loveGeneticLandscapeMutations2012
The 2012 study provided foundational insights into the genetic landscape of Burkitt lymphoma (BL), describing recurrent mutations in genes such as MYC, ID3, ARID1A, SMARCA4, and TP53. Subsequent research has both validated and expanded upon these findings. Although this study identified some genes that are commonly mutated in BL. Some of its novel findings are of questionable significance in BL.
- ID3 Mutations: The initial identification of ID3 mutations in approximately one-third of BL cases has been consistently corroborated. These mutations, particularly affecting the helix-loop-helix domain, are recognized as a hallmark of BL and are rare in other lymphomas.
- ARID1A and SMARCA4 Mutations: Mutations in ARID1A and SMARCA4, components of the SWI/SNF chromatin-remodeling complex, have been confirmed in BL. These mutations are often mutually exclusive, suggesting that alteration in one is sufficient to disrupt the complex's function.
- TP53 Mutations: Alterations in TP53 have been consistently observed in BL, underscoring its role in the disease's pathogenesis.
- GNA13 Mutations: The initial study noted mutations in GNA13. Further research has highlighted its role in BL, particularly in germinal center B cell–derived lymphomas.
- Additional Mutations: Subsequent studies have identified mutations in genes such as TCF3, CCND3, and DDX3X, which were not prominently featured in the 2012 study. These findings have enriched the understanding of BL's genetic complexity.
- CCT6B, SALL3, FTCD, and PC Mutations: The study reported mutations in a large number of genes including CCT6B, SALL3, FTCD, and PC. However, these findings have not been consistently replicated in subsequent research, suggesting they may be less central to BL's pathogenesis or represent less common alterations. Most of the genes from this study are now in Tier 3.
| Entity | Tier 1 genes | Tier 2 genes | Tier 3 genes |
|---|---|---|---|
| BL | 5 | 7 | 48 |
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sankey-beta
This study, New Tier 1, 5
New Tier 1, BL Tier 1, 5
This study, New Tier 2, 7
New Tier 2, BL Tier 2, 7
This study, New Tier 3, 48
New Tier 3, BL Tier 3, 48
All other BL studies, BL Tier 1, 27
All other BL studies, BL Tier 2, 65
All other BL studies, BL Tier 3, 22
| New gene | BL tier | Average variant quality | QC outcome |
|---|---|---|---|
| ARID1A | 1 | ||
| BCL6 | 1 | ★ ★ ★ ★ ☆ | PASS |
| CREBBP | 1 | ★ ★ ★ ★ ☆ | PASS |
| GNA13 | 1 | ||
| PTEN | 1 |
| New gene | BL tier | Average variant quality | QC outcome |
|---|---|---|---|
| CARD4 | 2 | ★ ★ ★ ★ ☆ | PASS |
| CDC73 | 2 | ★ ★ ★ ☆ ☆ | PASS |
| EZH2 | 2 | ★ ★ ★ ★ ★ | PASS |
| GGTLA4 | 2 | ★ ★ ★ ★ ☆ | PASS |
| NBEAL1 | 2 | ★ ★ ★ ★ ☆ | PASS |
| P2RY2 | 2 | ★ ★ ★ ★ ☆ | PASS |
| RANBP6 | 2 | ★ ★ ★ ★ ★ | PASS |
| New gene | BL tier | Average variant quality | QC outcome |
|---|---|---|---|
| ACAD9 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| ACE | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| ATP2C2 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| BRAF | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| BRD4 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| BTG2 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| C6orf27 | 3 | Germline | FAIL |
| CAD | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| CCT6B | 3 | Germline | FAIL |
| CDH17 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| COL4A2 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| CYB5D1 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| CYP4F22 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| DLGAP1 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| DTX1 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| EIF2C4 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| EML2 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| ENTPD3 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| EPHB2 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| FAM129B | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| FGFR3 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| FTCD | 3 | Germline | FAIL |
| GRIK5 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| ICK | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| ITPR3 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| KIFC3 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| MAP3K6 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| MYH10 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| NOTCH1 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| NRXN2 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| PC | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| POLRMT | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| POR | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| PRSS22 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| PTPRN | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| RBP3 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| RET | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| SALL3 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| SAPS2 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| SBF1 | 3 | ★ ★ ☆ ☆ ☆ | FAIL |
| SF3B1 | 3 | ★ ★ ★ ★ ☆ | FAIL |
| SHANK1 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| SLC29A2 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| SYNGAP1 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| TBC1D9B | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| TIGD6 | 3 | ★ ☆ ☆ ☆ ☆ | FAIL |
| TPST2 | 3 | ☆ ☆ ☆ ☆ ☆ | FAIL |
| ZNF229 | 3 | Germline | FAIL |
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