papers/abateDistinctViralMutational2015.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @abateDistinctViralMutational2015a
6
+# @abateDistinctViralMutational2015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|0|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, BL Tier 1, 0
27 27
This study, New Tier 2, 1
28 28
New Tier 2, BL Tier 2, 1
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 156
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 32
32
+All other BL studies, BL Tier 2, 71
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
### Tier 2
papers/albuquerqueEnhancingKnowledgeDiscovery2017.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @albuquerqueEnhancingKnowledgeDiscovery2017a
6
+# @albuquerqueEnhancingKnowledgeDiscovery2017
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|4|6|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 3
26
-New Tier 1, DLBCL Tier 1, 3
27
-This study, New Tier 2, 0
28
-New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 125
30
-All other DLBCL studies, DLBCL Tier 2, 198
25
+This study, New Tier 1, 4
26
+New Tier 1, DLBCL Tier 1, 4
27
+This study, New Tier 2, 6
28
+New Tier 2, DLBCL Tier 2, 6
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 121
32
+All other DLBCL studies, DLBCL Tier 2, 204
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -36,8 +39,19 @@ All other DLBCL studies, DLBCL Tier 2, 198
36 39
|New gene|DLBCL tier|
37 40
|:-|:-:|
38 41
|[BTK](../BTK)|1 |
42
+|[SETD1B](../SETD1B)|1 |
43
+|[SPEN](../SPEN)|1 |
39 44
|[TET2](../TET2)|1 |
40
-|[TMSB4X](../TMSB4X)|1 |
45
+
46
+### Tier 2
47
+|New gene|DLBCL tier|
48
+|:-|:-:|
49
+|[ASXL3](../ASXL3)|2 |
50
+|[CEP164](../CEP164)|2 |
51
+|[DNMT3B](../DNMT3B)|2 |
52
+|[ERAP2](../ERAP2)|2 |
53
+|[UBR5](../UBR5)|2 |
54
+|[UHRF1BP1](../UHRF1BP1)|2 |
41 55
42 56
43 57
# Details
papers/arthurGenomewideDiscoverySomatic2018.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @arthurGenomewideDiscoverySomatic2018
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|8|12|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|14|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 8
26
-New Tier 1, DLBCL Tier 1, 8
27
-This study, New Tier 2, 12
28
-New Tier 2, DLBCL Tier 2, 12
29
-All other DLBCL studies, DLBCL Tier 1, 120
30
-All other DLBCL studies, DLBCL Tier 2, 186
25
+This study, New Tier 1, 2
26
+New Tier 1, DLBCL Tier 1, 2
27
+This study, New Tier 2, 14
28
+New Tier 2, DLBCL Tier 2, 14
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 123
32
+All other DLBCL studies, DLBCL Tier 2, 196
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,14 +38,8 @@ All other DLBCL studies, DLBCL Tier 2, 186
35 38
### Tier 1
36 39
|New gene|DLBCL tier|
37 40
|:-|:-:|
38
-|[BCL7A](../BCL7A)|1 |
39
-|[ETV6](../ETV6)|1 |
40
-|[GRHPR](../GRHPR)|1 |
41
-|[LCOR](../LCOR)|1 |
42
-|[MEF2C](../MEF2C)|1 |
43
-|[OSBPL10](../OSBPL10)|1 |
44
-|[PIM2](../PIM2)|1 |
45
-|[ZC3H12A](../ZC3H12A)|1 |
41
+|[FBXO11](../FBXO11)|1 |
42
+|[RFX7](../RFX7)|1 |
46 43
47 44
### Tier 2
48 45
|New gene|DLBCL tier|
... ...
@@ -55,21 +52,13 @@ All other DLBCL studies, DLBCL Tier 2, 186
55 52
|[MALAT1](../MALAT1)|2 |
56 53
|[NEAT1](../NEAT1)|2 |
57 54
|[RFTN1](../RFTN1)|2 |
55
+|[RHEX](../RHEX)|2 |
58 56
|[SERPINA9](../SERPINA9)|2 |
59 57
|[ST6GAL1](../ST6GAL1)|2 |
60 58
|[TBC1D4](../TBC1D4)|2 |
59
+|[USP7](../USP7)|2 |
61 60
|[ZCCHC7](../ZCCHC7)|2 |
62 61
63 62
64
-## Data Availability
65
-
66
-|**Repository**|**Accession**|
67
-|-|-|
68
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000532.v18.p6 |
69
-|[EGA](https://ega-archive.org/)|EGAD00001003783|
70
-|[EGA](https://ega-archive.org/)|EGAD00001004142|
71
-
72
-
73
-
74 63
# Details
75 64
papers/barariaCathepsinAlterationsInduce2020.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @barariaCathepsinAlterationsInduce2020c
6
+# @barariaCathepsinAlterationsInduce2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, FL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, FL Tier 2, 0
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 50
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 53
32
+All other FL studies, FL Tier 2, 59
33
+All other FL studies, FL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/beaLandscapeSomaticMutations2013.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @beaLandscapeSomaticMutations2013
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|11|16|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MCL|11|16|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 11
26 26
New Tier 1, MCL Tier 1, 11
27 27
This study, New Tier 2, 16
28 28
New Tier 2, MCL Tier 2, 16
29
+This study, New Tier 3, 0
30
+New Tier 3, MCL Tier 3, 0
29 31
All other MCL studies, MCL Tier 1, 12
30 32
All other MCL studies, MCL Tier 2, 30
33
+All other MCL studies, MCL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/bohleRoleEarlyBcell2013.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @bohleRoleEarlyBcell2013
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/braggioGenomicAnalysisMarginal2012.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @braggioGenomicAnalysisMarginal2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, MZL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MZL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 41
30 32
All other MZL studies, MZL Tier 2, 74
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/burkhardtClinicalRelevanceMolecular2022.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @burkhardtClinicalRelevanceMolecular2022b
6
+# @burkhardtClinicalRelevanceMolecular2022
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|25|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|0|25|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, BL Tier 1, 0
27 27
This study, New Tier 2, 25
28 28
New Tier 2, BL Tier 2, 25
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 132
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 32
32
+All other BL studies, BL Tier 2, 47
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
### Tier 2
papers/chapuyMolecularSubtypesDiffuse2018.md
... ...
@@ -3,14 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @chapuyMolecularSubtypesDiffuse2018b
6
+# @chapuyMolecularSubtypesDiffuse2018
7 7
## Summary of novel genes
8 8
9
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail Rate|
10
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
-|DLBCL|19|2|17| 10\* | 7 | 41% |
12
-
13
-
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|10|13|6|
14 12
```mermaid
15 13
---
16 14
config:
... ...
@@ -24,48 +22,60 @@ config:
24 22
suffix: ' genes)'
25 23
---
26 24
sankey-beta
27
-New to this study, DLBCL Tier 1, 2
28
-New to this study, DLBCL Tier 2, 17
29
-DLBCL Tier 2, Pass QC, 10
30
-DLBCL Tier 2, Fail QC, 7
25
+This study, New Tier 1, 10
26
+New Tier 1, DLBCL Tier 1, 10
27
+This study, New Tier 2, 13
28
+New Tier 2, DLBCL Tier 2, 13
29
+This study, New Tier 3, 6
30
+New Tier 3, DLBCL Tier 3, 6
31
+All other DLBCL studies, DLBCL Tier 1, 115
32
+All other DLBCL studies, DLBCL Tier 2, 197
33
+All other DLBCL studies, DLBCL Tier 3, 381
31 34
```
32 35
33 36
## Novel genes reported in this study
34 37
35 38
### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[HIST1H1B](../HIST1H1B)|1 |
39
-|[LTB](../LTB)|1 |
39
+|New gene|DLBCL tier| Average variant quality | QC outcome |
40
+|:-|:-:|:-:|:-:|
41
+|[EEF1A1](../EEF1A1)|1 || |
42
+|[HIST1H1B](../HIST1H1B)|1 || |
43
+|[HIST1H2AM](../HIST1H2AM)|1 || |
44
+|[HIST2H2BE](../HIST2H2BE)|1 || |
45
+|[HLA-C](../HLA-C)|1 || |
46
+|[HVCN1](../HVCN1)|1 || |
47
+|[LTB](../LTB)|1 || |
48
+|[POU2AF1](../POU2AF1)|1 || |
49
+|[SIN3A](../SIN3A)|1 || |
50
+|[ZC3H12A](../ZC3H12A)|1 || |
40 51
41 52
### Tier 2
42
-|Novel Gene|DLBCL tier|Average variant quality|QC outcome|
53
+|New gene|DLBCL tier| Average variant quality | QC outcome |
43 54
|:-|:-:|:-:|:-:|
44
-|[GABRA2](../GABRA2)|2 |TBD|TBD|
45
-|[COQ7](../COQ7)|2 |★ ★ ★ ☆ ☆ |**Pass**|
46
-|[CRIP1](../CRIP1)|2 |★ ★ ★ ☆ ☆ |**Pass**|
47
-|[DOCK1](../DOCK1)|2 |★ ★ ★ ☆ ☆ |**Pass**|
48
-|[NAV1](../NAV1)|2 |TBD|TBD|
49
-|[IL6](../IL6)|2 |★ ★ ★ ☆ ☆ |**Pass**|
50
-|[LYN](../LYN)|2 |★ ★ ★ ★ ☆ |**Pass**|
51
-|[PRPS1](../PRPS1)|2 |★ ★ ★ ★ ☆ |**Pass**|
52
-|[TLR2](../TLR2)|2 |★ ★ ★ ★ ☆ |**Pass**|
53
-|[ZNF423](../ZNF423)|2 |★ ★ ★ ☆ ☆ |**Pass**|
54
-|[FUT5](../FUT5)|2 |★ ☆ ☆ ☆ ☆ |**Fail**|
55
-|[RAD9A](../RAD9A)|2 |*No variants reported*|**Fail**|
56
-|[CCL4](../CCL4)|2 |*No variants reported*|**Fail**|
57
-|[SMEK1](../SMEK1)|2 |*No variants in paired samples*|**Fail**|
58
-|[NANOG](../NANOG)|2 |*No variants reported*|**Fail**|
59
-|[NLRP8](../NLRP8)|2 |★ ★ ☆ ☆ ☆ |**Fail**|
60
-|[PDE4DIP](../PDE4DIP)|2 |★ ★ ☆ ☆ ☆ |**Fail**|
55
+|[BCL11A](../BCL11A)|2 || |
56
+|[COQ7](../COQ7)|2 |★ ★ ★ ☆ ☆ |PASS |
57
+|[CRIP1](../CRIP1)|2 |★ ★ ★ ☆ ☆ |PASS |
58
+|[DOCK1](../DOCK1)|2 |★ ★ ★ ☆ ☆ |PASS |
59
+|[GABRA2](../GABRA2)|2 || |
60
+|[HLA-DMA](../HLA-DMA)|2 || |
61
+|[IGLL5](../IGLL5)|2 || |
62
+|[IL6](../IL6)|2 |★ ★ ★ ☆ ☆ |PASS |
63
+|[LYN](../LYN)|2 |★ ★ ★ ★ ☆ |PASS |
64
+|[NAV1](../NAV1)|2 || |
65
+|[PRPS1](../PRPS1)|2 |★ ★ ★ ★ ☆ |PASS |
66
+|[TLR2](../TLR2)|2 |★ ★ ★ ★ ☆ |PASS |
67
+|[ZNF423](../ZNF423)|2 |★ ★ ★ ☆ ☆ |PASS |
61 68
69
+### Tier 3
70
+|New gene|DLBCL tier| Average variant quality | QC outcome |
71
+|:-|:-:|:-:|:-:|
72
+|[CCL4](../CCL4)|3 |☆ ☆ ☆ ☆ ☆ |FAIL |
73
+|[FUT5](../FUT5)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
74
+|[NANOG](../NANOG)|3 |☆ ☆ ☆ ☆ ☆ |FAIL |
75
+|[NLRP8](../NLRP8)|3 |★ ★ ☆ ☆ ☆ |FAIL |
76
+|[PDE4DIP](../PDE4DIP)|3 |★ ★ ☆ ☆ ☆ |FAIL |
77
+|[RAD9A](../RAD9A)|3 |☆ ☆ ☆ ☆ ☆ |FAIL |
62 78
63
-## Data Availability
64
-
65
-|**Repository**|**Accession**|
66
-|-|-|
67
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v1.p1|
68
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000450.v3.p1|
69 79
70 80
# Details
71 81
papers/cheungAcquiredTNFRSF14Mutations2010.md
... ...
@@ -3,13 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @cheungAcquiredTNFRSF14Mutations2010a
6
+# @cheungAcquiredTNFRSF14Mutations2010
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|0|
12
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|1|0|0|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -24,19 +23,22 @@ config:
24 23
---
25 24
sankey-beta
26 25
This study, New Tier 1, 1
27
-New Tier 1, DLBCL Tier 1, 1
26
+New Tier 1, FL Tier 1, 1
28 27
This study, New Tier 2, 0
29
-New Tier 2, DLBCL Tier 2, 0
30
-All other DLBCL studies, DLBCL Tier 1, 127
31
-All other DLBCL studies, DLBCL Tier 2, 198
28
+New Tier 2, FL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 53
32
+All other FL studies, FL Tier 2, 59
33
+All other FL studies, FL Tier 3, 0
32 34
```
33 35
34 36
## Novel genes reported in this study
35 37
36 38
### Tier 1
37
-|New gene|FL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[TNFRSF14](../TNFRSF14)|1 |1 |
39
+|New gene|FL tier|
40
+|:-|:-:|
41
+|[TNFRSF14](../TNFRSF14)|1 |
40 42
41 43
42 44
# Details
papers/compagnoMutationsMultipleGenes2009.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @compagnoMutationsMultipleGenes2009a
6
+# @compagnoMutationsMultipleGenes2009
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/davisChronicActiveBcellreceptor2010.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @davisChronicActiveBcellreceptor2010
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[CD79B](../CD79B)|1 |
42
+
43
+
44
+# Details
45
+
papers/deschGenotypingCirculatingTumor2020.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @deschGenotypingCirculatingTumor2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|9|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 9
28 28
New Tier 2, PMBL Tier 2, 9
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 73
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 103
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/drevalGeneticSubdivisionsFollicular2023.md
... ...
