43a90d669b64e45188894bad500e92da0e43a699
papers/reddyGeneticFunctionalDrivers2017.md
| ... | ... | @@ -6,10 +6,9 @@ bibliography: 'morinlab.bib' |
| 6 | 6 | # @reddyGeneticFunctionalDrivers2017 |
| 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|59| 6|53|24|29|55%| |
|
| 12 | - |
|
| 9 | +|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes| |
|
| 10 | +|:-:|:-:|:-:|:-:| |
|
| 11 | +|DLBCL|8|26|26| |
|
| 13 | 12 | ```mermaid |
| 14 | 13 | --- |
| 15 | 14 | config: |
| ... | ... | @@ -23,86 +22,91 @@ config: |
| 23 | 22 | suffix: ' genes)' |
| 24 | 23 | --- |
| 25 | 24 | sankey-beta |
| 26 | -New to this study, DLBCL Tier 1, 6 |
|
| 27 | -New to this study, DLBCL Tier 2, 53 |
|
| 28 | -DLBCL Tier 2, Pass QC, 24 |
|
| 29 | -DLBCL Tier 2, Fail QC, 29 |
|
| 25 | +This study, New Tier 1, 8 |
|
| 26 | +New Tier 1, DLBCL Tier 1, 8 |
|
| 27 | +This study, New Tier 2, 26 |
|
| 28 | +New Tier 2, DLBCL Tier 2, 26 |
|
| 29 | +This study, New Tier 3, 26 |
|
| 30 | +New Tier 3, DLBCL Tier 3, 26 |
|
| 31 | +All other DLBCL studies, DLBCL Tier 1, 120 |
|
| 32 | +All other DLBCL studies, DLBCL Tier 2, 153 |
|
| 33 | +All other DLBCL studies, DLBCL Tier 3, 359 |
|
| 30 | 34 | ``` |
| 31 | 35 | |
| 32 | 36 | ## Novel genes reported in this study |
| 33 | 37 | |
| 34 | 38 | ### Tier 1 |
| 35 | - |
|
| 36 | -|Novel gene|DLBCL tier|Average variant quality| |
|
| 37 | -|:-|:-:|:-:| |
|
| 38 | -|[ATM](../ATM)|1 |★ ★ ★ ☆ ☆| |
|
| 39 | -|[BIRC6](../BIRC6)|1 |★ ★ ★ ☆ ☆| |
|
| 40 | -|[HNRNPU](../HNRNPU)|1 |★ ★ ★ ☆ ☆| |
|
| 41 | -|[SETD1B](../SETD1B)|1 |★ ★ ☆ ☆ ☆| |
|
| 42 | -|[TOX](../TOX)|1 |★ ★ ★ ☆ ☆| |
|
| 43 | -|[NOTCH2](../NOTCH2)|1|★ ★ ★ ☆ ☆| |
|
| 39 | +|New gene|DLBCL tier| Average variant quality | QC outcome | |
|
| 40 | +|:-|:-:|:-:|:-:| |
|
| 41 | +|[ATM](../ATM)|1 || | |
|
| 42 | +|[BIRC6](../BIRC6)|1 || | |
|
| 43 | +|[DDX3X](../DDX3X)|1 || | |
|
| 44 | +|[HNRNPU](../HNRNPU)|1 || | |
|
| 45 | +|[MGA](../MGA)|1 || | |
|
| 46 | +|[PTEN](../PTEN)|1 || | |
|
| 47 | +|[SF3B1](../SF3B1)|1 || | |
|
| 48 | +|[TOX](../TOX)|1 || | |
|
| 44 | 49 | |
| 45 | 50 | ### Tier 2 |
| 46 | - |
|
| 47 | -|Novel gene|DLBCL tier|Average variant quality|QC outcome| |
|
| 51 | +|New gene|DLBCL tier| Average variant quality | QC outcome | |
|
| 48 | 52 | |:-|:-:|:-:|:-:| |
| 49 | -|[ARID5B](../ARID5B)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 50 | -|[BTBD3](../BTBD3)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 51 | -|[SETD5](../SETD5)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 52 | -|[ATR](../ATR)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 53 | -|[BRINP3](../BRINP3)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 54 | -|[TGFBR2](../TGFBR2)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 55 | -|[TIPARP](../TIPARP)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 56 | -|[CASP8](../CASP8)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 57 | -|[CD22](../CD22)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 58 | -|[NF1](../NF1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 59 | -|[IKBKB](../IKBKB)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 60 | -|[JUNB](../JUNB)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 61 | -|[KCMF1](../KCMF1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 62 | -|[MAGT1](../MAGT1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 63 | -|[MECOM](../MECOM)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 64 | -|[PTPN6](../PTPN6)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 65 | -|[MET](../MET)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 66 | -|[ZFX](../ZFX)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 67 | -|[YY1](../YY1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 68 | -|[FOXP1](../FOXP1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 69 | -|[FUBP1](../FUBP1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 70 | -|[GOLGA5](../GOLGA5)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 71 | -|[MSH6](../MSH6)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 72 | -|[MCL1](../MCL1)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 73 | -|[ANKRD17](../ANKRD17)|2 |★ ★ ★ ☆ ☆|**Fail**| |
