Detection of single base alterations in genomic DNA by solid phase polymerase chain reaction on oligonucleotide microarrays

DNA microarray technology holds significant promise for human DNA diagnosti cs. A number of technical approaches directed at the parallel identificatio n of mutations or single nucleotide polymorphisms make use of polymerase-ba sed specificity, like minisequencing or allele-specific primer elongation. These techniques, however, require separate laborious sample amplification, preparation, and purification steps, making large-scale analyses time and cost consuming. Here, we address this challenge by applying an experimental setup using simultaneous solid and liquid phase PCR on polyethyleneimine-c oated glass slides, a novel microarray support allowing on-chip amplificati on reactions with exquisite specificity. A gene-specific oligonucleotide ti ling array contains covalently attached allele-specific primers which inter rogate single nucleotide positions within a genomic region of interest. Dur ing a thermal cycling reaction amplification products remain covalently bou nd to the solid support and can be visualized and analyzed by the incorpora tion of fluorescent dyes. Using the described procedure we unequivocally de fined the presence of point mutations in the human tumor suppressor gene p5 3 directly from a natural DNA source. This semi-multiplex solid phase ampli fication format allowed the rapid and correct identification of 20 nucleoti de positions from minute amounts of human genomic DNA. Our results suggest that this approach might constitute a vital component of future integrated DNA chip devices used in gene analysis. (C) 2001 Elsevier Science.