@@ -0,0 +1,70 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @drevalGeneticSubdivisionsFollicular2023
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|10|11|0|
12
+|DLBCL|20|1|0|
13
+```mermaid
14
+---
15
+config:
16
+ sankey:
17
+ showValues: true
18
+ linkColor: target
19
+ width: 600
20
+ height: 300
21
+ nodeAlignment: right
22
+ prefix: '('
23
+ suffix: ' genes)'
24
+---
25
+sankey-beta
26
+This study, New Tier 1, 10
27
+New Tier 1, FL Tier 1, 10
28
+This study, New Tier 2, 11
29
+New Tier 2, FL Tier 2, 11
30
+This study, New Tier 3, 0
31
+New Tier 3, FL Tier 3, 0
32
+All other FL studies, FL Tier 1, 44
33
+All other FL studies, FL Tier 2, 48
34
+All other FL studies, FL Tier 3, 0
35
+```
36
+
37
+## Novel genes reported in this study
38
+
39
+### Tier 1
40
+|New gene|FL tier|DLBCL tier|
41
+|:-|:-:|:-:|
42
+|[ACTB](../ACTB)|1 |1 |
43
+|[BCL6](../BCL6)|1 |1 |
44
+|[BTG1](../BTG1)|2 |1 |
45
+|[BTG2](../BTG2)|2 |1 |
46
+|[CD79B](../CD79B)|2 |1 |
47
+|[DUSP2](../DUSP2)|2 |1 |
48
+|[EBF1](../EBF1)|1 |1 |
49
+|[GNAI2](../GNAI2)|1 |1 |
50
+|[IRF4](../IRF4)|1 |1 |
51
+|[ITPKB](../ITPKB)|2 |1 |
52
+|[KLF2](../KLF2)|2 |1 |
53
+|[LTB](../LTB)|2 |1 |
54
+|[MYD88](../MYD88)|2 |1 |
55
+|[P2RY8](../P2RY8)|2 |1 |
56
+|[PIM1](../PIM1)|1 |1 |
57
+|[S1PR2](../S1PR2)|2 |1 |
58
+|[SOCS1](../SOCS1)|1 |1 |
59
+|[TBL1XR1](../TBL1XR1)|1 |1 |
60
+|[TMSB4X](../TMSB4X)|1 |1 |
61
+|[TNFAIP3](../TNFAIP3)|1 |1 |
62
+
63
+### Tier 2
64
+|New gene|FL tier|DLBCL tier|
65
+|:-|:-:|:-:|
66
+|[PTPRD](../PTPRD)|2 |2 |
67
+
68
+
69
+# Details
70
+
papers/dunsCharacterizationDLBCLPMBL2021.md
... ...
@@ -3,13 +3,13 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @dunsCharacterizationDLBCLPMBL2021b
6
+# @dunsCharacterizationDLBCLPMBL2021
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|6|8|
12
-|DLBCL|8|3|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|8|3|0|
12
+|PMBL|6|8|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -27,33 +27,36 @@ This study, New Tier 1, 6
27 27
New Tier 1, PMBL Tier 1, 6
28 28
This study, New Tier 2, 8
29 29
New Tier 2, PMBL Tier 2, 8
30
-All other PMBL studies, PMBL Tier 1, 70
31
-All other PMBL studies, PMBL Tier 2, 74
30
+This study, New Tier 3, 0
31
+New Tier 3, PMBL Tier 3, 0
32
+All other PMBL studies, PMBL Tier 1, 40
33
+All other PMBL studies, PMBL Tier 2, 104
34
+All other PMBL studies, PMBL Tier 3, 0
32 35
```
33 36
34 37
## Novel genes reported in this study
35 38
36 39
### Tier 1
37
-|New gene|PMBL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[CD83](../CD83)|1 |1 |
40
-|[CREBBP](../CREBBP)|1 |1 |
41
-|[DUSP2](../DUSP2)|1 |1 |
42
-|[FOXO1](../FOXO1)|2 |1 |
43
-|[IL4R](../IL4R)|1 |1 |
44
-|[MYC](../MYC)|2 |1 |
45
-|[PIM1](../PIM1)|1 |1 |
46
-|[SGK1](../SGK1)|1 |1 |
40
+|New gene|DLBCL tier|PMBL tier| Average variant quality | QC outcome |
41
+|:-|:-:|:-:|:-:|:-:|
42
+|[CD83](../CD83)|1 |1 || |
43
+|[CREBBP](../CREBBP)|1 |1 || |
44
+|[DUSP2](../DUSP2)|1 |1 || |
45
+|[FOXO1](../FOXO1)|1 |2 || |
46
+|[IL4R](../IL4R)|1 |1 || |
47
+|[MYC](../MYC)|1 |2 || |
48
+|[PIM1](../PIM1)|1 |1 || |
49
+|[SGK1](../SGK1)|1 |1 || |
47 50
48 51
### Tier 2
49
-|New gene|PMBL tier|DLBCL tier|
50
-|:-|:-:|:-:|
51
-|[BIRC3](../BIRC3)|2 |2 |
52
-|[HRNR](../HRNR)|2 | |
53
-|[LPHN3](../LPHN3)|2 | |
54
-|[MCL1](../MCL1)|2 |2 |
55
-|[RFTN1](../RFTN1)|2 |2 |
56
-|[WDR87](../WDR87)|2 | |
52
+|New gene|DLBCL tier|PMBL tier| Average variant quality | QC outcome |
53
+|:-|:-:|:-:|:-:|:-:|
54
+|[BIRC3](../BIRC3)|2 |2 || |
55
+|[HRNR](../HRNR)| |2 || |
56
+|[LPHN3](../LPHN3)| |2 || |
57
+|[MCL1](../MCL1)|2 |2 |★ ★ ★ ☆ ☆ |PASS |
58
+|[RFTN1](../RFTN1)|2 |2 || |
59
+|[WDR87](../WDR87)| |2 || |
57 60
58 61
59 62
# Details
papers/fanComprehensiveCharacterizationDriver2020.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @fanComprehensiveCharacterizationDriver2020b
6
+# @fanComprehensiveCharacterizationDriver2020
7 7
## Summary of novel genes
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|0|0|72|
11
+|DLBCL|1|0|73|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,17 +22,24 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, DLBCL Tier 1, 0
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-This study, New Tier 3, 72
30
-New Tier 3, DLBCL Tier 3, 72
31
-All other DLBCL studies, DLBCL Tier 1, 127
32
-All other DLBCL studies, DLBCL Tier 2, 172
33
-All other DLBCL studies, DLBCL Tier 3, 309
29
+This study, New Tier 3, 73
30
+New Tier 3, DLBCL Tier 3, 73
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 314
34 34
```
35 35
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[ACTG1](../ACTG1)|1 |
42
+
36 43
### Tier 3
37 44
|New gene|DLBCL tier|
38 45
|:-|:-:|
... ...
@@ -42,6 +49,7 @@ All other DLBCL studies, DLBCL Tier 3, 309
42 49
|[ATP6V0A1](../ATP6V0A1)|3 |
43 50
|[BRCA1](../BRCA1)|3 |
44 51
|[CBX3](../CBX3)|3 |
52
+|[CDH1](../CDH1)|3 |
45 53
|[CDKN1A](../CDKN1A)|3 |
46 54
|[CGN](../CGN)|3 |
47 55
|[CHEK2](../CHEK2)|3 |
papers/ganapathiGeneticLandscapeDural2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @ganapathiGeneticLandscapeDural2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, MZL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MZL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 41
30 32
All other MZL studies, MZL Tier 2, 74
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/gomezUltraDeepSequencingReveals2023.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @gomezUltraDeepSequencingReveals2023
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|2|5|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|2|9|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,10 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 2
26 26
New Tier 1, PMBL Tier 1, 2
27
-This study, New Tier 2, 5
28
-New Tier 2, PMBL Tier 2, 5
29
-All other PMBL studies, PMBL Tier 1, 74
30
-All other PMBL studies, PMBL Tier 2, 77
27
+This study, New Tier 2, 9
28
+New Tier 2, PMBL Tier 2, 9
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 44
32
+All other PMBL studies, PMBL Tier 2, 103
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -46,6 +49,10 @@ All other PMBL studies, PMBL Tier 2, 77
46 49
|[HLA-C](../HLA-C)|2 |
47 50
|[LIMD2](../LIMD2)|2 |
48 51
|[OR13C2](../OR13C2)|2 |
52
+|[PCDH7](../PCDH7)|2 |
53
+|[RDH12](../RDH12)|2 |
54
+|[SCN9A](../SCN9A)|2 |
55
+|[STRAP](../STRAP)|2 |
49 56
50 57
51 58
# Details
papers/grandeGenomewideDiscoverySomatic2019.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @grandeGenomewideDiscoverySomatic2019
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|9|4|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|11|2|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 9
26
-New Tier 1, BL Tier 1, 9
27
-This study, New Tier 2, 4
28
-New Tier 2, BL Tier 2, 4
29
-All other BL studies, BL Tier 1, 20
30
-All other BL studies, BL Tier 2, 153
25
+This study, New Tier 1, 11
26
+New Tier 1, BL Tier 1, 11
27
+This study, New Tier 2, 2
28
+New Tier 2, BL Tier 2, 2
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 21
32
+All other BL studies, BL Tier 2, 70
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,9 +38,11 @@ All other BL studies, BL Tier 2, 153
35 38
### Tier 1
36 39
|New gene|BL tier|
37 40
|:-|:-:|
41
+|[BACH2](../BACH2)|1 |
38 42
|[BCL7A](../BCL7A)|1 |
39 43
|[CHD8](../CHD8)|1 |
40 44
|[GNAI2](../GNAI2)|1 |
45
+|[HIST1H1E](../HIST1H1E)|1 |
41 46
|[KMT2D](../KMT2D)|1 |
42 47
|[RFX7](../RFX7)|1 |
43 48
|[SIN3A](../SIN3A)|1 |
... ...
@@ -48,9 +53,7 @@ All other BL studies, BL Tier 2, 153
48 53
### Tier 2
49 54
|New gene|BL tier|
50 55
|:-|:-:|
51
-|[BACH2](../BACH2)|2 |
52 56
|[CDKN2A](../CDKN2A)|2 |
53
-|[HIST1H1E](../HIST1H1E)|2 |
54 57
|[MIR142](../MIR142)|2 |
55 58
56 59
papers/gunawardanaRecurrentSomaticMutations2014.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @gunawardanaRecurrentSomaticMutations2014c
6
+# @gunawardanaRecurrentSomaticMutations2014
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/hubschmannMutationalMechanismsShaping2021.md
... ...
@@ -3,14 +3,13 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @hubschmannMutationalMechanismsShaping2021b
6
+# @hubschmannMutationalMechanismsShaping2021
7 7
## Summary of novel genes
8 8
9
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail rate |
10
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
-|DLBCL or FL|38|4|34|31|3| 9% |
12
-
13
-
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|2|16|0|
12
+|DLBCL|4|20|3|
14 13
```mermaid
15 14
---
16 15
config:
... ...
