Table 3.
RNA-seq results for genes not targeted by the diagnostic standard protocol using FISH or RT-PCR analysis. Additional gene fusions were detected in the IKZF1plus and B-other subtypes but not in hyperdiploid BCP-ALL. Fusions were detected in cases with aberrant but also with normal karyotypes as assessed by R-banding and FISH. The 5′-3′ orientation (➔) of fused coding gene regions to one another is indicated according to the spanning read observed in TopHat alignment (details in Tab.S3). Information on potential in frame fusions of the coding sequences (CDS) is based on TopHat spanning reads as well. Presence of all fusions, except IKZF1-DLG2, could be validated indirectly by array CGH, FISH, or retrospective banding analysis. Previous reports on fusion genes observed in this study are summarized
| Genetic subtype | Patient data | RNA-seq | Previous report on fusion gene | |||||
|---|---|---|---|---|---|---|---|---|
| Case no. | Sex | Age at diagnosis | Immunophenotype | Fusion | Orientation of fusion partners (observed CDS) | Corresponding aberration in aCGH (affected genes) | ||
| IKZF1plus | 32 | m | 17.0 | common-ALL (B-II) | EBF1-PDGFRB | ➔➔ (in and out of frame fusions) | pos (EBF1 and PDGFRB) | Roberts et al., 2014, NEJM |
| 33 | m | 13.1 | common-ALL (B-II) | ETV6-IKZF1 | ➔➔ (out of frame fusion) | pos (IKZF1) | no previous report | |
| 34 | m | 5.6 | common-ALL (B-II) | ETV6-NTRK3 | ➔➔ (in frame fusion) | pos (ETV6 and NTRK3) | Roberts et al., 2014, NEJM | |
| 35 | f | 2.5 | pre-B-ALL (B-III) | PAX5-MYO1G | ➔➔ (in and out of frame fusions) | pos (PAX5 and MYO1G) | no previous report | |
| 36 | m | 3.2 | common-ALL (B-II) | PAX5-NCOA6 | ➔➔ (in frame fusion) | pos (PAX5 and NCOA6) | no previous report | |
| 37 | f | 11.6 | common-ALL (B-II) | TERF2-JAK2 JAK2-TERF2 | ➔➔ (in frame fusions) | neg | Roberts et al., 2014, NEJM | |
| B-other | 47 | m | 2.4 | pro-B-ALL (B-I) | ETV6-IKZF1 IKZF1-DLG2 | ➔➔ (out of frame fusions) | pos (ETV6) | no previous report |
| 48 | f | 4.2 | pro-B-ALL (B-I) | EP300-ZNF384 | ➔➔ (in frame fusion) | pos (EP300) | Gocho et al., 2015, Leukemia | |
| 49 | m | 13.7 | common-ALL (B-II) | HOOK3-FGFR1 | ➔➔ (in frame fusion) | neg | Reshmi et al., 2017, Blood | |
| 50 | f | 12.9 | common-ALL (B-II) | MEF2D-BCL9 | ➔➔ (in frame fusions) | pos (MEF2D and BCL9) | Gu et al., 2016, Nat Commun | |
| 51 | m | 3.7 | common-ALL (B-II) | PAX5-DACH1 | ➔➔ (in frame fusion) | pos (PAX5 and DACH1) | Nebral et al., 2009, Leukemia | |
| 52 | f | 15.0 | pre-B-ALL (B-III) | PAX5-ETV6 | ➔➔ (fusion with non-coding ETV6 exon) | pos (PAX5 and ETV6) | Cazzaniga et al., 2001, Cancer Res | |
| 53 | f | 6.5 | common-ALL (B-II) | PAX5-LINC01251 | ➔➔ (fusion with non-coding RNA) | pos (PAX5 and LINC01251) | no previous report | |
| 54 | f | 8.1 | pre-B-ALL (B-III) | ZNF618-NUTM1 | ➔➔ (in frame fusion) | pos (NUTM1) | Gu et al., 2019, Nat Genet | |
| 55 | f | 2.2 | pre-B-ALL (B-III) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 56 | f | 3.1 | common-ALL (B-II) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 57 | f | 3.2 | common-ALL (B-II) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 58 | m | 3.2 | common-ALL (B-II) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 59 | m | 3.4 | common-ALL (B-II) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 60 | f | 4.2 | pre-B-ALL (B-III) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 61 | f | 5.6 | pre-B-ALL (B-III) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 62 | m | 10.3 | common-ALL (B-II) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | pos (P2RY8 and CRLF2) | Russell et al., 2009, Blood | |
| 63 | m | 7.3 | common-ALL (B-II) | P2RY8-CRLF2 | ➔➔ (fusion of P2RY8 non-coding exon 1 to CRLF2 coding region) | np | Russell et al., 2009, Blood | |