BL_genes.md
... ...
@@ -1,7 +1,48 @@
1 1
# BL genes
2 2
3
-## Origins of BL genes![sankey](BL_sankey-1.svg)
4
-
3
+## Origins of BL genes
4
+```mermaid
5
+---
6
+config:
7
+ sankey:
8
+ showValues: false
9
+ linkColor: target
10
+ width: 800
11
+ height: 1000
12
+ nodeAlignment: right
13
+---
14
+sankey-beta
15
+Grande 2019, BL Tier 1, 9
16
+Grande 2019, BL Tier 2, 4
17
+Richter 2012, BL Tier 1, 5
18
+Burkhardt 2022, BL Tier 2, 25
19
+Schmitz 2012, BL Tier 1, 3
20
+Schmitz 2012, BL Tier 2, 16
21
+Love 2012, BL Tier 1, 3
22
+Love 2012, BL Tier 2, 56
23
+Muppidi 2014, BL Tier 1, 1
24
+Muppidi 2014, BL Tier 2, 2
25
+Panea 2019, BL Tier 1, 4
26
+Panea 2019, BL Tier 2, 46
27
+Thomas 2023, BL Tier 1, 2
28
+Thomas 2023, BL Tier 2, 3
29
+BL, panel, 25
30
+panel, Burkhardt 2022, 25
31
+BL, WGS, 13
32
+WGS, Grande 2019, 13
33
+BL, RNA-seq/WGS/exome, 5
34
+RNA-seq/WGS/exome, Richter 2012, 5
35
+BL, exome, 59
36
+exome, Love 2012, 59
37
+BL, RNA-seq, 19
38
+RNA-seq, Schmitz 2012, 19
39
+BL, Sanger, 3
40
+Sanger, Muppidi 2014, 3
41
+BL, RNA-seq/exome, 50
42
+RNA-seq/exome, Panea 2019, 50
43
+BL, WGS, 5
44
+WGS, Thomas 2023, 5
45
+```
5 46
## Tier 1 BL genes
6 47
7 48
### *29 total*
FL_genes.md
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1 1
# FL genes
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-## Origins of FL genes![sankey](FL_sankey-1.svg)
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+## Origins of FL genes
4
+
5
+```mermaid
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
+Okosun 2016, FL Tier 1, 2
17
+Russler-germain 2023, FL Tier 1, 1
18
+Russler-germain 2023, FL Tier 2, 19
19
+Krysiak 2017, FL Tier 1, 17
20
+Krysiak 2017, FL Tier 2, 5
21
+Morin 2011, FL Tier 1, 14
22
+Morin 2011, FL Tier 2, 1
23
+Pasqualucci 2011, FL Tier 1, 2
24
+Hubschmann 2021, FL Tier 1, 2
25
+Hubschmann 2021, FL Tier 2, 15
26
+FL, WGS, 2
27
+WGS, Okosun 2016, 2
28
+FL, exome, 20
29
+exome, Russler-germain 2023, 20
30
+FL, exome, 2
31
+exome, Pasqualucci 2011, 2
32
+FL, WGS, 17
33
+WGS, Hubschmann 2021, 17
34
+FL, exome, 22
35
+exome, Krysiak 2017, 22
36
+FL, RNA-seq/WGS, 15
37
+RNA-seq/WGS, Morin 2011, 15
38
+```
4 39
5 40
## Tier 1 FL genes
6 41
Home.md
... ...