@@ -24,59 +23,70 @@ config:
24 23
suffix: ' genes)'
25 24
---
26 25
sankey-beta
27
-New to this study, FL or DLBCL Tier 1, 4
28
-New to this study, FL or DLBCL Tier 2, 34
29
-FL or DLBCL Tier 2, Pass QC, 31
30
-FL or DLBCL Tier 2, Fail QC, 3
26
+This study, New Tier 1, 4
27
+New Tier 1, DLBCL Tier 1, 4
28
+This study, New Tier 2, 20
29
+New Tier 2, DLBCL Tier 2, 20
30
+This study, New Tier 3, 3
31
+New Tier 3, DLBCL Tier 3, 3
32
+All other DLBCL studies, DLBCL Tier 1, 121
33
+All other DLBCL studies, DLBCL Tier 2, 190
34
+All other DLBCL studies, DLBCL Tier 3, 384
31 35
```
32 36
33 37
## Novel genes reported in this study
34 38
35 39
### Tier 1
36
-|New gene|FL tier|DLBCL tier|
37
-|:-|:-:|:-:|
38
-|[ACTG1](../ACTG1)|2 |1 |
39
-|[EEF1A1](../EEF1A1)|1 |1 |
40
-|[FBXO11](../FBXO11)| |1 |
41
-|[VMA21](../VMA21)|1 | |
40
+|New gene|FL tier|DLBCL tier| Average variant quality | QC outcome |
41
+|:-|:-:|:-:|:-:|:-:|
42
+|[ACTG1](../ACTG1)|2 |1 || |
43
+|[EEF1A1](../EEF1A1)|1 |1 || |
44
+|[HLA-DMB](../HLA-DMB)| |1 || |
45
+|[MEF2C](../MEF2C)|2 |1 || |
46
+|[VMA21](../VMA21)|1 | || |
42 47
43 48
### Tier 2
44
-|New gene|FL tier|DLBCL tier|Average variant quality|QC outcome|
49
+|New gene|FL tier|DLBCL tier| Average variant quality | QC outcome |
45 50
|:-|:-:|:-:|:-:|:-:|
46
-|[ADAMTS1](../ADAMTS1)| |2 |★ ★ ★ ☆ ☆ | **Pass** |
47
-|[ANKRD12](../ANKRD12)| |2 |★ ★ ★ ☆ ☆ | **Pass** |
48
-|[ATP6V1A](../ATP6V1A)|2 | |★ ★ ★ ★ ☆ | **Pass** |
49
-|[CADPS2](../CADPS2)| |2 |★ ★ ★ ★ ☆ | **Pass** |
50
-|[CDC42BPB](../CDC42BPB)|2 | |★ ★ ★ ☆ ☆|**Pass**|
51
-|[CNOT2](../CNOT2)| |2 |★ ★ ★ ★ ☆|**Pass**|
52
-|[CPNE8](../CPNE8)|2 | |★ ★ ★ ★ ☆|**Pass**|
53
-|[DHX15](../DHX15)|2 | |★ ★ ★ ★ ☆|**Pass**|
54
-|[DHX16](../DHX16)| |2 |★ ★ ★ ★ ☆|**Pass**|
55
-|[DNM2](../DNM2)| |2 |★ ★ ★ ☆ ☆|**Pass**|
56
-|[FZR1](../FZR1)|2 | |★ ★ ★ ☆ ☆|**Pass**|
57
-|[IKBKE](../IKBKE)| |2 |★ ★ ★ ★ ☆|**Pass**|
58
-|[IRF1](../IRF1)| |2 |★ ★ ★ ☆ ☆|**Pass**|
59
-|[JUP](../JUP)|2 | |★ ★ ★ ★ ☆|**Pass**|
60
-|[LAPTM5](../LAPTM5)|2 |2 |★ ★ ★ ★ ☆|**Pass**|
61
-|[LRP12](../LRP12)| |2 |★ ★ ★ ☆ ☆|**Pass**|
62
-|[MGEA5](../MGEA5)|2 | |★ ★ ★ ☆ ☆|**Pass**|
63
-|[MYCBP2](../MYCBP2)|2 | |★ ★ ★ ★ ☆|**Pass**|
64
-|[PDS5B](../PDS5B)|2 |2 |★ ★ ★ ☆ ☆|**Pass**|
65
-|[PNPO](../PNPO)| |2 |★ ★ ★ ☆ ☆|**Pass**|
66
-|[PPP4C](../PPP4C)|2 | |★ ★ ★ ★ ☆|**Pass**|
67
-|[PRKDC](../PRKDC)|2 |2 |★ ★ ★ ☆ ☆|**Pass**|
68
-|[RAC2](../RAC2)| |2 |★ ★ ★ ☆ ☆|**Pass**|
69
-|[RBM6](../RBM6)|2 | |★ ★ ★ ☆ ☆|**Pass**|
70
-|[SIAH2](../SIAH2)| |2 |★ ★ ★ ☆ ☆|**Pass**|
71
-|[SLC34A2](../SLC34A2)| |2 |★ ★ ★ ☆ ☆|**Pass**|
72
-|[TPP1](../TPP1)|2 | |★ ★ ★ ☆ ☆|**Pass**|
73
-|[TRAF6](../TRAF6)| |2 |★ ★ ★ ☆ ☆|**Pass**|
74
-|[UNC5B](../UNC5B)| |2 |★ ★ ★ ☆ ☆|**Pass**|
75
-|[WNK1](../WNK1)| |2 |★ ★ ★ ☆ ☆|**Pass**|
76
-|[ZNF217](../ZNF217)| |2 |★ ★ ★ ☆ ☆|**Pass**|
77
-|[HLA-DQA1](../HLA-DQA1)| |2 |★ ★☆ ☆ ☆|**Fail**|
78
-|[GAK](../GAK)| |2 |★ ★ ☆ ☆ ☆|**Fail**|
79
-|[NR2F2](../NR2F2)| |2 |★ ★ ☆ ☆ ☆|**Fail**|
51
+|[ADAMTS1](../ADAMTS1)| |2 |★ ★ ★ ☆ ☆ |PASS |
52
+|[ANKRD12](../ANKRD12)| |2 |★ ★ ★ ☆ ☆ |PASS |
53
+|[ATP6V1A](../ATP6V1A)|2 | || |
54
+|[CADPS2](../CADPS2)| |2 |★ ★ ★ ★ ☆ |PASS |
55
+|[CDC42BPB](../CDC42BPB)|2 | || |
56
+|[CNOT2](../CNOT2)| |2 |★ ★ ★ ★ ☆ |PASS |
57
+|[CPNE8](../CPNE8)|2 | || |
58
+|[DHX15](../DHX15)|2 | || |
59
+|[DHX16](../DHX16)| |2 |★ ★ ★ ★ ☆ |PASS |
60
+|[DNM2](../DNM2)| |2 |★ ★ ★ ☆ ☆ |PASS |
61
+|[FZR1](../FZR1)|2 | || |
62
+|[IKBKE](../IKBKE)| |2 |★ ★ ★ ★ ☆ |PASS |
63
+|[IRF1](../IRF1)| |2 |★ ★ ★ ☆ ☆ |PASS |
64
+|[JUP](../JUP)|2 | || |
65
+|[LAPTM5](../LAPTM5)|2 |2 |★ ★ ★ ★ ☆ |PASS |
66
+|[LRP12](../LRP12)| |2 |★ ★ ★ ☆ ☆ |PASS |
67
+|[MGEA5](../MGEA5)|2 | || |
68
+|[MYCBP2](../MYCBP2)|2 | || |
69
+|[PDS5B](../PDS5B)|2 |2 |★ ★ ★ ★ ☆ |PASS |
70
+|[PNPO](../PNPO)| |2 |★ ★ ★ ☆ ☆ |PASS |
71
+|[PPP4C](../PPP4C)|2 | || |
72
+|[PRKDC](../PRKDC)|2 |2 || |
73
+|[RAC2](../RAC2)| |2 |★ ★ ★ ☆ ☆ |PASS |
74
+|[RBM6](../RBM6)|2 | || |
75
+|[SIAH2](../SIAH2)| |2 |★ ★ ★ ☆ ☆ |PASS |
76
+|[SLC34A2](../SLC34A2)| |2 |★ ★ ★ ☆ ☆ |PASS |
77
+|[TPP1](../TPP1)|2 | || |
78
+|[TRAF6](../TRAF6)| |2 |★ ★ ★ ☆ ☆ |PASS |
79
+|[UNC5B](../UNC5B)| |2 |★ ★ ★ ☆ ☆ |PASS |
80
+|[WNK1](../WNK1)| |2 |★ ★ ★ ☆ ☆ |PASS |
81
+|[ZNF217](../ZNF217)| |2 |★ ★ ★ ☆ ☆ |PASS |
82
+
83
+### Tier 3
84
+|New gene|FL tier|DLBCL tier| Average variant quality | QC outcome |
85
+|:-|:-:|:-:|:-:|:-:|
86
+|[GAK](../GAK)| |3 |★ ★ ☆ ☆ ☆ |FAIL |
87
+|[HLA-DQA1](../HLA-DQA1)| |3 |★ ★ ☆ ☆ ☆ |FAIL |
88
+|[NR2F2](../NR2F2)| |3 |★ ★ ☆ ☆ ☆ |FAIL |
89
+
80 90
81 91
# Details
82 92
papers/jalladesExomeSequencingIdentifies2017.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @jalladesExomeSequencingIdentifies2017
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|2|26|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|2|26|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, MZL Tier 1, 2
27 27
This study, New Tier 2, 26
28 28
New Tier 2, MZL Tier 2, 26
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 40
30 32
All other MZL studies, MZL Tier 2, 48
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/jardinRecurrentMutationsExportin2016.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @jardinRecurrentMutationsExportin2016a
6
+# @jardinRecurrentMutationsExportin2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/johnstonCmycHypermutationBurkitt1992.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @johnstonCmycHypermutationBurkitt1992
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, BL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, BL Tier 2, 0
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 157
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 31
32
+All other BL studies, BL Tier 2, 72
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/khodabakhshiRecurrentTargetsAberrant2012.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @khodabakhshiRecurrentTargetsAberrant2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/krysiakRecurrentSomaticMutations2017.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @krysiakRecurrentSomaticMutations2017b
6
+# @krysiakRecurrentSomaticMutations2017
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|17|5|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|15|7|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 17
26
-New Tier 1, FL Tier 1, 17
27
-This study, New Tier 2, 5
28
-New Tier 2, FL Tier 2, 5
29
-All other FL studies, FL Tier 1, 49
30
-All other FL studies, FL Tier 2, 45
25
+This study, New Tier 1, 15
26
+New Tier 1, FL Tier 1, 15
27
+This study, New Tier 2, 7
28
+New Tier 2, FL Tier 2, 7
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 39
32
+All other FL studies, FL Tier 2, 52
33
+All other FL studies, FL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -45,9 +48,7 @@ All other FL studies, FL Tier 2, 45
45 48
|[HIST1H2AG](../HIST1H2AG)|1 |
46 49
|[HIST1H2AM](../HIST1H2AM)|1 |
47 50
|[HIST1H2BC](../HIST1H2BC)|1 |
48
-|[HIST1H2BD](../HIST1H2BD)|1 |
49 51
|[HIST1H2BG](../HIST1H2BG)|1 |
50
-|[HIST1H3G](../HIST1H3G)|1 |
51 52
|[HVCN1](../HVCN1)|1 |
52 53
|[POU2AF1](../POU2AF1)|1 |
53 54
|[POU2F2](../POU2F2)|1 |
... ...
@@ -58,7 +59,9 @@ All other FL studies, FL Tier 2, 45
58 59
|:-|:-:|
59 60
|[CXCR4](../CXCR4)|2 |
60 61
|[EGR1](../EGR1)|2 |
62
+|[HIST1H2BD](../HIST1H2BD)|2 |
61 63
|[HIST1H2BM](../HIST1H2BM)|2 |
64
+|[HIST1H3G](../HIST1H3G)|2 |
62 65
|[HIST1H3I](../HIST1H3I)|2 |
63 66
|[ZNF608](../ZNF608)|2 |
64 67
papers/kwanhianMicroRNA142Mutated202012.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @kwanhianMicroRNA142Mutated202012b
6
+# @kwanhianMicroRNA142Mutated202012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|0|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,18 +22,23 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 0
26
-New Tier 1, DLBCL Tier 1, 0
27
-This study, New Tier 2, 1
28
-New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 128
30
-All other DLBCL studies, DLBCL Tier 2, 197
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33
-### Tier 2
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
34 39
|New gene|DLBCL tier|
35 40
|:-|:-:|
36
-|[MIR142](../MIR142)|2 |
41
+|[MIR142](../MIR142)|1 |
37 42
38 43
39 44
# Details
papers/lenzOncogenicCARD11Mutations2008.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @lenzOncogenicCARD11Mutations2008
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/lohrDiscoveryPrioritizationSomatic2012.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @lohrDiscoveryPrioritizationSomatic2012a
6
+# @lohrDiscoveryPrioritizationSomatic2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|14|27|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,27 +22,67 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 3
26
-New Tier 1, DLBCL Tier 1, 3
27
-This study, New Tier 2, 1
28
-New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 125
30
-All other DLBCL studies, DLBCL Tier 2, 197
25
+This study, New Tier 1, 14
26
+New Tier 1, DLBCL Tier 1, 14
27
+This study, New Tier 2, 27
28
+New Tier 2, DLBCL Tier 2, 27
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 111
32
+All other DLBCL studies, DLBCL Tier 2, 183
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
34 37
35 38
### Tier 1
36
-|New gene|DLBCL tier|
37
-|:-|:-:|
38
-|[ACTB](../ACTB)|1 |
39
-|[KRAS](../KRAS)|1 |
40
-|[P2RY8](../P2RY8)|1 |
39
+|New gene|DLBCL tier| Average variant quality | QC outcome |
40
+|:-|:-:|:-:|:-:|
41
+|[ACTB](../ACTB)|1 || |
42
+|[DUSP2](../DUSP2)|1 || |
43
+|[ETV6](../ETV6)|1 || |
44
+|[HIST1H1E](../HIST1H1E)|1 || |
45
+|[HIST1H2BC](../HIST1H2BC)|1 || |
46
+|[HIST1H3B](../HIST1H3B)|1 || |
47
+|[HLA-A](../HLA-A)|1 || |
48
+|[HLA-B](../HLA-B)|1 || |
49
+|[JUNB](../JUNB)|1 |★ ★ ★ ☆ ☆ |PASS |
50
+|[KRAS](../KRAS)|1 || |
51
+|[P2RY8](../P2RY8)|1 || |
52
+|[POU2F2](../POU2F2)|1 || |
53
+|[TBL1XR1](../TBL1XR1)|1 || |
54
+|[UBE2A](../UBE2A)|1 || |
41 55
42 56
### Tier 2
43
-|New gene|DLBCL tier|
44
-|:-|:-:|
45
-|[PCLO](../PCLO)|2 |
57
+|New gene|DLBCL tier| Average variant quality | QC outcome |
58
+|:-|:-:|:-:|:-:|
59
+|[BCR](../BCR)|2 || |
60
+|[CPS1](../CPS1)|2 || |
61
+|[GABRA1](../GABRA1)|2 || |
62
+|[H1FOO](../H1FOO)|2 || |
63
+|[HIST1H2AL](../HIST1H2AL)|2 || |
64
+|[HIST1H2BO](../HIST1H2BO)|2 || |
65
+|[HIST1H3A](../HIST1H3A)|2 || |
66
+|[KRTAP5-5](../KRTAP5-5)|2 || |
67
+|[OR6K3](../OR6K3)|2 || |
68
+|[PASD1](../PASD1)|2 || |
69
+|[PCDHB6](../PCDHB6)|2 || |
70
+|[PCLO](../PCLO)|2 || |
71
+|[PDGFC](../PDGFC)|2 || |
72
+|[PTPN21](../PTPN21)|2 || |
73
+|[RBP3](../RBP3)|2 || |
74
+|[S1PR1](../S1PR1)|2 || |
75
+|[SLC38A8](../SLC38A8)|2 || |
76
+|[SLITRK6](../SLITRK6)|2 || |
77
+|[SRPX](../SRPX)|2 || |
78
+|[SYN2](../SYN2)|2 || |
79
+|[TBP](../TBP)|2 || |
80
+|[TMSL3](../TMSL3)|2 || |
81
+|[TNF](../TNF)|2 || |
82
+|[UNC5C](../UNC5C)|2 || |
83
+|[UNC5D](../UNC5D)|2 || |
84
+|[VAX1](../VAX1)|2 || |
85
+|[ZNF385B](../ZNF385B)|2 || |
46 86
47 87
48 88
# Details
papers/louissaintPediatrictypeNodalFollicular2016.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @louissaintPediatrictypeNodalFollicular2016a
6
+# @louissaintPediatrictypeNodalFollicular2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, FL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, FL Tier 2, 0
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 50
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 53
32
+All other FL studies, FL Tier 2, 59
33
+All other FL studies, FL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/loveGeneticLandscapeMutations2012.md
... ...
