Abstract

We report here a new mechanism for allelic discrimination—allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are manipulated such that an extra mismatch next to a SNP of interest is introduced between a target and a reference amplicon and a GC-clamp is added. Based on this new mechanism, novel SNP genotyping methods were developed, including a homogeneous fluorescence polarization (FP) competition assay that requires neither labeled primers/probes nor expensive enzymes/substrates. Using this novel genotyping technology, we were able to convert >95% of SNP sequences into genotyping assays that work well under a universal set of assay conditions and achieved 100% accuracy in clinical samples.

Keywords

GenotypingBiologyHolliday junctionMolecular Inversion ProbeSNP genotypingGeneticsAmpliconSNPAllelePolymerase chain reactionDNAGenotypeComputational biologySingle-nucleotide polymorphismGeneHomologous recombination

Affiliated Institutions

Related Publications

Publication Info

Year
2003
Type
article
Volume
13
Issue
7
Pages
1754-1764
Citations
132
Access
Closed

External Links

View on DOI.org

Social Impact

Altmetric
PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

132
OpenAlex

Cite This

Qinghong Yang, Alla Lishanski, Wendy Yang et al. (2003). Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring. Genome Research , 13 (7) , 1754-1764. https://doi.org/10.1101/gr.997703

Identifiers

DOI
10.1101/gr.997703