Sequences of primers and probes used for clonotypic assays
Probes . | Primers . |
|---|---|
| Quantitative clonotypic assays* | |
| jb1-1FAM | FAM-CAAGGCACCAGACTCACAGT-BHQ-1 |
| jb2-1FAM | FAM-AGCAGTTCTTCGGGCCAG-MGBNFQ |
| jb2-3FAM | FAM-CAGTATTTTGGCCCAGGCA-MGBNFQ |
| vb12jb2.3BM sense, patient no. 31 | 5′-AGTTATGGAGCGGGGGCTAGCAC-3′ |
| vb13jb2.3BM sense, patient no. 37 | 5′-AGTTCCATCGGAAGGACTAGTAC-3′ |
| vb6jb2.3PB sense, patient no. 39 | 5′-TGCGTATCCACCGGAGGAGAG-3′ |
| vb14jb2.3BM sense, patient no. 40 | 5′-AGCAGGGAGACTAGCGGTCACAC-3′ |
| vb23jb2.1PB sense, patient no. 40 | 5′-CATTGATTCCCTGTCCCGGGAAG-3′ |
| vb15jb2.3PB sense, patient no. 41 | 5′-CTGCGTATCTGTGTCCCCTGTCC-3′ |
| vb24jb2.5PB sense, patient no. 41 | 5′-GGTCTCTCCTCCTACTCTGC-3′ |
| vb7jb2.1PB sense, patient no. 42 | 5′-TGTAAGGGTAGGCCCCGGTG-3′ |
| CB antisense | 5′-CTGCTTCTGATGGCTCAAACAC-3′ |
| Clonotypic PCR assays on biopsy tissues† | |
| vb6 sense | 5′-TCTCAGGTGTGATCCAAATTCGGG-3′ |
| vb7 sense | 5′-CCTGAATGCCCCAACAGCTCTCTC-3′ |
| vb15 sense | 5′-CAGGCACAGGCTAAATTCTCCCTG-3′ |
| vb23 sense | 5′-GCAGGGTCCAGGTCAGGACCCCCA-3′ |
| vb24 sense | 5′-CCCAGTTTGGAAAGCCAGTGACCC-3′ |
| vb6jb2.3PB antisense, patient no. 39 | 5′-TGCGTATCCACCGGAGGAGAG-3′ |
| vb23jb2.1PB antisense, patient no. 40 | 5′-CATTGATTCCCTGTCCCGGGAAG-3′ |
| vb15jb2.3PB antisense, patient no. 41 | 5′-CTGCGTATCTGTGTCCCCTGTCC-3′ |
| vb24jb2.5PB antisense, patient no. 41 | 5′-GGTCTCTCCTCCTACTCTGC-3′ |
| vb7jb2.1PB antisense, patient no. 42 | 5′-TGTAAGGGTAGGCCCCGGTG-3′ |
| jb2.1 antisense | 5′-CCTTCTTACCTAGCACGGTGA-3′ |
| jb2.3 antisense | 5′-CCCGCTTACCGAGCACTGTCA-3′ |
| jb2.5 antisense | 5′-CGCGCACACCGAGCAC-3′ |
Probes . | Primers . |
|---|---|
| Quantitative clonotypic assays* | |
| jb1-1FAM | FAM-CAAGGCACCAGACTCACAGT-BHQ-1 |
| jb2-1FAM | FAM-AGCAGTTCTTCGGGCCAG-MGBNFQ |
| jb2-3FAM | FAM-CAGTATTTTGGCCCAGGCA-MGBNFQ |
| vb12jb2.3BM sense, patient no. 31 | 5′-AGTTATGGAGCGGGGGCTAGCAC-3′ |
| vb13jb2.3BM sense, patient no. 37 | 5′-AGTTCCATCGGAAGGACTAGTAC-3′ |
| vb6jb2.3PB sense, patient no. 39 | 5′-TGCGTATCCACCGGAGGAGAG-3′ |
| vb14jb2.3BM sense, patient no. 40 | 5′-AGCAGGGAGACTAGCGGTCACAC-3′ |
| vb23jb2.1PB sense, patient no. 40 | 5′-CATTGATTCCCTGTCCCGGGAAG-3′ |
| vb15jb2.3PB sense, patient no. 41 | 5′-CTGCGTATCTGTGTCCCCTGTCC-3′ |
| vb24jb2.5PB sense, patient no. 41 | 5′-GGTCTCTCCTCCTACTCTGC-3′ |
| vb7jb2.1PB sense, patient no. 42 | 5′-TGTAAGGGTAGGCCCCGGTG-3′ |
| CB antisense | 5′-CTGCTTCTGATGGCTCAAACAC-3′ |
| Clonotypic PCR assays on biopsy tissues† | |
| vb6 sense | 5′-TCTCAGGTGTGATCCAAATTCGGG-3′ |
| vb7 sense | 5′-CCTGAATGCCCCAACAGCTCTCTC-3′ |
| vb15 sense | 5′-CAGGCACAGGCTAAATTCTCCCTG-3′ |
| vb23 sense | 5′-GCAGGGTCCAGGTCAGGACCCCCA-3′ |
| vb24 sense | 5′-CCCAGTTTGGAAAGCCAGTGACCC-3′ |
| vb6jb2.3PB antisense, patient no. 39 | 5′-TGCGTATCCACCGGAGGAGAG-3′ |
| vb23jb2.1PB antisense, patient no. 40 | 5′-CATTGATTCCCTGTCCCGGGAAG-3′ |
| vb15jb2.3PB antisense, patient no. 41 | 5′-CTGCGTATCTGTGTCCCCTGTCC-3′ |
| vb24jb2.5PB antisense, patient no. 41 | 5′-GGTCTCTCCTCCTACTCTGC-3′ |
| vb7jb2.1PB antisense, patient no. 42 | 5′-TGTAAGGGTAGGCCCCGGTG-3′ |
| jb2.1 antisense | 5′-CCTTCTTACCTAGCACGGTGA-3′ |
| jb2.3 antisense | 5′-CCCGCTTACCGAGCACTGTCA-3′ |
| jb2.5 antisense | 5′-CGCGCACACCGAGCAC-3′ |
FAM-labeled and minor groove binder (MGB) or black hole quencher 1 (BHQ1) quenched probes were used for quantitative PCR. CB reverse primer was designed to cover both CB1 and CB2 chains
PB indicates primer designed from CDR3 sequence detected in peripheral blood; and BM, primer designed from BM-derived clonotype
Shown in Figure 4A, C
Shown in Figure 4B