@@ -6,10 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @loveGeneticLandscapeMutations2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Total| Tier 1| Tier 2| Tier 2 Pass| Tier 2 Fail| Fail rate |
10
-|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
11
-|BL|60|3|57|9|48| 84% |
12
-
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|5|7|48|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -23,85 +22,91 @@ config:
23 22
suffix: ' genes)'
24 23
---
25 24
sankey-beta
26
-New to this study, BL Tier 1, 3
27
-New to this study, BL Tier 2, 56
28
-BL Tier 2, Pass QC, 9
29
-BL Tier 2, Fail QC, 47
25
+This study, New Tier 1, 5
26
+New Tier 1, BL Tier 1, 5
27
+This study, New Tier 2, 7
28
+New Tier 2, BL Tier 2, 7
29
+This study, New Tier 3, 48
30
+New Tier 3, BL Tier 3, 48
31
+All other BL studies, BL Tier 1, 27
32
+All other BL studies, BL Tier 2, 65
33
+All other BL studies, BL Tier 3, 22
30 34
```
31 35
32 36
## Novel genes reported in this study
33 37
34 38
### Tier 1
35
-|New gene|BL tier|
36
-|:-|:-:|
37
-|[ARID1A](../ARID1A)|1 |
38
-|[GNA13](../GNA13)|1 |
39
-|[PTEN](../PTEN)|1 |
39
+|New gene|BL tier| Average variant quality | QC outcome |
40
+|:-|:-:|:-:|:-:|
41
+|[ARID1A](../ARID1A)|1 || |
42
+|[BCL6](../BCL6)|1 |★ ★ ★ ★ ☆ |PASS |
43
+|[CREBBP](../CREBBP)|1 |★ ★ ★ ★ ☆ |PASS |
44
+|[GNA13](../GNA13)|1 || |
45
+|[PTEN](../PTEN)|1 || |
40 46
41 47
### Tier 2
42
-|Novel gene|DLBCL tier|Average variant quality|QC outcome|
48
+|New gene|BL tier| Average variant quality | QC outcome |
43 49
|:-|:-:|:-:|:-:|
44
-|[BCL6](../BCL6)|2 |★ ★ ★ ★ ☆|**Pass**|
45
-|[CARD4](../CARD4)|2 |★ ★ ★ ★ ☆|**Pass**|
46
-|[CDC73](../CDC73)|2 |★ ★ ★ ☆ ☆|**Pass**|
47
-|[CREBBP](../CREBBP)|2 |★ ★ ★ ★ ☆|**Pass**|
48
-|[EZH2](../EZH2)|2 |★ ★ ★ ★ ★|**Pass**|
49
-|[GGTLA4](../GGTLA4)|2 |★ ★ ★ ★ ☆|**Pass**|
50
-|[P2RY2](../P2RY2)|2 |★ ★ ★ ★ ☆|**Pass**|
51
-|[NBEAL1](../NBEAL1)|2 |★ ★ ★ ★ ☆|**Pass**|
52
-|[RANBP6](../RANBP6)|2 |★ ★ ★ ★ ★|**Pass**|
53
-|[ACAD9](../ACAD9)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
54
-|[ACE](../ACE)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
55
-|[ATP2C2](../ATP2C2)|2 |★ ★ ☆ ☆ ☆|**Fail**|
56
-|[BRAF](../BRAF)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
57
-|[BRD4](../BRD4)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
58
-|[BTG2](../BTG2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
59
-|[C6orf27](../C6orf27)|2 |*Germline*|**Fail**|
60
-|[CAD](../CAD)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
61
-|[CCT6B](../CCT6B)|2 |*Germline*|**Fail**|
62
-|[CDH17](../CDH17)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
63
-|[COL4A2](../COL4A2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
64
-|[CYB5D1](../CYB5D1)|2 |★ ★ ☆ ☆ ☆|**Fail**|
65
-|[CYP4F22](../CYP4F22)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
66
-|[DLGAP1](../DLGAP1)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
67
-|[DTX1](../DTX1)|2|★ ☆ ☆ ☆ ☆|**Fail**|
68
-|[EIF2C4](../EIF2C4)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
69
-|[EML2](../EML2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
70
-|[ENTPD3](../ENTPD3)|2 |★ ★ ☆ ☆ ☆|**Fail**|
71
-|[EPHB2](../EPHB2)|2 |★ ★ ☆ ☆ ☆|**Fail**|
72
-|[FAM129B](../FAM129B)|2 |★ ★ ☆ ☆ ☆|**Fail**|
73
-|[FGFR3](../FGFR3)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
74
-|[FTCD](../FTCD)|2 |*Germline*|**Fail**|
75
-|[GRIK5](../GRIK5)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
76
-|[ICK](../ICK)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
77
-|[ITPR3](../ITPR3)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
78
-|[KIFC3](../KIFC3)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
79
-|[MAP3K6](../MAP3K6)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
80
-|[MYH10](../MYH10)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
81
-|[NOTCH1](../NOTCH1)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
82
-|[NRXN2](../NRXN2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
83
-|[PC](../PC)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
84
-|[POLRMT](../POLRMT)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
85
-|[POR](../POR)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
86
-|[PRSS22](../PRSS22)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
87
-|[PTPRN](../PTPRN)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
88
-|[RBP3](../RBP3)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
89
-|[RET](../RET)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
90
-|[SALL3](../SALL3)|2 |★ ★ ☆ ☆ ☆|**Fail**|
91
-|[SAPS2](../SAPS2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
92
-|[SBF1](../SBF1)|2 |★ ★ ☆ ☆ ☆|**Fail**|
93
-|[SF3B1](../SF3B1)|2 |★ ★ ★ ★ ☆|**Fail**|
94
-|[SHANK1](../SHANK1)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
95
-|[SLC29A2](../SLC29A2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
96
-|[SYNGAP1](../SYNGAP1)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
97
-|[TBC1D9B](../TBC1D9B)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
98
-|[TIGD6](../TIGD6)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
99
-|[TPST2](../TPST2)|2 |☆ ☆ ☆ ☆ ☆|**Fail**|
100
-|[ZNF229](../ZNF229)|2 |*Germline*|**Fail**|
50
+|[CARD4](../CARD4)|2 |★ ★ ★ ★ ☆ |PASS |
51
+|[CDC73](../CDC73)|2 |★ ★ ★ ☆ ☆ |PASS |
52
+|[EZH2](../EZH2)|2 |★ ★ ★ ★ ★ |PASS |
53
+|[GGTLA4](../GGTLA4)|2 |★ ★ ★ ★ ☆ |PASS |
54
+|[NBEAL1](../NBEAL1)|2 |★ ★ ★ ★ ☆ |PASS |
55
+|[P2RY2](../P2RY2)|2 |★ ★ ★ ★ ☆ |PASS |
56
+|[RANBP6](../RANBP6)|2 |★ ★ ★ ★ ★ |PASS |
101 57
102
-## See Also
58
+### Tier 3
59
+|New gene|BL tier| Average variant quality | QC outcome |
60
+|:-|:-:|:-:|:-:|
61
+|[ACAD9](../ACAD9)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
62
+|[ACE](../ACE)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
63
+|[ATP2C2](../ATP2C2)|3 |★ ★ ☆ ☆ ☆ |FAIL |
64
+|[BRAF](../BRAF)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
65
+|[BRD4](../BRD4)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
66
+|[BTG2](../BTG2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
67
+|[C6orf27](../C6orf27)|3 |*Germline*|FAIL |
68
+|[CAD](../CAD)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
69
+|[CCT6B](../CCT6B)|3 |*Germline*|FAIL |
70
+|[CDH17](../CDH17)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
71
+|[COL4A2](../COL4A2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
72
+|[CYB5D1](../CYB5D1)|3 |★ ★ ☆ ☆ ☆ |FAIL |
73
+|[CYP4F22](../CYP4F22)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
74
+|[DLGAP1](../DLGAP1)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
75
+|[DTX1](../DTX1)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
76
+|[EIF2C4](../EIF2C4)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
77
+|[EML2](../EML2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
78
+|[ENTPD3](../ENTPD3)|3 |★ ★ ☆ ☆ ☆ |FAIL |
79
+|[EPHB2](../EPHB2)|3 |★ ★ ☆ ☆ ☆ |FAIL |
80
+|[FAM129B](../FAM129B)|3 |★ ★ ☆ ☆ ☆ |FAIL |
81
+|[FGFR3](../FGFR3)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
82
+|[FTCD](../FTCD)|3 |*Germline*|FAIL |
83
+|[GRIK5](../GRIK5)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
84
+|[ICK](../ICK)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
85
+|[ITPR3](../ITPR3)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
86
+|[KIFC3](../KIFC3)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
87
+|[MAP3K6](../MAP3K6)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
88
+|[MYH10](../MYH10)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
89
+|[NOTCH1](../NOTCH1)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
90
+|[NRXN2](../NRXN2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
91
+|[PC](../PC)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
92
+|[POLRMT](../POLRMT)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
93
+|[POR](../POR)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
94
+|[PRSS22](../PRSS22)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
95
+|[PTPRN](../PTPRN)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
96
+|[RBP3](../RBP3)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
97
+|[RET](../RET)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
98
+|[SALL3](../SALL3)|3 |★ ★ ☆ ☆ ☆ |FAIL |
99
+|[SAPS2](../SAPS2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
100
+|[SBF1](../SBF1)|3 |★ ★ ☆ ☆ ☆ |FAIL |
101
+|[SF3B1](../SF3B1)|3 |★ ★ ★ ★ ☆ |FAIL |
102
+|[SHANK1](../SHANK1)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
103
+|[SLC29A2](../SLC29A2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
104
+|[SYNGAP1](../SYNGAP1)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
105
+|[TBC1D9B](../TBC1D9B)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
106
+|[TIGD6](../TIGD6)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
107
+|[TPST2](../TPST2)|3 |☆ ☆ ☆ ☆ ☆ |FAIL |
108
+|[ZNF229](../ZNF229)|3 |*Germline*|FAIL |
103 109
104
-The primary data supporting each of the mutations reported in this study can be viewed in [IGV reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/)
105 110
106 111
# Details
107 112
papers/mansouriFrequentNFKBIEDeletions2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @mansouriFrequentNFKBIEDeletions2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/mareschalWholeExomeSequencing2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @mareschalWholeExomeSequencing2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 2
26
-New Tier 1, DLBCL Tier 1, 2
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 126
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,7 +38,6 @@ All other DLBCL studies, DLBCL Tier 2, 198
35 38
### Tier 1
36 39
|New gene|DLBCL tier|
37 40
|:-|:-:|
38
-|[TBL1XR1](../TBL1XR1)|1 |
39 41
|[XPO1](../XPO1)|1 |
40 42
41 43
papers/morinFrequentMutationHistonemodifying2011.md
... ...
