About BCR
The BCR gene (BCR Activator of RhoGEF and GTPase) on chromosome 22q11 The t(9;22) Philadelphia chromosome fuses BCR to ABL1, generating a constitutively active tyrosine kinase driver of chronic myeloid leukemia. Key targets include Exons 1–23 (fusion breakpoints in introns 13–14) for comprehensive mutation screening.
Mutations: t(9;22) BCR-ABL1 fusion, BCR-ABL1 e13a2, e14a2 | GC content: 54% | Target exons: Exons 1–23 (fusion breakpoints in introns 13–14)
BCR Primer Design Challenges
- Chromosomal translocation detection: BCR-ABL1 fusion breakpoints vary (e13a2, e14a2, e1a2) requiring multiplex primer strategies
- BCR N-terminal oligomerization: The coiled-coil domain in exon 1 is critical for BCR-ABL1 activation and requires targeted detection
- Large introns: Intronic breakpoints span 5.8 kb requiring long-range PCR optimization
Recommended Primer Design Parameters for BCR
| Parameter | Standard Exons | Optimized Regions |
|---|---|---|
| Primer length | 20–22 nt | 22–25 nt |
| GC content | 45–55% | 50–60% |
| Tm | 58–62°C | 60–65°C |
| Amplicon size | 150–300 bp | 180–350 bp |
| Annealing temp | 58–60°C | 60–64°C (touchdown) |
| PCR additive | Standard | Optional 3–5% DMSO for problematic regions |
Recommended Primer Sequences for BCR
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| e13a2 fusion | 5′-ACAGCATTCCGCTGACCATC-3′ | 5′-CAGCTCACTGACCACTCGTC-3′ | 210 bp |
| e14a2 fusion | 5′-ATCCGTGGAGCTGCAGATGC-3′ | 5′-TCAGACCCTGAGGCTCAAAG-3′ | 225 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing BCR primers, avoid these clinically significant variants:
- rs45459197 (BCR intron 14) — Breakpoint cluster region variant
- rs45558697 (BCR exon 13) — e13a2 breakpoint-associated SNP
Clinical Validation Required
All BCR primers designed with VigyanLLM are for research use only. Clinical diagnostic applications require additional wet-lab validation, Sanger sequencing confirmation, and regulatory approval before patient use.
Design BCR Primers Now
Pre-configured with BCR-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.