About CDH1
The CDH1 gene (Cadherin 1) on chromosome 16q22 Germline mutations in CDH1 cause hereditary diffuse gastric cancer (HDGC) with ~70% lifetime risk, and lobular breast cancer. Key targets include Exons 1–16 for comprehensive mutation screening.
Mutations: Truncating, missense, promoter hypermethylation | GC content: 52% | Target exons: Exons 1–16
CDH1 Primer Design Challenges
- Promoter CpG methylation: Epigenetic silencing via promoter hypermethylation is a key inactivation mechanism requiring bisulfite-based primer design
- Large gene structure: 16 exons spanning ~100 kb with large introns (intron 1 = 27 kb) complicate genomic amplification
- Multiple mutation types: Missense, frameshift, splice-site, and large deletions require comprehensive primer coverage
Recommended Primer Design Parameters for CDH1
| 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 CDH1
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 7 (extracellular) | 5′-GAGGTGCTGTTGCCAGTCAT-3′ | 5′-CATCAGCAAGAGCATGAGCA-3′ | 168 bp |
| Exon 12 (cytoplasmic) | 5′-GCTCACAGTGTGTGACTGGA-3′ | 5′-ACCTTGAGAGGTGACGCTTG-3′ | 213 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing CDH1 primers, avoid these clinically significant variants:
- rs121964898 (R732Q) — Exon 12 missense variant in HDGC
- rs121964878 (1003C>T) — Premature stop in exon 7
Clinical Validation Required
All CDH1 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 CDH1 Primers Now
Pre-configured with CDH1-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.