@@ -8,8 +8,8 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|29|4|0|
12
-|FL|21|4|0|
11
+|FL|20|5|0|
12
+|DLBCL|31|3|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -23,59 +23,60 @@ config:
23 23
suffix: ' genes)'
24 24
---
25 25
sankey-beta
26
-This study, New Tier 1, 29
27
-New Tier 1, DLBCL Tier 1, 29
28
-This study, New Tier 2, 4
29
-New Tier 2, DLBCL Tier 2, 4
26
+This study, New Tier 1, 31
27
+New Tier 1, DLBCL Tier 1, 31
28
+This study, New Tier 2, 3
29
+New Tier 2, DLBCL Tier 2, 3
30 30
This study, New Tier 3, 0
31 31
New Tier 3, DLBCL Tier 3, 0
32
-All other DLBCL studies, DLBCL Tier 1, 100
33
-All other DLBCL studies, DLBCL Tier 2, 174
34
-All other DLBCL studies, DLBCL Tier 3, 385
32
+All other DLBCL studies, DLBCL Tier 1, 94
33
+All other DLBCL studies, DLBCL Tier 2, 207
34
+All other DLBCL studies, DLBCL Tier 3, 387
35 35
```
36 36
37 37
## Novel genes reported in this study
38 38
39 39
### Tier 1
40
-|New gene|DLBCL tier|FL tier|
40
+|New gene|FL tier|DLBCL tier|
41 41
|:-|:-:|:-:|
42 42
|[B2M](../B2M)|1 |1 |
43
-|[BCL10](../BCL10)|1 |2 |
43
+|[BCL10](../BCL10)|1 |1 |
44 44
|[BCL2](../BCL2)|1 |1 |
45 45
|[BCL6](../BCL6)|1 |1 |
46 46
|[BCL7A](../BCL7A)|1 |1 |
47
-|[BTG1](../BTG1)|1 |1 |
48
-|[BTG2](../BTG2)|1 |1 |
47
+|[BTG1](../BTG1)|2 |1 |
48
+|[BTG2](../BTG2)|2 |1 |
49 49
|[CARD11](../CARD11)|1 |1 |
50 50
|[CCND3](../CCND3)|1 |1 |
51
-|[CD58](../CD58)|1 | |
52
-|[CD70](../CD70)|1 |2 |
53
-|[CD79B](../CD79B)|1 |2 |
54
-|[ETS1](../ETS1)|1 | |
51
+|[CD58](../CD58)| |1 |
52
+|[CD70](../CD70)|2 |1 |
53
+|[CIITA](../CIITA)| |1 |
54
+|[ETS1](../ETS1)| |1 |
55
+|[FAS](../FAS)|1 |1 |
55 56
|[FOXO1](../FOXO1)|1 |1 |
56 57
|[GNA13](../GNA13)|1 |1 |
57 58
|[HIST1H1C](../HIST1H1C)|1 |1 |
58
-|[IKZF3](../IKZF3)|1 | |
59
+|[IKZF3](../IKZF3)| |1 |
59 60
|[IRF4](../IRF4)|1 |1 |
60 61
|[IRF8](../IRF8)|1 |1 |
61 62
|[KLHL6](../KLHL6)|1 |1 |
62 63
|[KMT2D](../KMT2D)|1 |1 |
63 64
|[MEF2B](../MEF2B)|1 |1 |
64
-|[S1PR2](../S1PR2)|1 |1 |
65
+|[S1PR2](../S1PR2)|2 |1 |
65 66
|[SGK1](../SGK1)|1 |1 |
66 67
|[SOCS1](../SOCS1)|1 |1 |
67
-|[TMEM30A](../TMEM30A)|1 |2 |
68
+|[STAT3](../STAT3)| |1 |
69
+|[TMEM30A](../TMEM30A)|2 |1 |
68 70
|[TNFRSF14](../TNFRSF14)|1 |1 |
69 71
|[TP53](../TP53)|1 |1 |
70
-|[ZFP36L1](../ZFP36L1)|1 | |
72
+|[ZFP36L1](../ZFP36L1)| |1 |
71 73
72 74
### Tier 2
73
-|New gene|DLBCL tier|FL tier|
75
+|New gene|FL tier|DLBCL tier|
74 76
|:-|:-:|:-:|
75
-|[CD274](../CD274)|2 | |
76
-|[CIITA](../CIITA)|2 | |
77
-|[FAT2](../FAT2)|2 | |
78
-|[RAPGEF1](../RAPGEF1)|2 | |
77
+|[CD274](../CD274)| |2 |
78
+|[FAT2](../FAT2)| |2 |
79
+|[RAPGEF1](../RAPGEF1)| |2 |
79 80
80 81
81 82
# Details
papers/morinGeneticLandscapesRelapsed2016.md
... ...
@@ -28,9 +28,9 @@ This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29 29
This study, New Tier 3, 0
30 30
New Tier 3, DLBCL Tier 3, 0
31
-All other DLBCL studies, DLBCL Tier 1, 127
32
-All other DLBCL studies, DLBCL Tier 2, 178
33
-All other DLBCL studies, DLBCL Tier 3, 385
31
+All other DLBCL studies, DLBCL Tier 1, 123
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34 34
```
35 35
36 36
## Novel genes reported in this study
papers/morinMutationalStructuralAnalysis2013.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|9|21|7|
11
+|DLBCL|9|23|7|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,13 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 9
26 26
New Tier 1, DLBCL Tier 1, 9
27
-This study, New Tier 2, 21
28
-New Tier 2, DLBCL Tier 2, 21
27
+This study, New Tier 2, 23
28
+New Tier 2, DLBCL Tier 2, 23
29 29
This study, New Tier 3, 7
30 30
New Tier 3, DLBCL Tier 3, 7
31
-All other DLBCL studies, DLBCL Tier 1, 120
32
-All other DLBCL studies, DLBCL Tier 2, 157
33
-All other DLBCL studies, DLBCL Tier 3, 378
31
+All other DLBCL studies, DLBCL Tier 1, 116
32
+All other DLBCL studies, DLBCL Tier 2, 187
33
+All other DLBCL studies, DLBCL Tier 3, 380
34 34
```
35 35
36 36
## Novel genes reported in this study
... ...
@@ -52,9 +52,11 @@ All other DLBCL studies, DLBCL Tier 3, 378
52 52
|New gene|DLBCL tier| Average variant quality | QC outcome |
53 53
|:-|:-:|:-:|:-:|
54 54
|[ABI3BP](../ABI3BP)|2 |★ ★ ★ ☆ ☆ |PASS |
55
+|[ARAP2](../ARAP2)|2 || |
55 56
|[CDH9](../CDH9)|2 |★ ★ ★ ☆ ☆ |PASS |
56 57
|[CNTNAP5](../CNTNAP5)|2 |★ ★ ★ ★ ☆ |PASS |
57 58
|[DNAH5](../DNAH5)|2 |★ ★ ★ ★ ☆ |PASS |
59
+|[DSEL](../DSEL)|2 || |
58 60
|[DSG4](../DSG4)|2 |★ ★ ★ ☆ ☆ |PASS |
59 61
|[FAT4](../FAT4)|2 |★ ★ ★ ☆ ☆ |PASS |
60 62
|[HDAC7](../HDAC7)|2 |★ ★ ★ ☆ ☆ |PASS |
... ...
@@ -62,7 +64,7 @@ All other DLBCL studies, DLBCL Tier 3, 378
62 64
|[IFNGR1](../IFNGR1)|2 |★ ★ ★ ★ ☆ |PASS |
63 65
|[MPDZ](../MPDZ)|2 |★ ★ ★ ★ ☆ |PASS |
64 66
|[NLRP5](../NLRP5)|2 |★ ★ ★ ☆ ☆ |PASS |
65
-|[ODZ3](../ODZ3)|2 |★ ★ ★ ☆ ☆ |PASS |
67
+|[ODZ2](../ODZ2)|2 |★ ★ ★ ☆ ☆ |PASS |
66 68
|[P2RX5](../P2RX5)|2 |★ ★ ★ ☆ ☆ |PASS |
67 69
|[PASK](../PASK)|2 |★ ★ ★ ★ ☆ |PASS |
68 70
|[PCDHB11](../PCDHB11)|2 |★ ★ ★ ☆ ☆ |PASS |
papers/morinSomaticMutationsAltering2010.md
... ...
@@ -3,7 +3,7 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @morinSomaticMutationsAltering2010a
6
+# @morinSomaticMutationsAltering2010
7 7
## Summary of novel genes
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
... ...
@@ -24,14 +24,14 @@ config:
24 24
---
25 25
sankey-beta
26 26
This study, New Tier 1, 1
27
-New Tier 1, FL Tier 1, 1
27
+New Tier 1, DLBCL Tier 1, 1
28 28
This study, New Tier 2, 0
29
-New Tier 2, FL Tier 2, 0
29
+New Tier 2, DLBCL Tier 2, 0
30 30
This study, New Tier 3, 0
31
-New Tier 3, FL Tier 3, 0
32
-All other FL studies, FL Tier 1, 65
33
-All other FL studies, FL Tier 2, 49
34
-All other FL studies, FL Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
32
+All other DLBCL studies, DLBCL Tier 1, 124
33
+All other DLBCL studies, DLBCL Tier 2, 210
34
+All other DLBCL studies, DLBCL Tier 3, 387
35 35
```
36 36
37 37
## Novel genes reported in this study
papers/mottokGenomicAlterationsCIITA2015.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @mottokGenomicAlterationsCIITA2015b
6
+# @mottokGenomicAlterationsCIITA2015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/mottokIntegrativeGenomicAnalysis2019.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @mottokIntegrativeGenomicAnalysis2019b
6
+# @mottokIntegrativeGenomicAnalysis2019
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|6|15|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|6|15|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 6
26 26
New Tier 1, PMBL Tier 1, 6
27 27
This study, New Tier 2, 15
28 28
New Tier 2, PMBL Tier 2, 15
29
-All other PMBL studies, PMBL Tier 1, 70
30
-All other PMBL studies, PMBL Tier 2, 67
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 40
32
+All other PMBL studies, PMBL Tier 2, 97
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/muppidiLossSignalingGa132014.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @muppidiLossSignalingGa132014b
6
+# @muppidiLossSignalingGa132014
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|2|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|1|2|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, BL Tier 1, 1
27 27
This study, New Tier 2, 2
28 28
New Tier 2, BL Tier 2, 2
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 155
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 31
32
+All other BL studies, BL Tier 2, 70
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/ngoOncogenicallyActiveMYD882011.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @ngoOncogenicallyActiveMYD882011a
6
+# @ngoOncogenicallyActiveMYD882011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/okosunRecurrentMTORC1activatingRRAGC2016.md
... ...
@@ -3,13 +3,13 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @okosunRecurrentMTORC1activatingRRAGC2016a
6
+# @okosunRecurrentMTORC1activatingRRAGC2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-|FL|3|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|3|0|0|
12
+|DLBCL|1|0|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -27,17 +27,20 @@ This study, New Tier 1, 3
27 27
New Tier 1, FL Tier 1, 3
28 28
This study, New Tier 2, 0
29 29
New Tier 2, FL Tier 2, 0
30
-All other FL studies, FL Tier 1, 63
31
-All other FL studies, FL Tier 2, 50
30
+This study, New Tier 3, 0
31
+New Tier 3, FL Tier 3, 0
32
+All other FL studies, FL Tier 1, 51
33
+All other FL studies, FL Tier 2, 59
34
+All other FL studies, FL Tier 3, 0
32 35
```
33 36
34 37
## Novel genes reported in this study
35 38
36 39
### Tier 1
37
-|New gene|DLBCL tier|FL tier|
40
+|New gene|FL tier|DLBCL tier|
38 41
|:-|:-:|:-:|
39
-|[ATP6AP1](../ATP6AP1)| |1 |
40
-|[ATP6V1B2](../ATP6V1B2)| |1 |
42
+|[ATP6AP1](../ATP6AP1)|1 | |
43
+|[ATP6V1B2](../ATP6V1B2)|1 | |
41 44
|[RRAGC](../RRAGC)|1 |1 |
42 45
43 46
papers/ottoGeneticLesionsTRAF32012.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @ottoGeneticLesionsTRAF32012a
6
+# @ottoGeneticLesionsTRAF32012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|2|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|2|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, PMBL Tier 1, 2
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 74
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 44
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/paneaWholeGenomeLandscape2019.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|BL|4|13|22|
11
+|BL|2|15|22|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,14 +22,14 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 4
26
-New Tier 1, BL Tier 1, 4
27
-This study, New Tier 2, 13
28
-New Tier 2, BL Tier 2, 13
25
+This study, New Tier 1, 2
26
+New Tier 1, BL Tier 1, 2
27
+This study, New Tier 2, 15
28
+New Tier 2, BL Tier 2, 15
29 29
This study, New Tier 3, 22
30 30
New Tier 3, BL Tier 3, 22
31
-All other BL studies, BL Tier 1, 25
32
-All other BL studies, BL Tier 2, 62
31
+All other BL studies, BL Tier 1, 30
32
+All other BL studies, BL Tier 2, 57
33 33
All other BL studies, BL Tier 3, 48
34 34
```
35 35
... ...
@@ -39,8 +39,6 @@ All other BL studies, BL Tier 3, 48
39 39
|New gene|BL tier| Average variant quality | QC outcome |
40 40
|:-|:-:|:-:|:-:|
41 41
|[BMP7](../BMP7)|1 || |
42
-|[EIF4A1](../EIF4A1)|1 || |
43
-|[EPPK1](../EPPK1)|1 || |
44 42
|[HNRNPU](../HNRNPU)|1 || |
45 43
46 44
### Tier 2
... ...
@@ -48,6 +46,8 @@ All other BL studies, BL Tier 3, 48
48 46
|:-|:-:|:-:|:-:|
49 47
|[CD83](../CD83)|2 |★ ★ ★ ☆ ☆ |PASS |
50 48
|[CXCR4](../CXCR4)|2 |★ ★ ★ ★ ☆ |PASS |
49
+|[EIF4A1](../EIF4A1)|2 || |
50
+|[EPPK1](../EPPK1)|2 || |
51 51
|[HIST1H3D](../HIST1H3D)|2 |★ ★ ★ ☆ ☆ |PASS |
52 52
|[HIST1H3I](../HIST1H3I)|2 |★ ★ ★ ★ ☆ |PASS |
53 53
|[HIST1H4J](../HIST1H4J)|2 |★ ★ ★ ☆ ☆ |PASS |
papers/pararajalingamCodingNoncodingDrivers2020.md
... ...
