About ESR1
The ESR1 gene (Estrogen Receptor 1) on chromosome 6q25 Ligand-binding domain mutations (Y537S, D538G) arise during aromatase inhibitor therapy and drive acquired endocrine resistance in metastatic breast cancer. Key targets include Exons 1–10 (LBD in exons 4–10) for comprehensive mutation screening.
Mutations: Y537S, Y537N, D538G, E380Q | GC content: 49% | Target exons: Exons 1–10 (LBD in exons 4–10)
ESR1 Primer Design Challenges
- Acquired resistance mutations: LBD mutations (Y537S, D538G) emerge during therapy requiring highly sensitive (>0.1% VAF) mutation detection
- Moderate-to-low GC (49%): Slightly AT-rich sequence in exons 1–2 requires modest Tm adjustments
- Multiple transcript isoforms: ERα-36 (truncated) and ERα-46 variant transcripts require isoform-specific 3' primers
Recommended Primer Design Parameters for ESR1
| 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 ESR1
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 8 (LBD Y537S) | 5′-GCTACAATCATCTGAGGTCC-3′ | 5′-CCTCTGACGGTAGACCTTCC-3′ | 208 bp |
| Exon 4 (DNA-binding) | 5′-GACACATGATCGGTCCGTCA-3′ | 5′-ACATCTCGGGTAGGTCACAG-3′ | 182 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing ESR1 primers, avoid these clinically significant variants:
- rs121908912 (Y537S) — Exon 8 LBD activating mutation, endocrine resistance
- rs121908913 (D538G) — Exon 8 LBD hotspot in metastatic breast cancer
Clinical Validation Required
All ESR1 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 ESR1 Primers Now
Pre-configured with ESR1-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.