49127922f5aa881551315296d96fb80ae1d40ffe
papers/paneaWholeGenomeLandscape2019.md
| ... | ... | @@ -6,11 +6,9 @@ bibliography: 'morinlab.bib' |
| 6 | 6 | # @paneaWholeGenomeLandscape2019 |
| 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|40|4|35|13 |22| 55% | |
|
| 12 | - |
|
| 13 | - |
|
| 9 | +|Entity| Tier 1 genes| Tier 2 genes|Tier 3 genes| |
|
| 10 | +|:-:|:-:|:-:|:-:| |
|
| 11 | +|BL|4|13|22| |
|
| 14 | 12 | ```mermaid |
| 15 | 13 | --- |
| 16 | 14 | config: |
| ... | ... | @@ -24,60 +22,70 @@ config: |
| 24 | 22 | suffix: ' genes)' |
| 25 | 23 | --- |
| 26 | 24 | sankey-beta |
| 27 | -New to this study, BL Tier 1, 4 |
|
| 28 | -New to this study, BL Tier 2, 36 |
|
| 29 | -BL Tier 2, Pass QC, 13 |
|
| 30 | -BL Tier 2, Fail QC, 23 |
|
| 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 |
|
| 29 | +This study, New Tier 3, 22 |
|
| 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 |
|
| 33 | +All other BL studies, BL Tier 3, 48 |
|
| 31 | 34 | ``` |
| 32 | 35 | |
| 33 | 36 | ## Novel genes reported in this study |
| 34 | 37 | |
| 35 | 38 | ### Tier 1 |
| 36 | -|Novel gene|BL tier| |
|
| 37 | -|:-|:-:| |
|
| 38 | -|[BMP7](../BMP7)|1 | |
|
| 39 | -|[EIF4A1](../EIF4A1)|1 | |
|
| 40 | -|[EPPK1](../EPPK1)|1 | |
|
| 41 | -|[HNRNPU](../HNRNPU)|1 | |
|
| 39 | +|New gene|BL tier| Average variant quality | QC outcome | |
|
| 40 | +|:-|:-:|:-:|:-:| |
|
| 41 | +|[BMP7](../BMP7)|1 || | |
|
| 42 | +|[EIF4A1](../EIF4A1)|1 || | |
|
| 43 | +|[EPPK1](../EPPK1)|1 || | |
|
| 44 | +|[HNRNPU](../HNRNPU)|1 || | |
|
| 42 | 45 | |
| 43 | 46 | ### Tier 2 |
| 44 | -|Novel Gene|BL tier|Average variant quality|QC outcome| |
|
| 47 | +|New gene|BL tier| Average variant quality | QC outcome | |
|
| 45 | 48 | |:-|:-:|:-:|:-:| |
| 46 | -|[HIST1H3I](../HIST1H3I)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 47 | -|[CXCR4](../CXCR4)|2 | ★ ★ ★ ★ ☆|**Pass**| |
|
| 48 | -|[IRF8](../IRF8)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 49 | -|[MCL1](../MCL1)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 50 | -|[CD83](../CD83)|2 | ★ ★ ★ ☆ ☆|**Pass**| |
|
| 51 | -|[PLCG2](../PLCG2)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 52 | -|[IGLL5](../IGLL5)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 53 | -|[HIST1H3D](../HIST1H3D)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 54 | -|[WNK2](../WNK2)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 55 | -|[HIST1H4J](../HIST1H4J)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 56 | -|[IKZF3](../IKZF3)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 57 | -|[ZFP36L1](../ZFP36L1)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 58 | -|[RNF144B](../RNF144B)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 59 | -|[ALPK2](../ALPK2)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 60 | -|[CD79B](../CD79B)|2 | ★ ★ ☆ ☆ ☆|**Fail**| |
|
| 61 | -|[CTCF](../CTCF)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 62 | -|[DNMT1](../DNMT1)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 63 | -|[ETS1](../ETS1)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 64 | -|[FZD3](../FZD3)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 65 | -|[HIST1H1C](../HIST1H1C)|2 | ★ ★ ☆ ☆ ☆|**Fail**| |
|
| 66 | -|[HIST1H2AG](../HIST1H2AG)|2 | ★ ★ ☆ ☆ ☆|**Fail**| |
|