|
| 74 | -|[CDC73](../CDC73)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 75 | -|[CHD1](../CHD1)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 76 | -|[CHD8](../CHD8)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 77 | -|[CHST2](../CHST2)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 78 | -|[DCAF6](../DCAF6)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 79 | -|[DDX10](../DDX10)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 80 | -|[DICER1](../DICER1)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 81 | -|[HRAS](../HRAS)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 82 | -|[LIN54](../LIN54)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 83 | -|[MAP4K4](../MAP4K4)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 84 | -|[MSH2](../MSH2)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 85 | -|[GNAS](../GNAS)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 86 | -|[MYB](../MYB)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 87 | -|[NCOR1](../NCOR1)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 88 | -|[NFKB2](../NFKB2)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 89 | -|[PHF6](../PHF6)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 90 | -|[PIK3CD](../PIK3CD)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 91 | -|[PTPRK](../PTPRK)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 92 | -|[ZFAT](../ZFAT)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 93 | -|[ARID1B](../ARID1B)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 94 | -|[RUNX1](../RUNX1)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 95 | -|[CBLB](../CBLB)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 96 | -|[SYK](../SYK)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 97 | -|[WAC](../WAC)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 98 | -|[ZBTB7A](../ZBTB7A)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 99 | -|[RARA](../RARA)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 100 | -|[DNMT3A](../DNMT3A)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 101 | -|[MARK1](../MARK1)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 53 | +|[ARID5B](../ARID5B)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 54 | +|[ATR](../ATR)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 55 | +|[BRINP3](../BRINP3)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 56 | +|[CASP8](../CASP8)|2 || | |
|
| 57 | +|[CD22](../CD22)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 58 | +|[FOXP1](../FOXP1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 59 | +|[FUBP1](../FUBP1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 60 | +|[GOLGA5](../GOLGA5)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 61 | +|[HNRNPD](../HNRNPD)|2 || | |
|
| 62 | +|[IKBKB](../IKBKB)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 63 | +|[IL16](../IL16)|2 || | |
|
| 64 | +|[JUNB](../JUNB)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 65 | +|[KCMF1](../KCMF1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 66 | +|[MAGT1](../MAGT1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 67 | +|[MCL1](../MCL1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 68 | +|[MECOM](../MECOM)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 69 | +|[MET](../MET)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 70 | +|[MSH6](../MSH6)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 71 | +|[NF1](../NF1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 72 | +|[PTPN6](../PTPN6)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 73 | +|[SETD5](../SETD5)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 74 | +|[TCL1A](../TCL1A)|2 || | |
|
