Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring | Zendy

Qinghong Yang | Zendy; Alla Lishanski | Zendy; Wendy Yang | Zendy; Sandra Hatcher | Zendy; Henrietta Seet | Zendy; Jeffrey P. Gregg | Zendy

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Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring

Author(s) -

Qinghong Yang,

Alla Lishanski,

Wendy Yang,

Sandra Hatcher,

Henrietta Seet,

Jeffrey P. Gregg

Publication year - 2003

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.997703

Subject(s) - genotyping , biology , holliday junction , molecular inversion probe , snp genotyping , genetics , amplicon , snp , allele , polymerase chain reaction , dna , genotype , computational biology , single nucleotide polymorphism , gene , homologous recombination

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.

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