@@ -6,10 +6,10 @@ bibliography: 'morinlab.bib'
6 6
# @pararajalingamCodingNoncodingDrivers2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|3|
12
-|MCL|6|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|4|0|
12
+|MCL|6|1|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -27,8 +27,11 @@ This study, New Tier 1, 6
27 27
New Tier 1, MCL Tier 1, 6
28 28
This study, New Tier 2, 1
29 29
New Tier 2, MCL Tier 2, 1
30
+This study, New Tier 3, 0
31
+New Tier 3, MCL Tier 3, 0
30 32
All other MCL studies, MCL Tier 1, 17
31 33
All other MCL studies, MCL Tier 2, 45
34
+All other MCL studies, MCL Tier 3, 0
32 35
```
33 36
34 37
## Novel genes reported in this study
... ...
@@ -41,7 +44,7 @@ All other MCL studies, MCL Tier 2, 45
41 44
|[EWSR1](../EWSR1)| |1 |
42 45
|[HNRNPH1](../HNRNPH1)|2 |1 |
43 46
|[NFKBIE](../NFKBIE)|1 |1 |
44
-|[S1PR1](../S1PR1)| |1 |
47
+|[S1PR1](../S1PR1)|2 |1 |
45 48
|[UBR5](../UBR5)|2 |1 |
46 49
47 50
papers/parryWholeExomeSequencing2013.md
... ...
@@ -6,10 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @parryWholeExomeSequencing2013
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|0|8|
12
-|DLBCL|3|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|0|7|0|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -25,29 +24,25 @@ config:
25 24
sankey-beta
26 25
This study, New Tier 1, 0
27 26
New Tier 1, MZL Tier 1, 0
28
-This study, New Tier 2, 8
29
-New Tier 2, MZL Tier 2, 8
27
+This study, New Tier 2, 7
28
+New Tier 2, MZL Tier 2, 7
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
30 31
All other MZL studies, MZL Tier 1, 42
31
-All other MZL studies, MZL Tier 2, 66
32
+All other MZL studies, MZL Tier 2, 67
33
+All other MZL studies, MZL Tier 3, 0
32 34
```
33 35
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|MZL tier|DLBCL tier|
38
-|:-|:-:|:-:|
39
-|[CREBBP](../CREBBP)|2 |1 |
40
-|[FBXO11](../FBXO11)|2 |1 |
41
-|[TRRAP](../TRRAP)|2 |1 |
42
-
43 36
### Tier 2
44
-|New gene|MZL tier|DLBCL tier|
45
-|:-|:-:|:-:|
46
-|[AMOTL1](../AMOTL1)|2 | |
47
-|[CBFA2T3](../CBFA2T3)|2 | |
48
-|[FAT4](../FAT4)|2 |2 |
49
-|[PLA2G4D](../PLA2G4D)|2 | |
50
-|[USH2A](../USH2A)|2 | |
37
+|New gene|MZL tier|
38
+|:-|:-:|
39
+|[AMOTL1](../AMOTL1)|2 |
40
+|[CBFA2T3](../CBFA2T3)|2 |
41
+|[CREBBP](../CREBBP)|2 |
42
+|[FAT4](../FAT4)|2 |
43
+|[FBXO11](../FBXO11)|2 |
44
+|[PLA2G4D](../PLA2G4D)|2 |
45
+|[USH2A](../USH2A)|2 |
51 46
52 47
53 48
# Details
papers/pasqualucciAnalysisCodingGenome2011.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @pasqualucciAnalysisCodingGenome2011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|3|4|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|3|35|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,10 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 3
26 26
New Tier 1, DLBCL Tier 1, 3
27
-This study, New Tier 2, 4
28
-New Tier 2, DLBCL Tier 2, 4
29
-All other DLBCL studies, DLBCL Tier 1, 125
30
-All other DLBCL studies, DLBCL Tier 2, 194
27
+This study, New Tier 2, 35
28
+New Tier 2, DLBCL Tier 2, 35
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 122
32
+All other DLBCL studies, DLBCL Tier 2, 175
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -42,10 +45,41 @@ All other DLBCL studies, DLBCL Tier 2, 194
42 45
### Tier 2
43 46
|New gene|DLBCL tier|
44 47
|:-|:-:|
48
+|[ADAMTSL3](../ADAMTSL3)|2 |
49
+|[AKAP8](../AKAP8)|2 |
50
+|[ANKLE2](../ANKLE2)|2 |
51
+|[BCL2L10](../BCL2L10)|2 |
52
+|[BRSK1](../BRSK1)|2 |
53
+|[C12orf35](../C12orf35)|2 |
54
+|[CAMTA1](../CAMTA1)|2 |
45 55
|[CD36](../CD36)|2 |
56
+|[CYTSB](../CYTSB)|2 |
57
+|[DCHS1](../DCHS1)|2 |
58
+|[DPYD](../DPYD)|2 |
59
+|[DSC3](../DSC3)|2 |
60
+|[DUSP27](../DUSP27)|2 |
61
+|[DUSP9](../DUSP9)|2 |
62
+|[FBXO31](../FBXO31)|2 |
63
+|[HMGB1](../HMGB1)|2 |
46 64
|[HNF1B](../HNF1B)|2 |
65
+|[KDM2B](../KDM2B)|2 |
66
+|[MAGEC3](../MAGEC3)|2 |
67
+|[MED12L](../MED12L)|2 |
68
+|[MTMR8](../MTMR8)|2 |
69
+|[MYO1G](../MYO1G)|2 |
47 70
|[MYOM2](../MYOM2)|2 |
71
+|[OFD1](../OFD1)|2 |
72
+|[PMS1](../PMS1)|2 |
73
+|[PPP2R5A](../PPP2R5A)|2 |
74
+|[RASGEF1A](../RASGEF1A)|2 |
75
+|[RGAG1](../RGAG1)|2 |
76
+|[SERPINA1](../SERPINA1)|2 |
77
+|[SMARCA1](../SMARCA1)|2 |
78
+|[TLL2](../TLL2)|2 |
48 79
|[TRAF3](../TRAF3)|2 |
80
+|[TSC22D1](../TSC22D1)|2 |
81
+|[ZNF521](../ZNF521)|2 |
82
+|[ZWILCH](../ZWILCH)|2 |
49 83
50 84
51 85
# Details
papers/pasqualucciHypermutationMultipleProtooncogenes2001.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @pasqualucciHypermutationMultipleProtooncogenes2001a
6
+# @pasqualucciHypermutationMultipleProtooncogenes2001
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|2|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|2|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, DLBCL Tier 1, 2
27 27
This study, New Tier 2, 2
28 28
New Tier 2, DLBCL Tier 2, 2
29
-All other DLBCL studies, DLBCL Tier 1, 126
30
-All other DLBCL studies, DLBCL Tier 2, 196
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 123
32
+All other DLBCL studies, DLBCL Tier 2, 208
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/pasqualucciInactivatingMutationsAcetyltransferase2011.md
... ...
@@ -3,13 +3,13 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @pasqualucciInactivatingMutationsAcetyltransferase2011a
6
+# @pasqualucciInactivatingMutationsAcetyltransferase2011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|0|
12
-|FL|2|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|2|0|0|
12
+|FL|2|0|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -24,11 +24,14 @@ config:
24 24
---
25 25
sankey-beta
26 26
This study, New Tier 1, 2
27
-New Tier 1, FL Tier 1, 2
27
+New Tier 1, DLBCL Tier 1, 2
28 28
This study, New Tier 2, 0
29
-New Tier 2, FL Tier 2, 0
30
-All other FL studies, FL Tier 1, 64
31
-All other FL studies, FL Tier 2, 50
29
+New Tier 2, DLBCL Tier 2, 0
30
+This study, New Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
32
+All other DLBCL studies, DLBCL Tier 1, 123
33
+All other DLBCL studies, DLBCL Tier 2, 210
34
+All other DLBCL studies, DLBCL Tier 3, 387
32 35
```
33 36
34 37
## Novel genes reported in this study
papers/pasqualucciInactivationPRDM1BLIMP12006.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @pasqualucciInactivationPRDM1BLIMP12006a
6
+# @pasqualucciInactivationPRDM1BLIMP12006
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/reddyGeneticFunctionalDrivers2017.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|10|24|26|
11
+|DLBCL|13|28|26|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,15 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 10
26
-New Tier 1, DLBCL Tier 1, 10
27
-This study, New Tier 2, 24
28
-New Tier 2, DLBCL Tier 2, 24
25
+This study, New Tier 1, 13
26
+New Tier 1, DLBCL Tier 1, 13
27
+This study, New Tier 2, 28
28
+New Tier 2, DLBCL Tier 2, 28
29 29
This study, New Tier 3, 26
30 30
New Tier 3, DLBCL Tier 3, 26
31
-All other DLBCL studies, DLBCL Tier 1, 119
32
-All other DLBCL studies, DLBCL Tier 2, 154
33
-All other DLBCL studies, DLBCL Tier 3, 359
31
+All other DLBCL studies, DLBCL Tier 1, 112
32
+All other DLBCL studies, DLBCL Tier 2, 182
33
+All other DLBCL studies, DLBCL Tier 3, 361
34 34
```
35 35
36 36
## Novel genes reported in this study
... ...
@@ -42,10 +42,13 @@ All other DLBCL studies, DLBCL Tier 3, 359
42 42
|[BIRC6](../BIRC6)|1 || |
43 43
|[DDX3X](../DDX3X)|1 || |
44 44
|[HNRNPU](../HNRNPU)|1 || |
45
-|[JUNB](../JUNB)|1 |★ ★ ★ ☆ ☆ |PASS |
46 45
|[MGA](../MGA)|1 || |
46
+|[PIM2](../PIM2)|1 || |
47 47
|[PTEN](../PTEN)|1 || |
48
+|[PTPN6](../PTPN6)|1 |★ ★ ★ ☆ ☆ |PASS |
48 49
|[SF3B1](../SF3B1)|1 || |
50
+|[SMARCA4](../SMARCA4)|1 || |
51
+|[TMSB4X](../TMSB4X)|1 || |
49 52
|[TOX](../TOX)|1 || |
50 53
|[ZNF292](../ZNF292)|1 || |
51 54
... ...
@@ -63,18 +66,22 @@ All other DLBCL studies, DLBCL Tier 3, 359
63 66
|[HNRNPD](../HNRNPD)|2 || |
64 67
|[IKBKB](../IKBKB)|2 |★ ★ ★ ☆ ☆ |PASS |
65 68
|[IL16](../IL16)|2 || |
69
+|[INO80](../INO80)|2 || |
70
+|[JAK1](../JAK1)|2 || |
71
+|[JAK3](../JAK3)|2 || |
66 72
|[KCMF1](../KCMF1)|2 |★ ★ ★ ☆ ☆ |PASS |
67 73
|[MAGT1](../MAGT1)|2 |★ ★ ★ ☆ ☆ |PASS |
68 74
|[MCL1](../MCL1)|2 |★ ★ ★ ☆ ☆ |PASS |
69 75
|[MECOM](../MECOM)|2 |★ ★ ★ ☆ ☆ |PASS |
70 76
|[MET](../MET)|2 |★ ★ ★ ☆ ☆ |PASS |
71 77
|[MSH6](../MSH6)|2 |★ ★ ★ ☆ ☆ |PASS |
72
-|[PTPN6](../PTPN6)|2 |★ ★ ★ ☆ ☆ |PASS |
73 78
|[SETD5](../SETD5)|2 |★ ★ ★ ☆ ☆ |PASS |
79
+|[STAT5B](../STAT5B)|2 || |
74 80
|[TCL1A](../TCL1A)|2 || |
75 81
|[TGFBR2](../TGFBR2)|2 |★ ★ ★ ☆ ☆ |PASS |
76 82
|[TIPARP](../TIPARP)|2 |★ ★ ★ ☆ ☆ |PASS |
77 83
|[YY1](../YY1)|2 |★ ★ ★ ☆ ☆ |PASS |
84
+|[ZEB2](../ZEB2)|2 || |
78 85
|[ZFX](../ZFX)|2 |★ ★ ★ ☆ ☆ |PASS |
79 86
80 87
### Tier 3
papers/reichelFlowSortingExome2015.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @reichelFlowSortingExome2015a
6
+# @reichelFlowSortingExome2015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|11|18|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|11|18|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 11
26 26
New Tier 1, PMBL Tier 1, 11
27 27
This study, New Tier 2, 18
28 28
New Tier 2, PMBL Tier 2, 18
29
-All other PMBL studies, PMBL Tier 1, 65
30
-All other PMBL studies, PMBL Tier 2, 64
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 35
32
+All other PMBL studies, PMBL Tier 2, 94
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/richterRecurrentMutationID32012.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @richterRecurrentMutationID32012a
6
+# @richterRecurrentMutationID32012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|5|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|5|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 5
26 26
New Tier 1, BL Tier 1, 5
27 27
This study, New Tier 2, 0
28 28
New Tier 2, BL Tier 2, 0
29
-All other BL studies, BL Tier 1, 24
30
-All other BL studies, BL Tier 2, 157
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 27
32
+All other BL studies, BL Tier 2, 72
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/ritzRecurrentMutationsSTAT62009.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @ritzRecurrentMutationsSTAT62009a
6
+# @ritzRecurrentMutationsSTAT62009
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/rossiAlterationBIRC3Multiple2011.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @rossiAlterationBIRC3Multiple2011a
6
+# @rossiAlterationBIRC3Multiple2011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|4|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|4|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 4
26 26
New Tier 1, MZL Tier 1, 4
27 27
This study, New Tier 2, 1
28 28
New Tier 2, MZL Tier 2, 1
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 38
30 32
All other MZL studies, MZL Tier 2, 73
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/rossiCodingGenomeSplenic2012.md
... ...
