Table 2.
Comparison of standard of care FISH results and OGM.
| Samples | FISH (% of Abnormal Cells) | OGM (fCN/VAF) | Concordance |
|---|---|---|---|
| 1 (non-diploid) | TP53/D17Z1 (4 × 81%) | Gain of chromosome 17 | Yes |
| FGFR3 (3 × 90%) | Gain of chromosomes 5, 6, 7, 9, 15, 19 | Ploidy * | |
| IGH (3 × 45%, 4 × 46%) | Gain of chromosome 14 | Yes | |
| MAFB (3 × 94%) | Ploidy * | ||
| 1p32/CDKN2C (3 × 88%) | Ploidy * | ||
| 1q21/CKS1B amplification (5 × 88%) | 1q21/CKS1B amplification (3.25/0.63) | Yes | |
| 2 | Deletion 17p/TP53 (1 × 6%) | Deletion 17p/TP53 (visual inspection) | Yes |
| t(14;16) (2F 98%) | t(14;16) (0.48) | Yes | |
| Deletion 1p32/CDKN2C (1 × 22%) | Deletion 1p32/CDKN2C (1.73/0.135) | Yes | |
| 1q21/CKS1B gain (3 × 71%) | 1q21/CKS1B gain (2.72/0.36) | Yes | |
| 3 | Deletion 17p/TP53 (1 × 95%) | Deletion 17p/TP53 (0.91/0.54) | Yes |
| t(11;14) (2F 77%, 3F 17%) | t(11;14) (0.55) | Yes | |
| 5 | Normal | Yes | |
| Gain of chromosomes 3, 5, 9, 11, 15, 19 | N/A | ||
| 6 | Deletion 17p/TP53 (1 × 75%) | Deletion 17p/TP53 (0.81/0.59) | Yes |
| Gain of chromosomes 3, 7, 11, 15 | N/A | ||
| 1q21/CKS1B gain (3 × 70%) | 1q21/CKS1B gain (2.86/0.43) | Yes | |
| 7 | t(4;14) (1F 97%) | t(4;14) (0.51) | Yes |
| 1q21/CKS1B amplification (4 × 96%) | 1q21/CKS1B amplification (4.36/1.18) | Yes | |
| 9 | IGH (1 × 6%) | Gain of chromosomes 3, 5, 9, 11, 15, 19, 21 | No |
| 12 (non-diploid) | TP53/D17Z1 (4 × 14%) | t(6;14) (0.52) | Ploidy * |
| FGFR3 (4 × 16%) | Ploidy * | ||
| IGH (3x 18%, 4 × 13%) | Yes | ||
| MAF (4 × 14%) | Ploidy * | ||
| MAFB (4 × 10%) | Ploidy * | ||
| 1p32/CDKN2C (4 × 12%) | Ploidy * | ||
| 1q21/CKS1B amplification (4 × 12%) | 1q amplification not detected | Ploidy * | |
| 18 | Deletion 17p/TP53 (1 × 98%) | Deletion 17p/TP53 (1.02/0.49) | Yes |
| Deletion 1p32/CDKN2C (1 × 96%) | Deletion 1p32/CDKN2C (1.05/0.47) | Yes | |
| Gain of chromosomes 3, 5, 7, 9, 11, 15, 21 | N/A | ||
| 24 | t(11;14) (2F 87%) | t(11;14) (0.24) | Yes |
| 1q21/CKS1B gain (3 × 95%) | 1q21/CKS1B gain (2.92/0.46) | Yes | |
| 25 | t(11;14) (2F 97%) | t(11;14) (0.69) | Yes |
| 30 | Gain of chromosomes 3, 5, 7, 15, 18, 19 | N/A | |
| 1q21/CKS1B gain (3 × 60%) | 1q21/CKS1B gain (2.41/0.20) | Yes | |
| 33 (non-diploid) | TP53/D17Z1 (2 × 17.5%, 3 × 70%) | Deletion 1p32/CDKN2C (1.37/0.32) | Ploidy * |
| FGFR3 (3 × 64%) | Gain of chromosomes 3, 5, 7, 9, 15 | Ploidy * | |
| MAFB (3 × 91%) | Ploidy * | ||