@@ -24,134 +24,132 @@ config:
24 24
nodeAlignment: right
25 25
---
26 26
sankey-beta
27
-
28
-Sanger, 2001, 4
29
-2001, Pasqualucci 2001, 4
30
-Pasqualucci 2001, DLBCL Tier 1, 3
31
-Pasqualucci 2001, DLBCL Tier 2, 1
32
-
33
-RNA-seq/WGS, 2011, 49
34
-2011, Morin 2011, 25
35
-Morin 2011, DLBCL Tier 1, 25
36
-2011, Morin 2011, 15
37
-Morin 2011, FL Tier 1, 14
38
-Morin 2011, FL Tier 2, 1
39
-2011, Pasqualucci 2011a, 7
40
-Pasqualucci 2011a, DLBCL Tier 1, 5
41
-Pasqualucci 2011a, DLBCL Tier 2, 2
42
-2011, Pasqualucci 2011b, 2
43
-Pasqualucci 2011b, FL Tier 1, 2
44
-Pasqualucci 2011b, DLBCL Tier 1, 2
45
-
46
-exome, 2012 exome studies, 68
47
-2012 exome studies, Richter 2012, 5
48
-2012 exome studies, Lohr 2012, 4
49
-2012 exome studies, Love 2012, 59
50
-
51
-Richter 2012, BL Tier 1, 5
27
+Albuquerque 2017, DLBCL Tier 1, 3
52 28
Lohr 2012, DLBCL Tier 1, 3
53 29
Lohr 2012, DLBCL Tier 2, 1
54
-Love 2012, BL Tier 1, 3
55
-Love 2012, BL Tier 2, 56
56
-
57
-RNA-seq, 2012 , 19
58
-2012 , Schmitz 2012, 19
59
-Schmitz 2012, BL Tier 1, 3
60
-Schmitz 2012, BL Tier 2, 16
61
-
62
-WGS, 2013 WGS studies, 40
63
-2013 WGS studies, Morin 2013, 40
30
+Pasqualucci 2001, DLBCL Tier 1, 2
31
+Pasqualucci 2001, DLBCL Tier 2, 2
32
+Mareschal 2016, DLBCL Tier 1, 2
33
+Arthur 2018, DLBCL Tier 1, 8
34
+Arthur 2018, DLBCL Tier 2, 12
35
+Morin 2016, DLBCL Tier 1, 2
64 36
Morin 2013, DLBCL Tier 1, 11
65 37
Morin 2013, DLBCL Tier 2, 29
66
-
67
-
68
-exome, 2013 exome studies, 19
69
-2013 exome studies, Zhang 2013, 19
38
+Pasqualucci 2011, DLBCL Tier 1, 2
39
+Hubschmann 2021, DLBCL Tier 1, 3
40
+Hubschmann 2021, DLBCL Tier 2, 20
41
+Chapuy 2018, DLBCL Tier 1, 2
42
+Chapuy 2018, DLBCL Tier 2, 17
43
+Pasqualucci 2011, DLBCL Tier 1, 3
44
+Pasqualucci 2011, DLBCL Tier 2, 4
45
+Reddy 2017, DLBCL Tier 1, 7
46
+Reddy 2017, DLBCL Tier 2, 53
70 47
Zhang 2013, DLBCL Tier 1, 11
71 48
Zhang 2013, DLBCL Tier 2, 8
72
-
73
-exome, 2014 exome studies, 3
74
-2014 exome studies, Muppidi 2014, 3
75
-Muppidi 2014, BL Tier 1, 1
76
-Muppidi 2014, BL Tier 2, 2
77
-
78
-exome, 2016 exome studies, 2
79
-2016 exome studies, Mareschal 2016, 2
80
-Mareschal 2016, DLBCL Tier 1, 2
81
-
82
-WGS, 2016 WGS studies, 2
83
-2016 WGS studies, Okosun 2016, 2
84
-Okosun 2016, FL Tier 1, 2
85
-
86
-exome, 2016 exome studies, 2
87
-2016 exome studies, Morin 2016, 2
88
-Morin 2016, DLBCL Tier 1, 2
89
-
90
-exome, 2017 exome studies, 85
91
-2017 exome studies, Krysiak 2017, 22
49
+Schmitz 2018, DLBCL Tier 1, 7
50
+Schmitz 2018, DLBCL Tier 2, 9
51
+Morin 2011, DLBCL Tier 1, 24
52
+Morin 2011, DLBCL Tier 2, 1
53
+DLBCL, DLBCL-exome, 7
54
+DLBCL-exome, Pasqualucci 2011, 7
55
+DLBCL, DLBCL-exome, 19
56
+DLBCL-exome, Chapuy 2018, 19
57
