Molecular Diagnostics & PCR Assay Design

We design robust PCR primers and probe-based assays for research and diagnostic workflows from singleplex tests to high-plex panels prioritizing specificity, reproducibility, and clear deliverables.

Typical outputs

Primer/probe sequences + Tm/GC/amplicon size
Specificity & off-target report
Multiplex compatibility checks
Ready-to-order table (CSV/Excel)

What we develop

PCR primers

Endpoint PCR and genotyping assays optimized for efficiency, specificity, and clean amplification.

qPCR / probe assays

Hydrolysis or hybridization probe sets, with attention to SNP/indel positioning and assay stability.

Multiplex & high-plex panels

Panel construction and balancing strategies for dozens to hundreds of targets (tiling or gene panels).

Polymorphism detection

Assays for discriminating individuals, lines, or populations using SNPs/indels and repeat-associated loci.

Where PCR diagnostics are applied

Pathogen detection and strain/variant screening
Genetic disorder testing and carrier screening (research use)
Paternity/kinship and identity testing (where permitted)
Forensics and criminal investigation support workflows
Polymorphism and marker-assisted selection in plants/animals
Site-directed mutagenesis and clone validation
Validation of sequencing or microarray findings
Targeted amplicon sequencing preparation (Illumina/ONT)

Quality controls we emphasize

Specificity

Genome/database mapping, off-target assessment, and masking of repeats.

Thermodynamics

Tm/GC balance, secondary structures, and primer–dimer risk checks.

Multiplexability

Cross-interactions, pool partitioning, and amplicon spacing for panels.

Practical deliverables

Ordering table, recommended cycling conditions, and assay notes.

How the workflow typically runs

Step 1

Inputs

Targets (FASTA), coordinates, or gene lists; organism/build; constraints (amplicon length, chemistry).

Step 2

Design

Candidate primer/probe generation with thermodynamic constraints and repeat-aware filtering.

Step 3

In-silico validation

Mapping/off-target checks, amplicon verification, and multiplex interaction scanning.

Step 4

Deliverables

Final assay table and reports; optional pooling guidance for high-plex panels.

Note on intended use

PrimerDigital provides assay design and in‑silico validation. Wet-lab validation, clinical verification, and regulatory approval (if applicable) must be performed by the customer in accordance with local regulations and quality management requirements.

Discuss your diagnostic project

Share target sequences, organism/build, and assay type. We will propose an efficient design strategy and deliverables.