Changes in CNA between diagnosis and xenograft
| Sample . | Gain or loss of CNA . | Cytoband . | Copy number . | Overlapping genes . | Overlapping miRNAs . |
|---|---|---|---|---|---|
| Lesions detected only in xenografts, not in matched diagnostic samples | |||||
| VHR-01 | Gain | 9p | Deletion | Many | 7 |
| Gain | 12p13 | cnLOH | Many, including ETV6 | 4 | |
| Gain | 22q | Amplification | Many | 26 | |
| VHR-02 | Gain | 9p21.3 | Deletion | C9orf53, CDKN2A, CDKN2BAS, CDKN2B Intron of ZCCHC7 | None |
| Gain | 9p13.2 | Deletion | None | ||
| VHR-03 | Gain | 7q22.3 | Deletion | PIK3CG | None |
| VHR-04 | Gain | 22q11.22 | Deletion | VPREB1, IgL | hsa-miR649 |
| SR-02 | Gain | 1p36.13 | Amplification | CROCCL1, ESPNP, MST1P2, MST1P9, NBPF1 | None |
| Gain | 1q23.3 | Deletion | None | ||
| Gain | 3q22.1 | Amplification | F11R, ITLN2 ALG1L2, LOC729375 | None | |
| HR-03 | Gain | 9q34.11; 22q11.23 | Amplification | BCR-ABL1, many | 13 |
| Gain | 1q | Amplification | Many | 45 | |
| Lesions not detected in xenografts, only in matched diagnostic samples | |||||
| VHR-02 | Loss | 4q31.3 | Deletion | 20.34% of FBXW7 | hsa-miR3140 |
| VHR-03 | Loss of CNA in subclone | 1q42.11-1q42.13 | Deletion | Many | 3 |
| Loss of CNA in subclone | 9p | Deletion | Many | 7 | |
| Loss of CNA in subclone | 14q12 | Deletion | AP4S1, C14orf126, COCH, HEATR5A, HECTD1, MIR624, STRN3 | None | |
| SR-02 | Loss | 7p21.3 | Amplification | None | None |
| HR-03 | Loss of CNA in subclone | 9p | Amplification | Many | 7 |
| Sample . | Gain or loss of CNA . | Cytoband . | Copy number . | Overlapping genes . | Overlapping miRNAs . |
|---|---|---|---|---|---|
| Lesions detected only in xenografts, not in matched diagnostic samples | |||||
| VHR-01 | Gain | 9p | Deletion | Many | 7 |
| Gain | 12p13 | cnLOH | Many, including ETV6 | 4 | |
| Gain | 22q | Amplification | Many | 26 | |
| VHR-02 | Gain | 9p21.3 | Deletion | C9orf53, CDKN2A, CDKN2BAS, CDKN2B Intron of ZCCHC7 | None |
| Gain | 9p13.2 | Deletion | None | ||
| VHR-03 | Gain | 7q22.3 | Deletion | PIK3CG | None |
| VHR-04 | Gain | 22q11.22 | Deletion | VPREB1, IgL | hsa-miR649 |
| SR-02 | Gain | 1p36.13 | Amplification | CROCCL1, ESPNP, MST1P2, MST1P9, NBPF1 | None |
| Gain | 1q23.3 | Deletion | None | ||
| Gain | 3q22.1 | Amplification | F11R, ITLN2 ALG1L2, LOC729375 | None | |
| HR-03 | Gain | 9q34.11; 22q11.23 | Amplification | BCR-ABL1, many | 13 |
| Gain | 1q | Amplification | Many | 45 | |
| Lesions not detected in xenografts, only in matched diagnostic samples | |||||
| VHR-02 | Loss | 4q31.3 | Deletion | 20.34% of FBXW7 | hsa-miR3140 |
| VHR-03 | Loss of CNA in subclone | 1q42.11-1q42.13 | Deletion | Many | 3 |
| Loss of CNA in subclone | 9p | Deletion | Many | 7 | |
| Loss of CNA in subclone | 14q12 | Deletion | AP4S1, C14orf126, COCH, HEATR5A, HECTD1, MIR624, STRN3 | None | |
| SR-02 | Loss | 7p21.3 | Amplification | None | None |
| HR-03 | Loss of CNA in subclone | 9p | Amplification | Many | 7 |
CNAs that changed from diagnosis to xenograft material (additional/lost deletions, amplifications, and cnLOH) are presented. If > 10 genes or 3 miRNAs were in one CNA, it was noted as many or the number was listed.