+DLBCL, DLBCL-WGS, 23
58
+DLBCL-WGS, Hubschmann 2021, 23
59
+DLBCL, DLBCL-WGS/exome, 2
60
+DLBCL, DLBCL-exome, 2
61
+DLBCL-exome, Pasqualucci 2011, 2
62
+DLBCL, DLBCL-RNA-seq/WGS, 25
63
+DLBCL-RNA-seq/WGS, Morin 2011, 25
64
+DLBCL, DLBCL-exome, 19
65
+DLBCL-exome, Zhang 2013, 19
66
+DLBCL, DLBCL-exome, 16
67
+DLBCL-exome, Schmitz 2018, 16
68
+DLBCL, DLBCL-exome, 60
69
+DLBCL-exome, Reddy 2017, 60
70
+DLBCL, DLBCL-exome, 4
71
+DLBCL-exome, Lohr 2012, 4
72
+DLBCL, DLBCL-exome, 3
73
+DLBCL-exome, Albuquerque 2017, 3
74
+DLBCL, DLBCL-exome, 2
75
+DLBCL-exome, Morin 2016, 2
76
+DLBCL, DLBCL-WGS, 40
77
+DLBCL-WGS, Morin 2013, 40
78
+DLBCL, DLBCL-exome, 2
79
+DLBCL-exome, Mareschal 2016, 2
80
+DLBCL, DLBCL-WGS, 20
81
+DLBCL-WGS, Arthur 2018, 20
82
+DLBCL, DLBCL-Sanger, 4
83
+DLBCL-Sanger, Pasqualucci 2001, 4
84
+Pasqualucci 2011, FL Tier 1, 2
85
+Hubschmann 2021, FL Tier 1, 2
86
+Hubschmann 2021, FL Tier 2, 15
92 87
Krysiak 2017, FL Tier 1, 17
93 88
Krysiak 2017, FL Tier 2, 5
94
-
95
-
96
-2017 exome studies, Albuquerque 2017, 3
97
-Albuquerque 2017, DLBCL Tier 1, 3
98
-
99
-2017 exome studies, Reddy 2017, 60
100
-Reddy 2017, DLBCL Tier 2, 50
101
-Reddy 2017, DLBCL Tier 1, 10
102
-
103
-exome, 2018 exome studies, 35
104
-2018 exome studies, Schmitz 2018, 16
105
-Schmitz 2018, DLBCL Tier 2, 7
106
-Schmitz 2018, DLBCL Tier 1, 9
107
-
108
-2018 exome studies, Chapuy 2018, 19
109
-Chapuy 2018, DLBCL Tier 2, 16
110
-Chapuy 2018, DLBCL Tier 1, 3
111
-
112
-WGS, 2018 WGS studies, 20
113
-2018 WGS studies, Arthur 2018, 20
114
-Arthur 2018, DLBCL Tier 2, 12
115
-Arthur 2018, DLBCL Tier 1, 8
116
-
117
-RNA-seq/exome,2019 ,47
118
-2019 , Panea 2019, 47
119
-Panea 2019, BL Tier 2, 43
89
+Morin 2011, FL Tier 1, 14
90
+Morin 2011, FL Tier 2, 1
91
+Okosun 2016, FL Tier 1, 2
92
+Russler-germain 2023, FL Tier 1, 1
93
+Russler-germain 2023, FL Tier 2, 19
94
+FL, FL-WGS, 17
95
+FL-WGS, Hubschmann 2021, 17
96
+FL, FL-exome, 2
97
+FL-exome, Pasqualucci 2011, 2
98
+FL, FL-RNA-seq/WGS, 15
99
+FL-RNA-seq/WGS, Morin 2011, 15
100
+FL, FL-exome, 22
101
+FL-exome, Krysiak 2017, 22
102
+FL, FL-exome, 20
103
+FL-exome, Russler-germain 2023, 20
104
+FL, FL-WGS, 2
105
+FL-WGS, Okosun 2016, 2
106
+Muppidi 2014, BL Tier 1, 1
107
+Muppidi 2014, BL Tier 2, 2
120 108
Panea 2019, BL Tier 1, 4
121
-
122
-WGS,2019 WGS studies,13
123
-2019 WGS studies, Grande 2019, 13
124
-Grande 2019, BL Tier 1, 8
125
-Grande 2019, BL Tier 2, 5
126
-
127
-exome, 2020 exome studies, 2
128
-2020 exome studies, Pararajalingam 2020, 2
129
-Pararajalingam 2020, DLBCL Tier 1, 2
130
-
131
-WGS, 2021 WGS studies, 40
132
-2021 WGS studies, Hubschmann 2021, 17
133
-2021 WGS studies, Hubschmann 2021, 23
134
-Hubschmann 2021, FL Tier 2, 15
135
