10-10 : Reddy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,9 +30,6 @@
24 30
|FL |No |No |0.000 | 0.000 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29
-
30 33
31 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPN6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPN6_protein_hg38.html)
32 35
... ...
@@ -39,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 42
![image](images/gene_expression/PTPN6_by_pathology.svg)
40 43
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41 44
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
45
+## References
46
+1. 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.
PTPRK.md
... ...
@@ -1,5 +1,11 @@
1 1
# PTPRK
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-10-10 : Reddy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,8 +30,6 @@
24 30
|FL |No |No |1.875 |5.021 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29 33
30 34
31 35
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRK_protein_hg38.html)
... ...
@@ -39,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
39 43
![image](images/gene_expression/PTPRK_by_pathology.svg)
40 44
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41 45
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
46
+## References
47
+1. 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.
PTPRN.md
... ...
@@ -1,5 +1,11 @@
1 1
# PTPRN
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |0 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PTPRN_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PTPRN_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 41
![image](images/gene_expression/PTPRN_by_pathology.svg)
39 42
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 43
<!-- BL: loveGeneticLandscapeMutations2012 -->
44
+## References
45
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
PXDNL.md
... ...
@@ -1,5 +1,11 @@
1 1
# PXDNL
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |1.165 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PXDNL_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PXDNL_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
38 41
![image](images/gene_expression/PXDNL_by_pathology.svg)
39 42
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
40 43
<!-- BL: paneaWholeGenomeLandscape2019 -->
44
+## References
45
+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;
PZP.md
... ...
@@ -1,5 +1,11 @@
1 1
# PZP
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2023-07-26 : Russler : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |1.723 |0 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
26
-
27 30
28 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/PZP_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/PZP_protein_hg38.html)
29 32
... ...
@@ -36,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
36 39
![image](images/gene_expression/PZP_by_pathology.svg)
37 40
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38 41
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
42
+## References
43
+1. 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.
RAC2.md
... ...
@@ -2,6 +2,13 @@
2 2
## History
3 3
Mutations in this gene were first described in BL in 2019 by Panea et al<sup>1</sup> and in DLBCL 2021 by Hübschmann et al.<sup>2</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2019-09-26 : Panea : BL
10
+ 2021-05-05 : Hübschmann : DLBCL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
RAD9A.md
... ...
@@ -1,5 +1,11 @@
1 1
# RAD9A
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2018-05-01 : Chapuy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,10 +30,6 @@
24 30
|FL |No |No |0 |0 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
29
-
30
-
31 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RAD9A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RAD9A_protein_hg38.html)
32 34
33 35
![image](images/proteinpaint/RAD9A_NM_004584.svg)
... ...
@@ -39,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
39 41
![image](images/gene_expression/RAD9A_by_pathology.svg)
40 42
<!-- ORIGIN: chapuyMolecularSubtypesDiffuse2018b -->
41 43
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
44
+## References
45
+1. 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
RANBP6.md
... ...
@@ -1,5 +1,11 @@
1 1
# RANBP6
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |0.000 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RANBP6_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RANBP6_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 41
![image](images/gene_expression/RANBP6_by_pathology.svg)
39 42
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 43
<!-- BL: loveGeneticLandscapeMutations2012 -->
44
+## References
45
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
RARA.pdf
... ...
Binary files /dev/null and b/RARA.pdf differ
RBM6.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in this gene were first described in DLBCL and FL in 2021 by Hübschmann et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2021-05-05 : Hübschmann : FL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
RBP3.md
... ...
@@ -1,5 +1,11 @@
1 1
# RBP3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |0.00 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RBP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RBP3_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 41
![image](images/gene_expression/RBP3_by_pathology.svg)
39 42
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 43
<!-- BL: loveGeneticLandscapeMutations2012 -->
44
+## References
45
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
REV3L.md
... ...
@@ -1,5 +1,11 @@
1 1
# REV3L
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2022-07-06 : Burkhardt : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |0.731 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/REV3L_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/REV3L_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 42
![image](images/gene_expression/REV3L_by_pathology.svg)
39 43
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40 44
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
45
+## References
46
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
RHEX.md
... ...
@@ -27,3 +27,4 @@
27 27
## RHEX Expression
28 28
![image](images/gene_expression/RHEX_by_pathology.svg)
29 29
<!-- ORIGIN: Unknown -->
30
+## References
RNF144B.md
... ...
