papers/morinFrequentMutationHistonemodifying2011.md
... ...
@@ -6,10 +6,10 @@ bibliography: 'morinlab.bib'
6 6
# @morinFrequentMutationHistonemodifying2011
7 7
## Summary of novel genes
8 8
9
-|Entity| Tier 1 genes| Tier 2 genes|
10
-|:-:|:-:|:-:|
11
-|DLBCL|27|1|
12
-|FL|19|4|
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|28|4|0|
12
+|FL|21|4|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -23,12 +23,15 @@ config:
23 23
suffix: ' genes)'
24 24
---
25 25
sankey-beta
26
-This study, New Tier 1, 27
27
-New Tier 1, DLBCL Tier 1, 27
28
-This study, New Tier 2, 1
29
-New Tier 2, DLBCL Tier 2, 1
26
+This study, New Tier 1, 28
27
+New Tier 1, DLBCL Tier 1, 28
28
+This study, New Tier 2, 4
29
+New Tier 2, DLBCL Tier 2, 4
30
+This study, New Tier 3, 0
31
+New Tier 3, DLBCL Tier 3, 0
30 32
All other DLBCL studies, DLBCL Tier 1, 101
31
-All other DLBCL studies, DLBCL Tier 2, 197
33
+All other DLBCL studies, DLBCL Tier 2, 174
34
+All other DLBCL studies, DLBCL Tier 3, 385
32 35
```
33 36
34 37
## Novel genes reported in this study
... ...
@@ -40,6 +43,7 @@ All other DLBCL studies, DLBCL Tier 2, 197
40 43
|[BCL10](../BCL10)|1 |2 |
41 44
|[BCL2](../BCL2)|1 |1 |
42 45
|[BCL6](../BCL6)|1 |1 |
46
+|[BCL7A](../BCL7A)|1 |1 |
43 47
|[BTG1](../BTG1)|1 |1 |
44 48
|[BTG2](../BTG2)|1 |1 |
45 49
|[CARD11](../CARD11)|1 |1 |
... ...
@@ -47,7 +51,6 @@ All other DLBCL studies, DLBCL Tier 2, 197
47 51
|[CD58](../CD58)|1 | |
48 52
|[CD70](../CD70)|1 |2 |
49 53
|[CD79B](../CD79B)|1 |2 |
50
-|[CIITA](../CIITA)|1 | |
51 54
|[ETS1](../ETS1)|1 | |
52 55
|[FOXO1](../FOXO1)|1 |1 |
53 56
|[GNA13](../GNA13)|1 |1 |
... ...
@@ -61,6 +64,7 @@ All other DLBCL studies, DLBCL Tier 2, 197
61 64
|[SGK1](../SGK1)|1 |1 |
62 65
|[SOCS1](../SOCS1)|1 |1 |
63 66
|[TMEM30A](../TMEM30A)|1 |2 |
67
+|[TNFRSF14](../TNFRSF14)|1 |1 |
64 68
|[TP53](../TP53)|1 |1 |
65 69
|[ZFP36L1](../ZFP36L1)|1 | |
66 70
... ...
@@ -68,13 +72,9 @@ All other DLBCL studies, DLBCL Tier 2, 197
68 72
|New gene|DLBCL tier|FL tier|
69 73
|:-|:-:|:-:|
70 74
|[CD274](../CD274)|2 | |
71
-
72
-
73
-## Data Availability
74
-
75
-|**Repository**|**Accession**|
76
-|-|-|
77
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000532.v18.p6 |
75
+|[CIITA](../CIITA)|2 | |
76
+|[FAT2](../FAT2)|2 | |
77
+|[RAPGEF1](../RAPGEF1)|2 | |
78 78
79 79
80 80
# Details
papers/morinGeneticLandscapesRelapsed2016.md
... ...
@@ -6,9 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @morinGeneticLandscapesRelapsed2016
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|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, DLBCL Tier 1, 2
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, 127
32
+All other DLBCL studies, DLBCL Tier 2, 178
33
+All other DLBCL studies, DLBCL Tier 3, 385
31 34
```
32 35
33 36
## Novel genes reported in this study
papers/morinMutationalStructuralAnalysis2013.md
... ...
