Universal DNA microarray method for multiplex detection of low abundance point mutations.
Cancers arise from the accumulation of multiple mutations in genes regulating cellular growth and differentiation. Identification of such mutations in numerous genes represents a significant challenge in genetic analysis, particularly when the majority of DNA in a tumor sample is from wild-type stroma. To overcome these difficulties, we have developed a new type of DNA microchip that combines polymerase chain reaction/ligase detection reaction (PCR/LDR) with "zip-code" hybridization. Suitably designed allele-specific LDR primers become covalently ligated to adjacent fluorescently labeled primers if and only if a mutation is present. The allele-specific LDR primers contain on their 5'-ends "zip-code complements" that are used to direct LDR products to specific zip-code addresses attached covalently to a three-dimensional gel-matrix array. Since zip-codes have no homology to either the target sequence or to other sequences in the genome, false signals due to mismatch hybridizations are not detected. The zip-code sequences remain constant and their complements can be appended to any set of LDR primers, making our zip-code arrays universal. Using the K- ras gene as a model system, multiplex PCR/LDR followed by hybridization to prototype 3x3 zip-code arrays correctly identified all mutations in tumor and cell line DNA. Mutations present at less than one per cent of the wild-type DNA level could be distinguished. Universal arrays may be used to rapidly detect low abundance mutations in any gene of interest.
Gerry
N P
NP
Department of Microbiology Hearst Microbiology Research Center, and Strang Cancer Prevention Center, Joan and Sanford I. Weill Medical College of Cornell University, 1300 York Ave., New York, Box 62, 10021, USA.
Witowski
N E
NE
Day
J
J
Hammer
R P
RP
Barany
G
G
Barany
F
F
D000483:Alleles; D020137:Base Pair Mismatch; D015374:Biosensing Techniques; D004252:DNA Mutational Analysis / Q000379:methods; D017931:DNA Primers; D005453:Fluorescence; D011905:Genes, ras; D006801:Humans; D008025:Ligases; D008214:Lymphocytes; D009693:Nucleic Acid Hybridization; D017354:Point Mutation / Q000235:genetics*; D016133:Polymerase Chain Reaction; D014407:Tumor Cells, Cultured
D017931:DNA Primers; D008025:Ligases