Microarray technology for mutation analysis of low-template DNA samples

Microarrays containing oligonucleotide mutation probes are emerging as useful platforms for the diagnosis of genetic disease. Herein, we describe the development and validation of an in-house microarray suitable for the diagnosis of common cystic fibrosis (CF) mutations in low-template DNA samples such as those taken for preimplantation genetic diagnosis and prenatal diagnosis. The success of the CF microarray was based on the ability to generate sufficient target DNA for hybridization to the array probes using either direct polymerase chain reaction (PCR) amplification or whole-genome amplification followed by PCR. From replicate experiments using target DNA carrying known CF mutations, it was possible to define strict diagnostic parameters for the accurate diagnosis of CF. This protocol serves as a general guide for DNA-testing laboratories to develop other microarray platforms that may eventually replace traditional PCR-based genetic testing in the near future.