@@ -1,5 +1,11 @@
1 1
# RNF144B
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-09-26 : Panea : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -28,8 +34,6 @@
28 34
|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29 35
|chr6 |25861094 |25868788|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A25861094%2D25868788)|NA |
30 36
31
-> [!NOTE]
32
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
33 37
34 38
35 39
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RNF144B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RNF144B_protein_hg38.html)
... ...
@@ -43,3 +47,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
43 47
![image](images/gene_expression/RNF144B_by_pathology.svg)
44 48
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
45 49
<!-- BL: paneaWholeGenomeLandscape2019 -->
50
+## References
51
+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;
RPL10.md
... ...
@@ -1,5 +1,11 @@
1 1
# RPL10
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2022-07-06 : Burkhardt : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |0.00 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/RPL10_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/RPL10_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
38 42
![image](images/gene_expression/RPL10_by_pathology.svg)
39 43
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
40 44
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
45
+## References
46
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
RPL22.md
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
35 35
![image](images/gene_expression/RPL22_by_pathology.svg)
36 36
<!-- ORIGIN: Unknown -->
37 37
<!-- BL: 2 -->
38
+## References
RUBCNL.md
... ...
@@ -22,3 +22,4 @@
22 22
## RUBCNL Expression
23 23
![image](images/gene_expression/RUBCNL_by_pathology.svg)
24 24
<!-- ORIGIN: Unknown -->
25
+## References
SAL3.md
... ...
@@ -1,5 +1,11 @@
1 1
# SAL3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2022-07-06 : Burkhardt : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -14,13 +20,6 @@
14 20
|BL |Thomas cohort |NA |
15 21
|BL |Panea cohort |NA |
16 22
17
-## Mutation pattern and selective pressure estimates
18
-
19
-|
20
-
21
-
22
-> [!NOTE]
23
-> First described in BL in 2022 by [Burkhardt B](https://pubmed.ncbi.nlm.nih.gov/35794096)
24 23
25 24
26 25
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAL3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAL3_protein_hg38.html)
... ...
@@ -32,3 +31,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
32 31
![image](images/gene_expression/SAL3_by_pathology.svg)
33 32
<!-- ORIGIN: burkhardtClinicalRelevanceMolecular2022b -->
34 33
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
34
+## References
35
+1. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
SALL3.md
... ...
@@ -1,5 +1,12 @@
1 1
# SALL3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+ 2014-05-08 : Zhang : MCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -25,8 +32,6 @@
25 32
|FL |No |No |1.660 | 0.000 |
26 33
27 34
28
-> [!NOTE]
29
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
30 35
31 36
32 37
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SALL3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SALL3_protein_hg38.html)
... ...
@@ -41,3 +46,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
41 46
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
42 47
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
43 48
<!-- BL: loveGeneticLandscapeMutations2012 -->
49
+## References
50
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
51
+2. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
SAMD9L.md
... ...
@@ -1,5 +1,11 @@
1 1
# SAMD9L
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,9 +30,6 @@
24 30
|FL |No |No |0.000 |0.000 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29
-
30 33
31 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAMD9L_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAMD9L_protein_hg38.html)
32 35
... ...
@@ -39,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
39 42
![image](images/gene_expression/SAMD9L_by_pathology.svg)
40 43
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 44
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
45
+## References
46
+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
SAPS2.md
... ...
@@ -1,5 +1,11 @@
1 1
# SAPS2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -14,13 +20,8 @@
14 20
|BL |Thomas cohort |NA |
15 21
|BL |Panea cohort |NA |
16 22
17
-## Mutation pattern and selective pressure estimates
18
-
19
-|
20 23
21 24
22
-> [!NOTE]
23
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
24 25
25 26
26 27
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SAPS2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SAPS2_protein_hg38.html)
... ...
@@ -32,3 +33,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
32 33
![image](images/gene_expression/SAPS2_by_pathology.svg)
33 34
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
34 35
<!-- BL: loveGeneticLandscapeMutations2012 -->
36
+## References
37
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
SARM1.md
... ...
@@ -1,5 +1,11 @@
1 1
# SARM1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2013-08-15 : Morin : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,8 +30,6 @@
24 30
|FL |No |No |0.000 |0 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29 33
30 34
31 35
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SARM1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SARM1_protein_hg38.html)
... ...
@@ -39,3 +43,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
39 43
![image](images/gene_expression/SARM1_by_pathology.svg)
40 44
<!-- ORIGIN: morinMutationalStructuralAnalysis2013 -->
41 45
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
46
+## References
47
+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
SEL1L3.md
... ...
