About HER2/ERBB2
The ERBB2 gene (also known as HER2, human epidermal growth factor receptor 2) on chromosome 17q12 encodes a receptor tyrosine kinase in the EGFR family. HER2 amplification and overexpression occur in ~20% of breast cancers and are key biomarkers for targeted therapy. ERBB2 spans ~40 kb with 27 coding exons.
NCBI Gene ID: 2064 | RefSeq: NM_004448.3 | Genomic: NC_000017.11 (39688492-39728990)
HER2/ERBB2 Primer Design Challenges
- Amplification quantification: qPCR requires reference gene co-amplification (e.g., RNaseP or TOP2A) for copy number normalization
- GC-rich regions: Exons 1–5 contain 60–70% GC content requiring optimized parameters
- Gene duplication: ERBB2 amplification in tumors requires primers that avoid homologous ERBB family members (EGFR, ERBB3, ERBB4)
- Alternative transcripts: Multiple splice variants (including a constitutively active truncated form) require careful transcript selection
- Clinical cut-offs: IHC/FISH correlation requires precise amplicon design for copy number assays
Recommended Primer Design Parameters for HER2/ERBB2
| Parameter | Standard Exons | GC-Rich Exons (1–5) |
|---|---|---|
| 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 | 62-65°C |
| PCR additive | Standard | Add 5% DMSO or 1M betaine |
Key SNPs to Avoid in Primer Binding Sites
When designing HER2/ERBB2 primers, avoid these significant variants:
- rs1136201 (p.Ile655Val) — Common polymorphism in transmembrane domain, associated with cancer risk
- rs1058808 (p.Pro1170Ala) — C-terminal variant in exon 27
- rs4252633 (p.Trp452Cys) — Extracellular domain missense variant
Clinical Validation Required
All HER2/ERBB2 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.
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