| 67 | -|[HIST1H2BK](../HIST1H2BK)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 68 | -|[KCNK10](../KCNK10)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 69 | -|[MME](../MME)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 70 | -|[MTOR](../MTOR)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 71 | -|[PABPC4L](../PABPC4L)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 72 | -|[PCDHA11](../PCDHA11)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 73 | -|[PDZRN3](../PDZRN3)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 74 | -|[PIK3R1](../PIK3R1)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 75 | -|[PXDNL](../PXDNL)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
|
| 76 | -|[SNTB2](../SNTB2)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 77 | -|[WDR7](../WDR7)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
|
| 78 | -|[HIST1H3H](../HIST1H3H)|2 |☆ ☆ ☆ ☆ ☆|**Fail**| |
|
| 79 | -|[HIST1H3J](../HIST1H3J)|2 |☆ ☆ ☆ ☆ ☆|**Fail**| |
|
| 80 | -|[HIST1H2AM](../HIST1H2AM)|2 | ☆ ☆ ☆ ☆ ☆|**Fail**| |
|
| 49 | +|[CD83](../CD83)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 50 | +|[CXCR4](../CXCR4)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 51 | +|[HIST1H3D](../HIST1H3D)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 52 | +|[HIST1H3I](../HIST1H3I)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 53 | +|[HIST1H4J](../HIST1H4J)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 54 | +|[IGLL5](../IGLL5)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 55 | +|[IKZF3](../IKZF3)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 56 | +|[IRF8](../IRF8)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 57 | +|[MCL1](../MCL1)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 58 | +|[PLCG2](../PLCG2)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 59 | +|[RNF144B](../RNF144B)|2 |★ ★ ★ ☆ ☆ |PASS | |
|
| 60 | +|[WNK2](../WNK2)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 61 | +|[ZFP36L1](../ZFP36L1)|2 |★ ★ ★ ★ ☆ |PASS | |
|
| 62 | + |
|
| 63 | +### Tier 3 |
|
| 64 | +|New gene|BL tier| Average variant quality | QC outcome | |
|
| 65 | +|:-|:-:|:-:|:-:| |
|
| 66 | +|[ALPK2](../ALPK2)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 67 | +|[CD79B](../CD79B)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 68 | +|[CTCF](../CTCF)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 69 | +|[DNMT1](../DNMT1)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 70 | +|[ETS1](../ETS1)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 71 | +|[FZD3](../FZD3)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 72 | +|[HIST1H1C](../HIST1H1C)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 73 | +|[HIST1H2AG](../HIST1H2AG)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 74 | +|[HIST1H2AM](../HIST1H2AM)|3 |☆ ☆ ☆ ☆ ☆ |FAIL | |
|
| 75 | +|[HIST1H2BK](../HIST1H2BK)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 76 | +|[HIST1H3H](../HIST1H3H)|3 |☆ ☆ ☆ ☆ ☆ |FAIL | |
|
| 77 | +|[HIST1H3J](../HIST1H3J)|3 |☆ ☆ ☆ ☆ ☆ |FAIL | |
|
| 78 | +|[KCNK10](../KCNK10)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 79 | +|[MME](../MME)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 80 | +|[MTOR](../MTOR)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 81 | +|[PABPC4L](../PABPC4L)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 82 | +|[PCDHA11](../PCDHA11)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 83 | +|[PDZRN3](../PDZRN3)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 84 | +|[PIK3R1](../PIK3R1)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 85 | +|[PXDNL](../PXDNL)|3 |★ ☆ ☆ ☆ ☆ |FAIL | |
|
| 86 | +|[SNTB2](../SNTB2)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 87 | +|[WDR7](../WDR7)|3 |★ ★ ☆ ☆ ☆ |FAIL | |
|
| 88 | + |
|
| 81 | 89 | |
| 82 | 90 | # Details |
| 83 | 91 |