About ERCC1
The ERCC1 gene (ERCC Excision Repair 1) on chromosome 19q13 Expression levels and polymorphisms in ERCC1 influence response to platinum-based chemotherapy in non-small cell lung and ovarian cancers. Key targets include Exons 1–10 for comprehensive mutation screening.
Mutations: Asn118Asn (rs11615), C8092A (rs3212986) | GC content: 54% | Target exons: Exons 1–10
ERCC1 Primer Design Challenges
- Polymorphism-as-biomarker: rs11615 (N118N) and rs3212986 (C8092A) are common SNPs that may influence mRNA stability and therapeutic prediction
- Balanced GC (54%): Standard PCR conditions suitable but requires Mg2+ optimization for some GC-rich intron 2 regions
- Alternative splicing: ERCC1-202 (lacks exon 8) and ERCC1-204 (lacks exons 2–3) transcripts require splice-aware primer design
Recommended Primer Design Parameters for ERCC1
| 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 ERCC1
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 4 (rs11615) | 5′-CAAGAGGAGGCAATGTGGAC-3′ | 5′-TGACACTCTGGGAGGTAGCA-3′ | 160 bp |
| Exon 10 (3' UTR) | 5′-CCCTGGGAGTTTAGAGAAGC-3′ | 5′-ACTCAGGAGTGCACATCAAG-3′ | 218 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing ERCC1 primers, avoid these clinically significant variants:
- rs11615 (N118N) — Exon 4 synonymous variant, therapy response marker
- rs3212986 (C8092A) — 3' UTR variant, platinum sensitivity
Clinical Validation Required
All ERCC1 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 ERCC1 Primers Now
Pre-configured with ERCC1-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.