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A surface invasive cleavage assay for highly parallel SNP analysis
Author(s) -
Lu Manchun,
Shortreed Michael R.,
Hall Jeff G.,
Wang Liman,
Berggren Travis,
Stevens Priscilla Wilkins,
Kelso David M.,
Lyamichev Victor,
Neri Bruce,
Smith Lloyd M.
Publication year - 2002
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.10071
Subject(s) - cleavage (geology) , biology , oligonucleotide , molecular inversion probe , single nucleotide polymorphism , dna , gene , microbiology and biotechnology , genetics , computational biology , combinatorial chemistry , chemistry , genotype , paleontology , fracture (geology)
The structure‐specific invasive cleavage of single‐stranded DNA by 5′ nucleases is a useful means for sensitive detection of single‐nucleotide polymorphisms or SNPs. The solution‐phase invasive cleavage reaction has sufficient sensitivity for direct detection of as few as 600 target molecules with no prior target amplification. One approach to the parallelization of SNP analysis is to adapt the invasive cleavage reaction to an addressed array format. Two surface invasive cleavage reaction strategies were designed and tested using the polymorphic site in codon 158 of the human ApoE gene as a model system, with a synthetic oligonucleotide as target. The upstream oligonucleotide, which is required for the invasive cleavage reaction, was either added in solution (strategy 1), or co‐immobilized on the surface along with the probe oligonucleotide (strategy 2). Both strategies showed target‐concentration and time‐dependent amplification of signal. Parameters that govern the rate of the surface‐invasive cleavage reactions are discussed. Hum Mutat 19:416–422, 2002. © 2002 Wiley‐Liss, Inc.