@@ -6,10 +6,9 @@ bibliography: 'morinlab.bib'
6 6
# @morinMutationalStructuralAnalysis2013
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 |38|9|29|22|7| 24% |
12
-
9
+|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes|
10
+|:-:|:-:|:-:|:-:|
11
+|DLBCL|10|21|7|
13 12
```mermaid
14 13
---
15 14
config:
... ...
@@ -23,65 +22,69 @@ config:
23 22
suffix: ' genes)'
24 23
---
25 24
sankey-beta
26
-New to this study, DLBCL Tier 1, 9
27
-New to this study, DLBCL Tier 2, 29
28
-DLBCL Tier 2, Pass QC, 22
29
-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, 21
28
+New Tier 2, DLBCL Tier 2, 21
29
+This study, New Tier 3, 7
30
+New Tier 3, DLBCL Tier 3, 7
31
+All other DLBCL studies, DLBCL Tier 1, 119
32
+All other DLBCL studies, DLBCL Tier 2, 157
33
+All other DLBCL studies, DLBCL Tier 3, 378
30 34
```
31 35
32 36
## Novel genes reported in this study
33 37
34 38
### Tier 1
35
-|New gene|DLBCL tier|
36
-|:-|:-:|
37
-|[CD83](../CD83)|1 |
38
-|[CDKN2A](../CDKN2A)|1 |
39
-|[GNAI2](../GNAI2)|1 |
40
-|[HIST1H1D](../HIST1H1D)|1 |
41
-|[HIST1H2AC](../HIST1H2AC)|1 |
42
-|[IKZF3](../IKZF3)|1 |
43
-|[MPEG1](../MPEG1)|1 |
44
-|[RB1](../RB1)|1 |
45
-|[TAF1](../TAF1)|1 |
39
+|New gene|DLBCL tier| Average variant quality | QC outcome |
40
+|:-|:-:|:-:|:-:|
41
+|[CD83](../CD83)|1 || |
42
+|[CDKN2A](../CDKN2A)|1 || |
43
+|[GNAI2](../GNAI2)|1 || |
44
+|[HIST1H1D](../HIST1H1D)|1 || |
45
+|[HIST1H2AC](../HIST1H2AC)|1 || |
46
+|[IKZF3](../IKZF3)|1 || |
47
+|[MPEG1](../MPEG1)|1 || |
48
+|[RB1](../RB1)|1 || |
49
+|[TAF1](../TAF1)|1 || |
50
+|[ZNF608](../ZNF608)|1 || |
46 51
47 52
### Tier 2
48
-|Novel Gene|DLBCL Tier|Average variant quality|QC outcome|
49
-|:--|:-:|:--:|:-:|
50
-|[ABI3BP](../ABI3BP)|2 |★ ★ ★ ☆ ☆|**Pass**|
51
-|[CDH9](../CDH9)|2 |★ ★ ★ ☆ ☆|**Pass**|
52
-|[CNTNAP5](../CNTNAP5)|2 |★ ★ ★ ★ ☆|**Pass**|
53
-|[DNAH5](../DNAH5)|2 |★ ★ ★ ★ ☆|**Pass**|
54
-|[DSG4](../DSG4)|2 |★ ★ ★ ☆ ☆|**Pass**|
55
-|[FAT4](../FAT4)|2 |★ ★ ★ ☆ ☆|**Pass**|
56
-|[HDAC7](../HDAC7)|2 |★ ★ ★ ☆ ☆|**Pass**|
57
-|[HIST1H2AG](../HIST1H2AG)|2 |★ ★ ★ ☆ ☆|**Pass**|
58
-|[IFNGR1](../IFNGR1)|2 |★ ★ ★ ★ ☆|**Pass**|
59
-|[LRRN3](../LRRN3)|2 |★ ★ ★ ★ ★|**Pass**|
