CYSTIC-FIBROSIS MUTATION DETECTION BY HYBRIDIZATION TO LIGHT-GENERATED DNA-PROBE ARRAYS

We have combined photochemistry and photolithography with solid phase DNA synthesis chemistry to form a new technology that makes high densi ty oligonucleotide probe array synthesis possible, Hybridization to th ese two dimensional arrays containing hundreds or thousands of oligonu cleotide probes provides a powerful DNA sequence analysis tool. Two ty pes of light generated DNA probe arrays have been used to test for a v ariety of mutations in the cystic fibrosis transmembrane conductance r egulator (CFTR) gene. One array, made up of 428 probes, was designed t o scan through the length of CFTR exon 11 and identify differences fro m the wild type reference sequence. The second type of array contained 1480 probes chosen to detect known deletions, insertions, or base sub stitution mutations. The validity of the probe arrays was established by hybridizing them with fluorescently labeled control oligonucleotide targets, Characterized mutant CFTR genomic DNA samples were then used to further test probe array hybridization specificity, Finally, ten u nknown patient samples were genotyped using tile CFTR probe array assa y, The genotype assignments were identical to those obtained by PCR pr oduct restriction fragment analysis. Our results show that light gener ated DNA probe arrays are highly effective in analyzing complex mutati on and polymorphism patterns in a relatively large gene such as CFTR. (C) 1996 Wiley Liss, Inc.