DOI: 10.1101/gr.997703. Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring

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

10.1101/gr.997703

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

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.

Bibliography

Yang, Q., Lishanski, A., Yang, W., Hatcher, S., Seet, H., & Gregg, J. P. (2003). Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring. Genome Research, 13(7), 1754â1764.

Authors 6

Qinghong Yang (first)
Alla Lishanski (additional)
Wendy Yang (additional)
Sandra Hatcher (additional)
Henrietta Seet (additional)
Jeffrey P. Gregg (additional)

References 5 Referenced 99

10.1146/annurev.genom.2.1.235
10.1093/clinchem/46.9.1464 / Clin. Chem. (2000)
10.1093/nar/28.9.e42 / Nucleic Acids Res. (2000)
10.1006/jmbi.1993.1159
10.1146/annurev.genet.31.1.213

Dates

Type	When
Created	22 years, 1 month ago (July 27, 2003, 1:25 a.m.)
Deposited	3 years, 9 months ago (Nov. 18, 2021, 2:23 p.m.)
Indexed	1 year, 3 months ago (June 5, 2024, 11:34 a.m.)
Issued	22 years, 2 months ago (July 1, 2003)
Published	22 years, 2 months ago (July 1, 2003)
Published Online	22 years, 2 months ago (July 1, 2003)
Published Print	22 years, 2 months ago (July 1, 2003)

Funders 0

None

BibTeX

@article{Yang_2003, title={Allele-Specific Holliday Junction Formation: A New Mechanism of Allelic Discrimination for SNP Scoring}, volume={13}, ISSN={1088-9051}, url={http://dx.doi.org/10.1101/gr.997703}, DOI={10.1101/gr.997703}, number={7}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Yang, Qinghong and Lishanski, Alla and Yang, Wendy and Hatcher, Sandra and Seet, Henrietta and Gregg, Jeffrey P.}, year={2003}, month=jul, pages={1754–1764} }

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