RT Journal
A1 Kajiyama, Tomoharu
A1 Miyahara, Yuji
A1 Kricka, Larry J.
A1 Wilding, Peter
A1 Graves, David J.
A1 Surrey, Saul
A1 Fortina, Paolo
T1 Genotyping on a Thermal Gradient DNA Chip
JF Genome Research 
JO Genome Research 
YR 2003 
FD March 01 
VO 13 
IS 3 
SP 467 
OP 475 
DO 10.1101/gr.790603 
UL http://genome.cshlp.org/content/13/3/467.abstract 
AB Silicon-based chips with discrete, independently temperature-controlled islands have been developed for use in DNA microarray hybridization studies. Each island, containing a heater made of a diffusion layer and a temperature sensor based on a p–n junction, is created on a silicon dioxide/nitride surface by anisotropic etching. Different reactive groups are subsequently added to the surface of the islands, and allele-specific oligonucleotide probes are attached to discrete spots on the chip. Hybridization is performed with Cy5-tagged single-stranded targets derived by PCR from genomic DNA. Results are assessed by measuring fluorescence of bound dye-tagged targets after hybridization and washing. Temperatures at each island can be set at different values to obtain optimal distinction between perfect matches and mismatches. This approach facilitates definition of optimal temperatures for probe/target annealing and for distinction between perfectly matched versus mismatched solution-phase targets. The thermal gradient DNA chips were then tested for genotyping, and the results for four different loci in two genes are presented. Unambiguous typing was achieved for clinically relevant loci within the factor VII and hemochromatosis genes.