Comparison of RNA-seq to standard-of-care cytogenetic testing to identify fusion genes
| Rearrangements identified . | Standard test, n . | RNA-seq (additional findings to standard testing), n . | RNA-seq/standard test, % . | Comment . | |
|---|---|---|---|---|---|
| B-ALL | |||||
| BCR-ABL1 | 4 | 3 | 75 | Missed BCR-ABL1 (1). RNA-Seq performed on sample taken 8 d after commencement of induction. | |
| KMT2A rearrangement | 6 | 4 | 66.7 | Missed KMT2A-MLLT1 (1) and KMT2A-X (1). Low expression of KMT2A in these samples (Figure 3A) | |
| ETV6-RUNX1 | 20 | 20 | 100 | — | |
| TCF3-PBX1 | 2 | 2 | 100 | — | |
| IL3-IGH | 1 | 0 | 0 | Missed IL3-IGH (1) | |
| Undefined/B-other | |||||
| ABL1 rearrangement | 2 | 2 | 100 | — | |
| JAK2 rearrangement | 0 | 0 (2) | — | PAX5-JAK2 (2) | |
| CRLF2 rearrangement | 9 | 8 (1) | 88.9 | Missed IGH-CRLF2 (1). P2RY8-CRLF2 (1) | |
| ETV6 rearrangement | 4 | 3 (2) | 75 | Missed ETV6 rearrangement (1). CHST11-VSP8 (1)fusion found in this patient by RNA-Seq. Suggesting of a more complex Chr3/12 rearrangement. Two ETV6 rearrangements found in 1 patient: ETV6-MDH2 + ETV6-ATP5SL (1) | |
| ZNF384 rearrangement | 1 | 1 (1) | 100 | TCF3-ZNF384 (1) | |
| PAX5 rearrangement | 1 | 1 (1) | 100 | PAX5-AUTS2 (1) | |
| Additional findings in patients otherwise classified | 0 | 0 (5) | — | PAX5-LINC01400 (hyperdiploid, 1); PAX5-ARHGAP22 (hypodiploid, 1); PAX5-NOL4L (P2RY8-CRLF2, 1); PAX5-MSMP (IGH-CRLF2, 1); IKZF1-CEP170+ADSS-IKZF1 (ETV6-CLN6, 1) | |
| T-ALL | |||||
| Undefined/T-other | |||||
| LMO2 rearrangement | 2 | 2 (1) | 100 | LMO2-TRA (1) | |
| KMT2A rearrangement | 1 | 1 | 100 | — | |
| NUP214-ABL1 | 1 | 1 | 100 | — | |
| MYC rearrangement | 1 | 0 | 0 | Missed TRA-MYC (1) | |
| Other | 1 | 0 (4) | 0 | PTEN-ATAD1 (1); BCOR-KDM6A+PHF16-BCOR (1); TCF7-CSF1R (1); TP53-WDR7 (1) | |
| Additional findings in patients otherwise classified | 0 | 0 (1) | — | ETV6-CRX (ETP-ALL,1) | |
| Total | 56 | 48 (18) | 85.7 | ||
| Rearrangements identified . | Standard test, n . | RNA-seq (additional findings to standard testing), n . | RNA-seq/standard test, % . | Comment . | |
|---|---|---|---|---|---|
| B-ALL | |||||
| BCR-ABL1 | 4 | 3 | 75 | Missed BCR-ABL1 (1). RNA-Seq performed on sample taken 8 d after commencement of induction. | |
| KMT2A rearrangement | 6 | 4 | 66.7 | Missed KMT2A-MLLT1 (1) and KMT2A-X (1). Low expression of KMT2A in these samples (Figure 3A) | |
| ETV6-RUNX1 | 20 | 20 | 100 | — | |
| TCF3-PBX1 | 2 | 2 | 100 | — | |
| IL3-IGH | 1 | 0 | 0 | Missed IL3-IGH (1) | |
| Undefined/B-other | |||||
| ABL1 rearrangement | 2 | 2 | 100 | — | |
| JAK2 rearrangement | 0 | 0 (2) | — | PAX5-JAK2 (2) | |
| CRLF2 rearrangement | 9 | 8 (1) | 88.9 | Missed IGH-CRLF2 (1). P2RY8-CRLF2 (1) | |
| ETV6 rearrangement | 4 | 3 (2) | 75 | Missed ETV6 rearrangement (1). CHST11-VSP8 (1)fusion found in this patient by RNA-Seq. Suggesting of a more complex Chr3/12 rearrangement. Two ETV6 rearrangements found in 1 patient: ETV6-MDH2 + ETV6-ATP5SL (1) | |
| ZNF384 rearrangement | 1 | 1 (1) | 100 | TCF3-ZNF384 (1) | |
| PAX5 rearrangement | 1 | 1 (1) | 100 | PAX5-AUTS2 (1) | |
| Additional findings in patients otherwise classified | 0 | 0 (5) | — | PAX5-LINC01400 (hyperdiploid, 1); PAX5-ARHGAP22 (hypodiploid, 1); PAX5-NOL4L (P2RY8-CRLF2, 1); PAX5-MSMP (IGH-CRLF2, 1); IKZF1-CEP170+ADSS-IKZF1 (ETV6-CLN6, 1) | |
| T-ALL | |||||
| Undefined/T-other | |||||
| LMO2 rearrangement | 2 | 2 (1) | 100 | LMO2-TRA (1) | |
| KMT2A rearrangement | 1 | 1 | 100 | — | |
| NUP214-ABL1 | 1 | 1 | 100 | — | |
| MYC rearrangement | 1 | 0 | 0 | Missed TRA-MYC (1) | |
| Other | 1 | 0 (4) | 0 | PTEN-ATAD1 (1); BCOR-KDM6A+PHF16-BCOR (1); TCF7-CSF1R (1); TP53-WDR7 (1) | |
| Additional findings in patients otherwise classified | 0 | 0 (1) | — | ETV6-CRX (ETP-ALL,1) | |
| Total | 56 | 48 (18) | 85.7 | ||
Bold typeface indicates fusions that were identified by RNA-seq only.