@@ -0,0 +1,69 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @rossiCodingGenomeSplenic2012
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|10|11|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 10
26
+New Tier 1, MZL Tier 1, 10
27
+This study, New Tier 2, 11
28
+New Tier 2, MZL Tier 2, 11
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
31
+All other MZL studies, MZL Tier 1, 32
32
+All other MZL studies, MZL Tier 2, 63
33
+All other MZL studies, MZL Tier 3, 0
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|MZL tier|
40
+|:-|:-:|
41
+|[ARID1A](../ARID1A)|1 |
42
+|[DTX1](../DTX1)|1 |
43
+|[EP300](../EP300)|1 |
44
+|[KMT2D](../KMT2D)|1 |
45
+|[NOTCH1](../NOTCH1)|1 |
46
+|[NOTCH2](../NOTCH2)|1 |
47
+|[SIN3A](../SIN3A)|1 |
48
+|[SPEN](../SPEN)|1 |
49
+|[TBL1XR1](../TBL1XR1)|1 |
50
+|[TP53](../TP53)|1 |
51
+
52
+### Tier 2
53
+|New gene|MZL tier|
54
+|:-|:-:|
55
+|[CD79A](../CD79A)|2 |
56
+|[EGR1](../EGR1)|2 |
57
+|[EGR2](../EGR2)|2 |
58
+|[GPS2](../GPS2)|2 |
59
+|[HIST1H2AG](../HIST1H2AG)|2 |
60
+|[HIST1H2BK](../HIST1H2BK)|2 |
61
+|[MCRS1](../MCRS1)|2 |
62
+|[MSL2](../MSL2)|2 |
63
+|[SWAP70](../SWAP70)|2 |
64
+|[TRRAP](../TRRAP)|2 |
65
+|[WAC](../WAC)|2 |
66
+
67
+
68
+# Details
69
+
papers/rossiCodingGenomeSplenic2012c.md
... ...
@@ -1,67 +0,0 @@
1
----
2
-title: ''
3
-bibliography: 'morinlab.bib'
4
----
5
-
6
-# @rossiCodingGenomeSplenic2012c
7
-## Summary of novel genes
8
-
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|12|2|
12
-|MZL|10|11|
13
-```mermaid
14
----
15
-config:
16
- sankey:
17
- showValues: true
18
- linkColor: target
19
- width: 600
20
- height: 300
21
- nodeAlignment: right
22
- prefix: '('
23
- suffix: ' genes)'
24
----
25
-sankey-beta
26
-This study, New Tier 1, 10
27
-New Tier 1, MZL Tier 1, 10
28
-This study, New Tier 2, 11
29
-New Tier 2, MZL Tier 2, 11
30
-All other MZL studies, MZL Tier 1, 32
31
-All other MZL studies, MZL Tier 2, 63
32
-```
33
-
34
-## Novel genes reported in this study
35
-
36
-### Tier 1
37
-|New gene|DLBCL tier|MZL tier|
38
-|:-|:-:|:-:|
39
-|[ARID1A](../ARID1A)|1 |1 |
40
-|[DTX1](../DTX1)|1 |1 |
41
-|[EP300](../EP300)|1 |1 |
42
-|[HIST1H2BK](../HIST1H2BK)|1 |2 |
43
-|[KMT2D](../KMT2D)|1 |1 |
44
-|[NOTCH1](../NOTCH1)|1 |1 |
45
-|[NOTCH2](../NOTCH2)|1 |1 |
46
-|[SIN3A](../SIN3A)|1 |1 |
47
-|[SPEN](../SPEN)|1 |1 |
48
-|[TBL1XR1](../TBL1XR1)|1 |1 |
49
-|[TP53](../TP53)|1 |1 |
50
-|[TRRAP](../TRRAP)|1 |2 |
51
-
52
-### Tier 2
53
-|New gene|DLBCL tier|MZL tier|
54
-|:-|:-:|:-:|
55
-|[CD79A](../CD79A)| |2 |
56
-|[EGR1](../EGR1)| |2 |
57
-|[EGR2](../EGR2)| |2 |
58
-|[GPS2](../GPS2)| |2 |
59
-|[HIST1H2AG](../HIST1H2AG)|2 |2 |
60
-|[MCRS1](../MCRS1)| |2 |
61
-|[MSL2](../MSL2)| |2 |
62
-|[SWAP70](../SWAP70)| |2 |
63
-|[WAC](../WAC)|2 |2 |
64
-
65
-
66
-# Details
67
-
papers/rushtonGeneticEvolutionaryPatterns2020.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @rushtonGeneticEvolutionaryPatterns2020
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/russler-germainMutationsAssociatedProgression2023.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @russler-germainMutationsAssociatedProgression2023b
6
+# @russler-germainMutationsAssociatedProgression2023
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|FL|1|19|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|FL|2|18|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 1
26
-New Tier 1, FL Tier 1, 1
27
-This study, New Tier 2, 19
28
-New Tier 2, FL Tier 2, 19
29
-All other FL studies, FL Tier 1, 65
30
-All other FL studies, FL Tier 2, 31
25
+This study, New Tier 1, 2
26
+New Tier 1, FL Tier 1, 2
27
+This study, New Tier 2, 18
28
+New Tier 2, FL Tier 2, 18
29
+This study, New Tier 3, 0
30
+New Tier 3, FL Tier 3, 0
31
+All other FL studies, FL Tier 1, 52
32
+All other FL studies, FL Tier 2, 41
33
+All other FL studies, FL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,13 +38,13 @@ All other FL studies, FL Tier 2, 31
35 38
### Tier 1
36 39
|New gene|FL tier|
37 40
|:-|:-:|
41
+|[BCL10](../BCL10)|1 |
38 42
|[CD83](../CD83)|1 |
39 43
40 44
### Tier 2
41 45
|New gene|FL tier|
42 46
|:-|:-:|
43 47
|[ABL2](../ABL2)|2 |
44
-|[BCL10](../BCL10)|2 |
45 48
|[CD70](../CD70)|2 |
46 49
|[CILP](../CILP)|2 |
47 50
|[CYP2A6](../CYP2A6)|2 |
papers/sarkozyMutationalLandscapeGray2021.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @sarkozyMutationalLandscapeGray2021a
6
+# @sarkozyMutationalLandscapeGray2021
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|5|6|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|5|6|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 5
26 26
New Tier 1, PMBL Tier 1, 5
27 27
This study, New Tier 2, 6
28 28
New Tier 2, PMBL Tier 2, 6
29
-All other PMBL studies, PMBL Tier 1, 71
30
-All other PMBL studies, PMBL Tier 2, 76
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 41
32
+All other PMBL studies, PMBL Tier 2, 106
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/schmitzBurkittLymphomaPathogenesis2012.md
... ...
@@ -6,10 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @schmitzBurkittLymphomaPathogenesis2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|2|3|
12
-|BL|4|16|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|4|15|0|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -25,41 +24,43 @@ config:
25 24
sankey-beta
26 25
This study, New Tier 1, 4
27 26
New Tier 1, BL Tier 1, 4
28
-This study, New Tier 2, 16
29
-New Tier 2, BL Tier 2, 16
30
-All other BL studies, BL Tier 1, 25
31
-All other BL studies, BL Tier 2, 141
27
+This study, New Tier 2, 15
28
+New Tier 2, BL Tier 2, 15
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 28
32
+All other BL studies, BL Tier 2, 57
33
+All other BL studies, BL Tier 3, 70
32 34
```
33 35
34 36
## Novel genes reported in this study
35 37
36 38
### Tier 1
37
-|New gene|DLBCL tier|BL tier|
38
-|:-|:-:|:-:|
39
-|[DDX3X](../DDX3X)|1 |1 |
40
-|[FOXO1](../FOXO1)|1 |1 |
41
-|[ID3](../ID3)|2 |1 |
42
-|[TCF3](../TCF3)| |1 |
39
+|New gene|BL tier|
40
+|:-|:-:|
41
+|[DDX3X](../DDX3X)|1 |
42
+|[FOXO1](../FOXO1)|1 |
43
+|[PCBP1](../PCBP1)|1 |
44
+|[TCF3](../TCF3)|1 |
43 45
44 46
### Tier 2
45
-|New gene|DLBCL tier|BL tier|
46
-|:-|:-:|:-:|
47
-|[C16orf48](../C16orf48)| |2 |
48
-|[DHCR7](../DHCR7)| |2 |
49
-|[ELP2](../ELP2)| |2 |
50
-|[EXOSC6](../EXOSC6)| |2 |
51
-|[FLYWCH1](../FLYWCH1)| |2 |
52
-|[GTSE1](../GTSE1)| |2 |
53
-|[KANK2](../KANK2)| |2 |
54
-|[MKI67](../MKI67)| |2 |
55
-|[MYO18A](../MYO18A)| |2 |
56
-|[NCOR2](../NCOR2)|2 |2 |
57
-|[PCBP1](../PCBP1)|2 |2 |
58
-|[PDCD11](../PDCD11)| |2 |
59
-|[TOP2A](../TOP2A)| |2 |
60
-|[WDR90](../WDR90)| |2 |
61
-|[WHAMM](../WHAMM)| |2 |
62
-|[YY1AP1](../YY1AP1)| |2 |
47
+|New gene|BL tier|
48
+|:-|:-:|
49
+|[C16orf48](../C16orf48)|2 |
50
+|[DHCR7](../DHCR7)|2 |
51
+|[ELP2](../ELP2)|2 |
52
+|[EXOSC6](../EXOSC6)|2 |
53
+|[FLYWCH1](../FLYWCH1)|2 |
54
+|[GTSE1](../GTSE1)|2 |
55
+|[KANK2](../KANK2)|2 |
56
+|[MKI67](../MKI67)|2 |
57
+|[MYO18A](../MYO18A)|2 |
58
+|[NCOR2](../NCOR2)|2 |
59
+|[PDCD11](../PDCD11)|2 |
60
+|[TOP2A](../TOP2A)|2 |
61
+|[WDR90](../WDR90)|2 |
62
+|[WHAMM](../WHAMM)|2 |
63
+|[YY1AP1](../YY1AP1)|2 |
63 64
64 65
65 66
# Details
papers/schmitzGeneticsPathogenesisDiffuse2018.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @schmitzGeneticsPathogenesisDiffuse2018a
6
+# @schmitzGeneticsPathogenesisDiffuse2018
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|7|9|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|4|14|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,12 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 7
26
-New Tier 1, DLBCL Tier 1, 7
27
-This study, New Tier 2, 9
28
-New Tier 2, DLBCL Tier 2, 9
25
+This study, New Tier 1, 4
26
+New Tier 1, DLBCL Tier 1, 4
27
+This study, New Tier 2, 14
28
+New Tier 2, DLBCL Tier 2, 14
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
29 31
All other DLBCL studies, DLBCL Tier 1, 121
30
-All other DLBCL studies, DLBCL Tier 2, 189
32
+All other DLBCL studies, DLBCL Tier 2, 196
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -35,10 +38,7 @@ All other DLBCL studies, DLBCL Tier 2, 189
35 38
### Tier 1
36 39
|New gene|DLBCL tier|
37 40
|:-|:-:|
38
-|[CXCR5](../CXCR5)|1 |
39
-|[DDX3X](../DDX3X)|1 |
40
-|[DTX1](../DTX1)|1 |
41
-|[HIST2H2BE](../HIST2H2BE)|1 |
41
+|[GRHPR](../GRHPR)|1 |
42 42
|[ITPKB](../ITPKB)|1 |
43 43
|[NOL9](../NOL9)|1 |
44 44
|[WEE1](../WEE1)|1 |
... ...
@@ -46,15 +46,20 @@ All other DLBCL studies, DLBCL Tier 2, 189
46 46
### Tier 2
47 47
|New gene|DLBCL tier|
48 48
|:-|:-:|
49
+|[CXCR5](../CXCR5)|2 |
50
+|[EIF2AK3](../EIF2AK3)|2 |
49 51
|[FOXC1](../FOXC1)|2 |
50 52
|[GPC5](../GPC5)|2 |
51 53
|[GSG2](../GSG2)|2 |
54
+|[ID3](../ID3)|2 |
52 55
|[KLHL21](../KLHL21)|2 |
53 56
|[LAMA5](../LAMA5)|2 |
54 57
|[MYBPC2](../MYBPC2)|2 |
55 58
|[PAPOLG](../PAPOLG)|2 |
56 59
|[PRKDC](../PRKDC)|2 |
60
+|[SEL1L3](../SEL1L3)|2 |
57 61
|[TAP1](../TAP1)|2 |
62
+|[UBE2J1](../UBE2J1)|2 |
58 63
59 64
60 65
# Details
papers/schmitzTNFAIP3A20Tumor2009.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @schmitzTNFAIP3A20Tumor2009a
6
+# @schmitzTNFAIP3A20Tumor2009
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/schneiderAlterationsCD58Gene2015.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @schneiderAlterationsCD58Gene2015a
6
+# @schneiderAlterationsCD58Gene2015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/schollMutationsRegionFAS2007.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @schollMutationsRegionFAS2007
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/shinBRAFV600EMAP2K12015.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @shinBRAFV600EMAP2K12015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|0|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|0|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, DLBCL Tier 1, 0
27 27
This study, New Tier 2, 1
28 28
New Tier 2, DLBCL Tier 2, 1
29
-All other DLBCL studies, DLBCL Tier 1, 128
30
-All other DLBCL studies, DLBCL Tier 2, 197
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 125
32
+All other DLBCL studies, DLBCL Tier 2, 209
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
### Tier 2
papers/spinaGeneticsNodalMarginal2016.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @spinaGeneticsNodalMarginal2016b
6
+# @spinaGeneticsNodalMarginal2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|8|23|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|8|23|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 8
26 26
New Tier 1, MZL Tier 1, 8
27 27
This study, New Tier 2, 23
28 28
New Tier 2, MZL Tier 2, 23
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 34
30 32
All other MZL studies, MZL Tier 2, 51
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -56,6 +59,7 @@ All other MZL studies, MZL Tier 2, 51
56 59
|[CDC42BPB](../CDC42BPB)|2 |
57 60
|[CDKN2A](../CDKN2A)|2 |
58 61
|[CLGN](../CLGN)|2 |
62
+|[CNBP](../CNBP)|2 |
59 63
|[CNKSR2](../CNKSR2)|2 |
60 64
|[GPR98](../GPR98)|2 |
61 65
|[LRP1B](../LRP1B)|2 |
... ...