| 1q21/CKS1B (3 × 81%, 4 × 14%) | 1q21/CKS1B gain by visual inspection | Yes | |
| 37 | t(11;14) (1F 89%) | t(11;14) (0.45) | Yes |
| 1q21/CKS1B gain (3 × 49%) | 1q21/CKS1B gain (2.32/0.16) | Yes | |
| 38 | Gain of chromosomes 9, 11, 15, 19 | N/A | |
| 1q21/CKS1B gain (3 × 91%) | 1q21/CKS1B gain (3.05/0.53) | Yes | |
| 41 | t(11;14) (2F 96%) | t(11;14) (0.25) | Yes |
| 1q21/CKS1B gain (3 × 95%) | 1q21/CKS1B gain (2.99/0.49) | Yes | |
| 42 | Gain of chromosomes 5, 9, 11, 15, 18, 19 | N/A | |
| Deletion 17p/TP53 (1 × 45%) | Deletion 17p/TP53 by visual inspection | Yes | |
| Deletion 1p32/CDKN2C (1 × 78%, 0 × 12%) | Deletion 1p32 CNV (1.08/0.46), SV targeted deletion CDKN2C (0.9/0.22) | Yes | |
| 43 | Gain of chromosomes 3, 5, 7, 9, 11, 17, 18, 19 | N/A | |
| Deletion 17p/TP53 (1 × 97%%) | Deletion 17p/TP53 (1.04/0.48) | Yes | |
| 1q21/CKS1B amplification (3 × 29%, 4 × 42%; 5 × 19%) | 1q21/CKS1B amplification (3.59/0.8) | Yes | |
| 44 (non-diploid) | TP53/D17Z1 (3 × 5%, 4 × 17%, 5 × 41%) | Gain of chromosome 17 | Yes |
| FGFR3 (3 × 59%) | Ploidy * | ||
| MAF (3 × 35%) | Ploidy * | ||
| t(14;20) (2F 66%, 3F 43%) | t(14;20) (0.28) | Yes | |
| 1p32/CDKN2C (3 × 50,4%) | Deletion 1p32/CDKN2C (1.72/0.14) | Ploidy * | |
| 1q21/CKS1B amplification (3 × 4%, 4 × 21%, 5 × 45%) | 1q21/CKS1B gain (2.55/0.68) | Ploidy * | |
| 45 (non-diploid) | TP53/D17Z1 (3 × 67%) | Deletion 1p32/CDKN2C (1.42/0.29) | Ploidy * |
| t(4;14) (2F: 8%; 3F: 85%) | t(4;14) (0.28) | Yes | |
| 1q21/CKS1B amplification (5 × 4%, 6 × 28%, 7 × 49%, 8 × 12%) | 1q21/CSK1B amplification (4.15/1.08) | Ploidy * |
FISH results, showing the copy number and the percentage of positive cells, were compared to the fractional copy number (fCN) and variant allele frequency (VAF) values obtained by OGM for the 17p/TP53 deletion, various IGH translocations and chromosome 1 abnormalities. Probe targeting TP53/D17Z1 loci, t(4;14), t(14;16) and t(14;20) dual-color dual-fusion probes and probe for detection of 1p32/CDKN2C deletion and 1q21/CKS1B amplification were used for every sample. For patients with IGH translocations, the number of fusion signals is reported. If not otherwise specified, results were consistent with the normal FISH signal pattern expected with the specific probe. Samples with non-diploid genomes are indicated. Ploidy * refers to cases with non-diploid genomes where concordance could not be readily evaluated. N/A: not assessed by FISH.