60
-|[MPDZ](../MPDZ)|2 |★ ★ ★ ★ ☆|**Pass**|
61
-|[NLRP5](../NLRP5)|2 |★ ★ ★ ☆ ☆|**Pass**|
62
-|[ODZ3](../ODZ3)|2 |★ ★ ★ ☆ ☆|**Pass**|
63
-|[P2RX5](../P2RX5)|2 |★ ★ ★ ☆ ☆|**Pass**|
64
-|[PASK](../PASK)|2 |★ ★ ★ ★ ☆|**Pass**|
65
-|[PCDHB11](../PCDHB11)|2 |★ ★ ★ ☆ ☆|**Pass**|
66
-|[PDS5B](../PDS5B)|2 |★ ★ ★ ★ ☆|**Pass**|
67
-|[PRKCB](../PRKCB)|2 |★ ★ ★ ★ ☆|**Pass**|
68
-|[SAMD9L](../SAMD9L)|2 |★ ★ ★ ☆ ☆|**Pass**|
69
-|[SRRM2](../SRRM2)|2 |★ ★ ★ ☆ ☆|**Pass**|
70
-|[SYPL1](../SYPL1)|2 |★ ★ ★ ☆ ☆|**Pass**|
71
-|[WDFY3](../WDFY3)|2 |★ ★ ★ ★ ☆|**Pass**|
72
-|[POGZ](../POGZ)|2 |★ ★ ☆ ☆ ☆|**Fail**|
73
-|[PKD1](../PKD1)|2 |★ ★ ☆ ☆ ☆|**Fail**|
74
-|[IER2](../IER2)|2 |★ ☆ ☆ ☆ ☆|**Fail**|
75
-|[FAM38B](../FAM38B)|2 |★ ★ ☆ ☆ ☆|**Fail**|
76
-|[FNDC1](../FNDC1)|2 |★ ★ ☆ ☆ ☆|**Fail**|
77
-|[PTPN23](../PTPN23)|2 |★ ★ ☆ ☆ ☆|**Fail**|
78
-|[SARM1](../SARM1)|2 |★ ★ ☆ ☆ ☆|**Fail**|
53
+|New gene|DLBCL tier| Average variant quality | QC outcome |
54
+|:-|:-:|:-:|:-:|
55
+|[ABI3BP](../ABI3BP)|2 |★ ★ ★ ☆ ☆ |PASS |
56
+|[CDH9](../CDH9)|2 |★ ★ ★ ☆ ☆ |PASS |
57
+|[CNTNAP5](../CNTNAP5)|2 |★ ★ ★ ★ ☆ |PASS |
58
+|[DNAH5](../DNAH5)|2 |★ ★ ★ ★ ☆ |PASS |
59
+|[DSG4](../DSG4)|2 |★ ★ ★ ☆ ☆ |PASS |
60
+|[FAT4](../FAT4)|2 |★ ★ ★ ☆ ☆ |PASS |
61
+|[HDAC7](../HDAC7)|2 |★ ★ ★ ☆ ☆ |PASS |
62
+|[HIST1H2AG](../HIST1H2AG)|2 |★ ★ ★ ☆ ☆ |PASS |
63
+|[IFNGR1](../IFNGR1)|2 |★ ★ ★ ★ ☆ |PASS |
64
+|[MPDZ](../MPDZ)|2 |★ ★ ★ ★ ☆ |PASS |
65
+|[NLRP5](../NLRP5)|2 |★ ★ ★ ☆ ☆ |PASS |
66
+|[ODZ3](../ODZ3)|2 |★ ★ ★ ☆ ☆ |PASS |
67
+|[P2RX5](../P2RX5)|2 |★ ★ ★ ☆ ☆ |PASS |
68
+|[PASK](../PASK)|2 |★ ★ ★ ★ ☆ |PASS |
69
+|[PCDHB11](../PCDHB11)|2 |★ ★ ★ ☆ ☆ |PASS |
70
+|[PDS5B](../PDS5B)|2 |★ ★ ★ ★ ☆ |PASS |
71
+|[PRKCB](../PRKCB)|2 |★ ★ ★ ★ ☆ |PASS |
72
+|[SAMD9L](../SAMD9L)|2 |★ ★ ★ ☆ ☆ |PASS |
73
+|[SRRM2](../SRRM2)|2 |★ ★ ★ ☆ ☆ |PASS |
74
+|[SYPL1](../SYPL1)|2 |★ ★ ★ ☆ ☆ |PASS |
75
+|[WDFY3](../WDFY3)|2 |★ ★ ★ ★ ☆ |PASS |
79 76
80
-## Data Availability
77
+### Tier 3
78
+|New gene|DLBCL tier| Average variant quality | QC outcome |
79
+|:-|:-:|:-:|:-:|
80
+|[FAM38B](../FAM38B)|3 |★ ★ ☆ ☆ ☆ |FAIL |
81
+|[FNDC1](../FNDC1)|3 |★ ★ ☆ ☆ ☆ |FAIL |
82