-Hubschmann 2021, FL Tier 1, 2
136
-Hubschmann 2021, DLBCL Tier 1, 4
137
-Hubschmann 2021, DLBCL Tier 2, 19
138
-
139
-exome, 2023 exome studies, 20
140
-2023 exome studies, Russler-Germain 2023, 20
141
-Russler-Germain 2023, FL Tier 1, 1
142
-Russler-Germain 2023, FL Tier 2, 19
143
-
144
-Panel, panel studies, 25
145
-panel studies, Burkhardt 2022, 25
146
-Burkhardt 2022, BL Tier 2, 25
147
-
148
-WGS, 2023 WGS studies, 3
149
-2023 WGS studies, Thomas 2023, 3
150
-Thomas 2023, BL Tier 2, 1
109
+Panea 2019, BL Tier 2, 46
151 110
Thomas 2023, BL Tier 1, 2
152
-
111
+Thomas 2023, BL Tier 2, 3
112
+Grande 2019, BL Tier 1, 9
113
+Grande 2019, BL Tier 2, 4
114
+Richter 2012, BL Tier 1, 5
115
+Burkhardt 2022, BL Tier 2, 25
116
+Schmitz 2012, BL Tier 1, 3
117
+Schmitz 2012, BL Tier 2, 16
118
+Love 2012, BL Tier 1, 3
119
+Love 2012, BL Tier 2, 56
120
+BL, BL-RNA-seq/exome, 50
121
+BL-RNA-seq/exome, Panea 2019, 50
122
+BL, BL-Sanger, 3
123
+BL-Sanger, Muppidi 2014, 3
124
+BL, BL-WGS, 5
125
+BL-WGS, Thomas 2023, 5
126
+BL, BL-panel, 25
127
+BL-panel, Burkhardt 2022, 25
128
+BL, BL-WGS, 13
129
+BL-WGS, Grande 2019, 13
130
+BL, BL-RNA-seq/WGS/exome, 5
131
+BL-RNA-seq/WGS/exome, Richter 2012, 5
132
+BL, BL-exome, 59
133
+BL-exome, Love 2012, 59
134
+BL, BL-RNA-seq, 19
135
+BL-RNA-seq, Schmitz 2012, 19
136
+Zhang 2014, MCL Tier 1, 2
137
+Zhang 2014, MCL Tier 2, 26
138
+Bea 2013, MCL Tier 1, 11
139
+Bea 2013, MCL Tier 2, 16
140
+Nadeu 2020, MCL Tier 1, 3
141
+Nadeu 2020, MCL Tier 2, 2
142
+Pararajalingam 2020, MCL Tier 1, 6
143
+Pararajalingam 2020, MCL Tier 2, 1
144
+MCL, MCL-WGS/exome, 27
145
+MCL-WGS/exome, Bea 2013, 27
146
+MCL, MCL-WGS/exome, 7
147
+MCL-WGS/exome, Pararajalingam 2020, 7
148
+MCL, MCL-WGS, 5
149
+MCL-WGS, Nadeu 2020, 5
150
+MCL, MCL-exome, 28
151
+MCL-exome, Zhang 2014, 28
153 152
```
154
-
155 153
## B-cell Lymphoma aSHM targets
156 154
[hg19 coordinates](ashm)
157 155
MCL_genes.md
... ...
@@ -1,6 +1,34 @@
1 1
# MCL genes
2 2
3
-## Origins of MCL genes![sankey](MCL_sankey-1.svg)
3
+## Origins of MCL genes
4
+```mermaid
5
+---
6
+config:
7
+ sankey:
8
+ showValues: false
9
+ linkColor: target
10
+ width: 800
11
+ height: 1000
12
+ nodeAlignment: right
13
+---
14
+sankey-beta
15
+Zhang 2014, MCL Tier 1, 2
16
+Zhang 2014, MCL Tier 2, 26
17
+Nadeu 2020, MCL Tier 1, 3
18
+Nadeu 2020, MCL Tier 2, 2
19
+Pararajalingam 2020, MCL Tier 1, 6
20
+Pararajalingam 2020, MCL Tier 2, 1
21
+Bea 2013, MCL Tier 1, 11
22
+Bea 2013, MCL Tier 2, 16
23
+MCL, exome, 28
24
+exome, Zhang 2014, 28
25
+MCL, WGS/exome, 7
26
+WGS/exome, Pararajalingam 2020, 7
27
+MCL, WGS, 5
28
+WGS, Nadeu 2020, 5
29
+MCL, WGS/exome, 27
30
+WGS/exome, Bea 2013, 27
31
+```
4 32
5 33
## Tier 1 MCL genes
6 34