About BRCA2
The BRCA2 gene (BRCA2 DNA Repair Associated) on chromosome 13q13 Germline loss-of-function mutations in BRCA2 confer lifetime breast cancer risk of ~69% and ovarian cancer risk of ~17%. Key targets include Exons 2–27 for comprehensive mutation screening.
Mutations: Truncating, frameshift, 6174delT, 999del5 | GC content: 41% | Target exons: Exons 2–27
BRCA2 Primer Design Challenges
- Very low GC content (41%): BRCA2 has among the lowest GC content of cancer genes, causing weak primer-template stability
- Large coding sequence: 27 exons spanning 11.4 kb require 120+ tiled amplicons for full mutation screening
- Multitude of founder mutations: Population-specific frameshifts (6174delT in Ashkenazi, 999del5 in Icelandic) need targeted genotyping
Recommended Primer Design Parameters for BRCA2
| Parameter | Standard Exons | Low-GC / AT-Rich 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 | Longer primers (24–28 nt), lower annealing Tₘ |
Recommended Primer Sequences for BRCA2
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 9 (Icelandic del) | 5′-CCTGTGAAGACAGTGACAGC-3′ | 5′-ACACAGCTTGTAGGGACTCC-3′ | 172 bp |
| Exon 11 (6174delT) | 5′-AAGGTGCATGGCTACAGCTG-3′ | 5′-TCTGTGCTGTGACTTTGCTG-3′ | 244 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing BRCA2 primers, avoid these clinically significant variants:
- rs80359550 (6174delT) — Ashkenazi Jewish founder frameshift in exon 11
- rs80359671 (999del5) — Icelandic founder mutation in exon 9
Clinical Validation Required
All BRCA2 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 BRCA2 Primers Now
Pre-configured with BRCA2-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.