+|[IER2](../IER2)|3 |★ ☆ ☆ ☆ ☆ |FAIL |
83
+|[PKD1](../PKD1)|3 |★ ★ ☆ ☆ ☆ |FAIL |
84
+|[POGZ](../POGZ)|3 |★ ★ ☆ ☆ ☆ |FAIL |
85
+|[PTPN23](../PTPN23)|3 |★ ★ ☆ ☆ ☆ |FAIL |
86
+|[SARM1](../SARM1)|3 |★ ★ ☆ ☆ ☆ |FAIL |
81 87
82
-|**Repository**|**Accession**|
83
-|-|-|
84
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000532.v18.p6 |
85 88
86 89
# Details
87 90
papers/morinSomaticMutationsAltering2010a.md
... ...
@@ -6,10 +6,10 @@ bibliography: 'morinlab.bib'
6 6
# @morinSomaticMutationsAltering2010a
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
+|FL|1|0|0|
12
+|DLBCL|1|0|0|
13 13
```mermaid
14 14
---
15 15
config:
... ...
@@ -27,23 +27,20 @@ This study, New Tier 1, 1
27 27
New Tier 1, FL Tier 1, 1
28 28
This study, New Tier 2, 0
29 29
New Tier 2, FL Tier 2, 0
30
+This study, New Tier 3, 0
31
+New Tier 3, FL Tier 3, 0
30 32
All other FL studies, FL Tier 1, 65
31
-All other FL studies, FL Tier 2, 50
33
+All other FL studies, FL Tier 2, 49
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 42
|[EZH2](../EZH2)|1 |1 |
40 43
41
-## Data Availability
42
-
43
-|**Repository**|**Accession**|
44
-|-|-|
45
-|[dbGAP](https://www.ncbi.nlm.nih.gov/gap/)| phs000532.v18.p6 |
46
-
47 44
48 45
# Details
49 46
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|13|14|271|
11
+|DLBCL|12|14|271|
12 12
```mermaid
13 13
---
14 14
config:
... ...
@@ -22,13 +22,13 @@ config:
22 22
suffix: ' genes)'
23 23
---
24 24
sankey-beta
25
-This study, New Tier 1, 13
26
-New Tier 1, DLBCL Tier 1, 13
25
+This study, New Tier 1, 12
26
+New Tier 1, DLBCL Tier 1, 12
27 27
This study, New Tier 2, 14
28 28
New Tier 2, DLBCL Tier 2, 14
29 29
This study, New Tier 3, 271
30 30
New Tier 3, DLBCL Tier 3, 271
31
-All other DLBCL studies, DLBCL Tier 1, 116
31
+All other DLBCL studies, DLBCL Tier 1, 117
32 32
All other DLBCL studies, DLBCL Tier 2, 164
33 33
All other DLBCL studies, DLBCL Tier 3, 114
34 34
```
... ...
@@ -50,7 +50,6 @@ All other DLBCL studies, DLBCL Tier 3, 114
50 50
|[OSBPL10](../OSBPL10)|1 |
51 51
|[RHOA](../RHOA)|1 |
52 52
|[TRRAP](../TRRAP)|1 |
53
-|[ZNF608](../ZNF608)|1 |
54 53
55 54
### Tier 2
56 55
|New gene|DLBCL tier|