@@ -69,7 +73,6 @@ All other MZL studies, MZL Tier 2, 51
69 73
|[STXBP5](../STXBP5)|2 |
70 74
|[TAF1](../TAF1)|2 |
71 75
|[TCTN2](../TCTN2)|2 |
72
-|[ZNF9](../ZNF9)|2 |
73 76
74 77
75 78
# Details
papers/tanakaFrequentIncidenceSomatic1992.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @tanakaFrequentIncidenceSomatic1992
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/thomasGeneticSubgroupsInform2023.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @thomasGeneticSubgroupsInform2023
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|2|3|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|2|4|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -24,10 +24,13 @@ config:
24 24
sankey-beta
25 25
This study, New Tier 1, 2
26 26
New Tier 1, BL Tier 1, 2
27
-This study, New Tier 2, 3
28
-New Tier 2, BL Tier 2, 3
29
-All other BL studies, BL Tier 1, 27
30
-All other BL studies, BL Tier 2, 154
27
+This study, New Tier 2, 4
28
+New Tier 2, BL Tier 2, 4
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 30
32
+All other BL studies, BL Tier 2, 68
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
... ...
@@ -44,6 +47,7 @@ All other BL studies, BL Tier 2, 154
44 47
|[CDKN2C](../CDKN2C)|2 |
45 48
|[EBF1](../EBF1)|2 |
46 49
|[EHD1](../EHD1)|2 |
50
+|[TET2](../TET2)|2 |
47 51
48 52
49 53
# Details
papers/thomasMutationalAnalysisIkappaBalpha2004.md
... ...
@@ -0,0 +1,45 @@
1
+---
2
+title: ''
3
+bibliography: 'morinlab.bib'
4
+---
5
+
6
+# @thomasMutationalAnalysisIkappaBalpha2004
7
+## Summary of novel genes
8
+
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+```mermaid
13
+---
14
+config:
15
+ sankey:
16
+ showValues: true
17
+ linkColor: target
18
+ width: 600
19
+ height: 300
20
+ nodeAlignment: right
21
+ prefix: '('
22
+ suffix: ' genes)'
23
+---
24
+sankey-beta
25
+This study, New Tier 1, 1
26
+New Tier 1, DLBCL Tier 1, 1
27
+This study, New Tier 2, 0
28
+New Tier 2, DLBCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
34
+```
35
+
36
+## Novel genes reported in this study
37
+
38
+### Tier 1
39
+|New gene|DLBCL tier|
40
+|:-|:-:|
41
+|[NFKBIA](../NFKBIA)|1 |
42
+
43
+
44
+# Details
45
+
papers/tiacciBRAFMutationsHairycell2011.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @tiacciBRAFMutationsHairycell2011a
6
+# @tiacciBRAFMutationsHairycell2011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, DLBCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, DLBCL Tier 2, 0
29
-All other DLBCL studies, DLBCL Tier 1, 127
30
-All other DLBCL studies, DLBCL Tier 2, 198
29
+This study, New Tier 3, 0
30
+New Tier 3, DLBCL Tier 3, 0
31
+All other DLBCL studies, DLBCL Tier 1, 124
32
+All other DLBCL studies, DLBCL Tier 2, 210
33
+All other DLBCL studies, DLBCL Tier 3, 387
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/tiacciPervasiveMutationsJAKSTAT2018.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @tiacciPervasiveMutationsJAKSTAT2018b
6
+# @tiacciPervasiveMutationsJAKSTAT2018
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|9|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|9|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 9
28 28
New Tier 2, PMBL Tier 2, 9
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 73
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 103
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/vandenbrandRecurrentMutationsGenes2017.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @vandenbrandRecurrentMutationsGenes2017
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|0|2|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|0|2|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, MZL Tier 1, 0
27 27
This study, New Tier 2, 2
28 28
New Tier 2, MZL Tier 2, 2
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 42
30 32
All other MZL studies, MZL Tier 2, 72
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
### Tier 2
papers/viganoSomaticIL4RMutations2018.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @viganoSomaticIL4RMutations2018b
6
+# @viganoSomaticIL4RMutations2018
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, PMBL Tier 2, 0
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 82
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 112
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/wenigerMutationsTumorSuppressor2006.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @wenigerMutationsTumorSuppressor2006a
6
+# @wenigerMutationsTumorSuppressor2006
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|1|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|1|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, PMBL Tier 1, 1
27 27
This study, New Tier 2, 1
28 28
New Tier 2, PMBL Tier 2, 1
29
-All other PMBL studies, PMBL Tier 1, 75
30
-All other PMBL studies, PMBL Tier 2, 81
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 45
32
+All other PMBL studies, PMBL Tier 2, 111
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/wienandGenomicAnalysesFlowsorted2019.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @wienandGenomicAnalysesFlowsorted2019b
6
+# @wienandGenomicAnalysesFlowsorted2019
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|PMBL|4|3|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|PMBL|4|3|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 4
26 26
New Tier 1, PMBL Tier 1, 4
27 27
This study, New Tier 2, 3
28 28
New Tier 2, PMBL Tier 2, 3
29
-All other PMBL studies, PMBL Tier 1, 72
30
-All other PMBL studies, PMBL Tier 2, 79
29
+This study, New Tier 3, 0
30
+New Tier 3, PMBL Tier 3, 0
31
+All other PMBL studies, PMBL Tier 1, 42
32
+All other PMBL studies, PMBL Tier 2, 109
33
+All other PMBL studies, PMBL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/wildaInactivationARFMDM2p53Pathway2004.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @wildaInactivationARFMDM2p53Pathway2004
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, BL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, BL Tier 2, 0
29
-All other BL studies, BL Tier 1, 28
30
-All other BL studies, BL Tier 2, 157
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 31
32
+All other BL studies, BL Tier 2, 72
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/wuGeneticHeterogeneityPrimary2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @wuGeneticHeterogeneityPrimary2016
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MCL|1|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 1
26 26
New Tier 1, MCL Tier 1, 1
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MCL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MCL Tier 3, 0
29 31
All other MCL studies, MCL Tier 1, 22
30 32
All other MCL studies, MCL Tier 2, 46
33
+All other MCL studies, MCL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/yanBCRTLRSignaling2012.md
... ...
@@ -3,12 +3,12 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @yanBCRTLRSignaling2012a
6
+# @yanBCRTLRSignaling2012
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MZL|2|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MZL|2|0|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, MZL Tier 1, 2
27 27
This study, New Tier 2, 0
28 28
New Tier 2, MZL Tier 2, 0
29
+This study, New Tier 3, 0
30
+New Tier 3, MZL Tier 3, 0
29 31
All other MZL studies, MZL Tier 1, 40
30 32
All other MZL studies, MZL Tier 2, 74
33
+All other MZL studies, MZL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/yildizActivatingSTAT6Mutations2015.md
... ...
@@ -3,13 +3,13 @@ title: ''
3 3
bibliography: 'morinlab.bib'
4 4
---
5 5
6
-# @yildizActivatingSTAT6Mutations2015c
6
+# @yildizActivatingSTAT6Mutations2015
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|1|0|
12
-|FL|1|0|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|1|0|0|
12
+|FL|1|0|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -27,8 +27,11 @@ This study, New Tier 1, 1
27 27
New Tier 1, DLBCL Tier 1, 1
28 28
This study, New Tier 2, 0
29 29
New Tier 2, DLBCL Tier 2, 0
30
-All other DLBCL studies, DLBCL Tier 1, 127
31
-All other DLBCL studies, DLBCL Tier 2, 198
30
+This study, New Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
32
+All other DLBCL studies, DLBCL Tier 1, 124
33
+All other DLBCL studies, DLBCL Tier 2, 210
34
+All other DLBCL studies, DLBCL Tier 3, 387
32 35
```
33 36
34 37
## Novel genes reported in this study
papers/zhangGeneticHeterogeneityDiffuse2013.md
... ...
@@ -8,7 +8,7 @@ bibliography: 'morinlab.bib'
8 8
9 9
|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10 10
|:-:|:-:|:-:|:-:|
11
-|DLBCL|12|14|271|
11
+|DLBCL|11|8|272|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,15 +22,15 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 12
26
-New Tier 1, DLBCL Tier 1, 12
27
-This study, New Tier 2, 14
28
-New Tier 2, DLBCL Tier 2, 14
29
-This study, New Tier 3, 271
30
-New Tier 3, DLBCL Tier 3, 271
31
-All other DLBCL studies, DLBCL Tier 1, 117
32
-All other DLBCL studies, DLBCL Tier 2, 164
33
-All other DLBCL studies, DLBCL Tier 3, 114
25
+This study, New Tier 1, 11
26
+New Tier 1, DLBCL Tier 1, 11
27
+This study, New Tier 2, 8
28
+New Tier 2, DLBCL Tier 2, 8
29
+This study, New Tier 3, 272
30
+New Tier 3, DLBCL Tier 3, 272
31
+All other DLBCL studies, DLBCL Tier 1, 114
32
+All other DLBCL studies, DLBCL Tier 2, 202
33
+All other DLBCL studies, DLBCL Tier 3, 115
34 34
```
35 35
36 36
## Novel genes reported in this study
... ...
@@ -49,7 +49,6 @@ All other DLBCL studies, DLBCL Tier 3, 114
49 49
|[NOTCH2](../NOTCH2)|1 |
50 50
|[OSBPL10](../OSBPL10)|1 |
51 51
|[RHOA](../RHOA)|1 |
52
-|[TRRAP](../TRRAP)|1 |
53 52
54 53
### Tier 2
55 54
|New gene|DLBCL tier|
... ...
@@ -57,17 +56,11 @@ All other DLBCL studies, DLBCL Tier 3, 114
57 56
|[ANKRD17](../ANKRD17)|2 |
58 57
|[BTBD3](../BTBD3)|2 |
59 58
|[DDX10](../DDX10)|2 |
60
-|[INO80](../INO80)|2 |
61
-|[JAK1](../JAK1)|2 |
62
-|[JAK3](../JAK3)|2 |
63 59
|[NF1](../NF1)|2 |
64 60
|[PIK3CD](../PIK3CD)|2 |
65 61
|[PIK3R1](../PIK3R1)|2 |
66 62
|[SETD2](../SETD2)|2 |
67 63
|[SMEK1](../SMEK1)|2 |
68
-|[STAT5B](../STAT5B)|2 |
69
-|[UBR5](../UBR5)|2 |
70
-|[ZEB2](../ZEB2)|2 |
71 64
72 65
### Tier 3
73 66
|New gene|DLBCL tier|
... ...
@@ -321,6 +314,7 @@ All other DLBCL studies, DLBCL Tier 3, 114
321 314
|[TPRKB](../TPRKB)|3 |
322 315
|[TRIM37](../TRIM37)|3 |
323 316
|[TRIP11](../TRIP11)|3 |
317
+|[TRRAP](../TRRAP)|3 |
324 318
|[TSC2](../TSC2)|3 |
325 319
|[TSHZ2](../TSHZ2)|3 |
326 320
|[UHRF1BP1L](../UHRF1BP1L)|3 |
papers/zhangGenomicLandscapeMantle2014.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @zhangGenomicLandscapeMantle2014
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|MCL|2|26|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|MCL|2|26|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 2
26 26
New Tier 1, MCL Tier 1, 2
27 27
This study, New Tier 2, 26
28 28
New Tier 2, MCL Tier 2, 26
29
+This study, New Tier 3, 0
30
+New Tier 3, MCL Tier 3, 0
29 31
All other MCL studies, MCL Tier 1, 21
30 32
All other MCL studies, MCL Tier 2, 20
33
+All other MCL studies, MCL Tier 3, 0
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/zhouSporadicEndemicBurkitt2019.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @zhouSporadicEndemicBurkitt2019
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|BL|0|1|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|BL|0|1|0|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -26,8 +26,11 @@ This study, New Tier 1, 0
26 26
New Tier 1, BL Tier 1, 0
27 27
This study, New Tier 2, 1
28 28
New Tier 2, BL Tier 2, 1
29
-All other BL studies, BL Tier 1, 29
30
-All other BL studies, BL Tier 2, 156
29
+This study, New Tier 3, 0
30
+New Tier 3, BL Tier 3, 0
31
+All other BL studies, BL Tier 1, 32
32
+All other BL studies, BL Tier 2, 71
33
+All other BL studies, BL Tier 3, 70
31 34
```
32 35
33 36
### Tier 2