Genotyping / Allele Discrimination

Feature documentation: Genotyping / Allele Discrimination

Score primers for SNP genotyping assays (allele-specific PCR).

Overview

The genotyping module evaluates primer suitability for allele-specific PCR:

• SNP Position - 3’ terminal = best discrimination
• Mismatch Type - Transversions discriminate better than transitions
• Tm Difference - Higher delta Tm = better specificity

Python API

score_genotyping_primer_api

from primerlab.api import score_genotyping_primer_api

result = score_genotyping_primer_api(
    primer_sequence="ATGCGATCGATCGATCGA",
    snp_position=0,        # Distance from 3' end
    ref_allele="A",
    alt_allele="T",
)

print(f"Grade: {result['grade']}")
print(f"Delta Tm: {result['delta_tm']}°C")
print(f"Specificity: {result['specificity']}")

SNP Position Guidelines

Position from 3’	Weight	Discrimination
0 (terminal)	1.0	Best
1	0.7	Good
2	0.4	Acceptable
3	0.2	Marginal
4+	<0.2	Poor

Mismatch Type Scoring

Transversions (purine ↔ pyrimidine) provide better discrimination:

Mismatch	Score	Type
A↔T	1.0	Transversion (best)
G↔T	0.95	Transversion
A↔C	0.9	Transversion
G↔C	0.85	Transversion
A↔G	0.6	Transition
C↔T	0.6	Transition

Tm Discrimination

Delta Tm	Specificity	Score
≥8°C	Excellent	100
≥5°C	Good	85
≥3°C	Moderate	70
≥1.5°C	Marginal	55
<1.5°C	Poor	40

Use Cases

1. SNP Genotyping - Detect known variants
2. Mutation Screening - Quick PCR-based detection
3. Allele-Specific PCR (AS-PCR) - Distinguish alleles

See Also

• Species Specificity
• Probe Binding