@@ -40,3 +40,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
40 40
## SEL1L3 Expression
41 41
![image](images/gene_expression/SEL1L3_by_pathology.svg)
42 42
<!-- ORIGIN: Unknown -->
43
+## References
SESN1.md
... ...
@@ -35,3 +35,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
35 35
## SESN1 Expression
36 36
![image](images/gene_expression/SESN1_by_pathology.svg)
37 37
<!-- ORIGIN: Unknown -->
38
+## References
SHANK1.md
... ...
@@ -1,5 +1,11 @@
1 1
# SHANK1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,9 +29,6 @@
23 29
|FL |No |No |2.138 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
-
29 32
30 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SHANK1_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SHANK1_protein_hg38.html)
31 34
... ...
@@ -38,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 41
![image](images/gene_expression/SHANK1_by_pathology.svg)
39 42
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 43
<!-- BL: loveGeneticLandscapeMutations2012 -->
44
+## References
45
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
SHROOM3.md
... ...
@@ -1,5 +1,11 @@
1 1
# SHROOM3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2023-07-26 : Russler-Germain : FL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,8 +27,6 @@
21 27
|FL |No |No |0.774 |0 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
26 30
27 31
28 32
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SHROOM3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SHROOM3_protein_hg38.html)
... ...
@@ -36,3 +40,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
36 40
![image](images/gene_expression/SHROOM3_by_pathology.svg)
37 41
<!-- ORIGIN: russler-germainMutationsAssociatedProgression2023a -->
38 42
<!-- FL: russler-germainMutationsAssociatedProgression2023a -->
43
+## References
44
+1. 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.
SI.md
... ...
@@ -1,5 +1,11 @@
1 1
# SI
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-05-08 : Zhang : MCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |0.455 |1.135 |
22 28
23 29
24
-> [!NOTE]
25
-> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
26
-
27 30
28 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SI_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SI_protein_hg38.html)
29 32
... ...
@@ -36,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
36 39
![image](images/gene_expression/SI_by_pathology.svg)
37 40
<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 41
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
42
+## References
43
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.
SIAH2.md
... ...
@@ -1,5 +1,12 @@
1 1
# SIAH2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2015-02-12 : Reichel : PMBL
8
+ 2021-05-05 : Hübschmann : DLBCL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -41,3 +48,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
41 48
<!-- ORIGIN: reichelFlowSortingExome2015a -->
42 49
<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
43 50
<!-- PMBL: reichelFlowSortingExome2015a -->
51
+## References
52
+1. 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
53
+2. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
SLC29A2.md
... ...
@@ -1,5 +1,11 @@
1 1
# SLC29A2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -23,8 +29,6 @@
23 29
|FL |No |No |0 |0 |
24 30
25 31
26
-> [!NOTE]
27
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28 32
29 33
30 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SLC29A2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SLC29A2_protein_hg38.html)
... ...
@@ -38,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
38 42
![image](images/gene_expression/SLC29A2_by_pathology.svg)
39 43
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40 44
<!-- BL: loveGeneticLandscapeMutations2012 -->
45
+## References
46
+1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
SLC34A2.md
... ...
@@ -1,5 +1,11 @@
1 1
# SLC34A2
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2021-05-05 : Hübschmann : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,10 +30,6 @@
24 30
|FL |No |No |1.687 |0 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
29
-
30
-
31 33
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SLC34A2_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SLC34A2_protein_hg38.html)
32 34
33 35
![image](images/proteinpaint/SLC34A2_NM_006424.svg)
... ...
@@ -39,3 +41,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
39 41
![image](images/gene_expression/SLC34A2_by_pathology.svg)
40 42
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
41 43
<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
44
+## References
45
+1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
SMC1A.md
... ...
@@ -1,5 +1,11 @@
1 1
# SMC1A
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
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+timeline
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+ title Publication timing
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+ 2014-05-08 : Zhang : MCL
8
+```
3 9
## Relevance tier by entity
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5 11
|Entity|Tier|Description |
... ...
@@ -21,9 +27,6 @@
21 27
|FL |No |No |0 |0 |
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23 29
24
-> [!NOTE]
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-> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
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-
27 30
28 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SMC1A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SMC1A_protein_hg38.html)
29 32
... ...
@@ -36,3 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
36 39
![image](images/gene_expression/SMC1A_by_pathology.svg)
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<!-- ORIGIN: zhangGenomicLandscapeMantle2014 -->
38 41
<!-- MCL: zhangGenomicLandscapeMantle2014 -->
42
+## References
43
+1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996.