| 75 | +|[TGFBR2](../TGFBR2)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 76 | +|[TIPARP](../TIPARP)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 77 | +|[YY1](../YY1)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 78 | +|[ZFX](../ZFX)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 102 | 79 | |
| 103 | -## See Also |
|
| 80 | +### Tier 3 |
|
| 81 | +|New gene|DLBCL tier| Average variant quality | QC outcome | |
|
| 82 | +|:-|:-:|:-:|:-:| |
|
| 83 | +|[ARID1B](../ARID1B)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 84 | +|[CBLB](../CBLB)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 85 | +|[CDC73](../CDC73)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 86 | +|[CDH8](../CDH8)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 87 | +|[CHD1](../CHD1)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 88 | +|[CHST2](../CHST2)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 89 | +|[DCAF6](../DCAF6)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 90 | +|[DICER1](../DICER1)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 91 | +|[DNMT3A](../DNMT3A)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 92 | +|[GNAS](../GNAS)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 93 | +|[HRAS](../HRAS)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 94 | +|[LIN54](../LIN54)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 95 | +|[MAP4K4](../MAP4K4)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 96 | +|[MARK1](../MARK1)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 97 | +|[MSH2](../MSH2)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 98 | +|[MYB](../MYB)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 99 | +|[NCOR1](../NCOR1)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 100 | +|[NFKB2](../NFKB2)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 101 | +|[PHF6](../PHF6)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 102 | +|[PTPRK](../PTPRK)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 103 | +|[RARA](../RARA)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 104 | +|[RUNX1](../RUNX1)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 105 | +|[SYK](../SYK)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 106 | +|[WAC](../WAC)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 107 | +|[ZBTB7A](../ZBTB7A)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 108 | +|[ZFAT](../ZFAT)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 104 | 109 | |
| 105 | -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/Reddy/igv_reports/) along with mutations unique to the GAMBL re-analysis.[@drevalRevisitingReddyDLBCL2023] |
|
| 106 | 110 | |
| 107 | -# References |
|
| 111 | +# Details |
|
| 108 | 112 |
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|16|13|271| |
|
| 11 | +|DLBCL|14|13|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, 16 |
|
| 26 | -New Tier 1, DLBCL Tier 1, 16 |
|
| 25 | +This study, New Tier 1, 14 |
|
| 26 | +New Tier 1, DLBCL Tier 1, 14 |
|
| 27 | 27 | This study, New Tier 2, 13 |
| 28 | 28 | New Tier 2, DLBCL Tier 2, 13 |
| 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, 112 |
|
| 31 | +All other DLBCL studies, DLBCL Tier 1, 114 |
|
| 32 | 32 | All other DLBCL studies, DLBCL Tier 2, 166 |
| 33 | 33 | All other DLBCL studies, DLBCL Tier 3, 114 |
| 34 | 34 | ``` |
| ... | ... | @@ -39,14 +39,12 @@ All other DLBCL studies, DLBCL Tier 3, 114 |
| 39 | 39 | |New gene|DLBCL tier| |
| 40 | 40 | |:-|:-:| |
| 41 | 41 | |[ARID1A](../ARID1A)|1 | |
| 42 | -|[BCL7A](../BCL7A)|1 | |
|
| 43 | 42 | |[DTX1](../DTX1)|1 | |
| 44 | 43 | |[FBXW7](../FBXW7)|1 | |
| 45 | 44 | |[HIST1H2BK](../HIST1H2BK)|1 | |
| 46 | 45 | |[KLHL14](../KLHL14)|1 | |
| 47 | 46 | |[KMT2C](../KMT2C)|1 | |
| 48 | 47 | |[LRRN3](../LRRN3)|1 | |
| 49 | -|[MGA](../MGA)|1 | |
|
| 50 | 48 | |[MTOR](../MTOR)|1 | |
| 51 | 49 | |[NOTCH2](../NOTCH2)|1 | |
| 52 | 50 | |[OSBPL10](../OSBPL10)|1 | |