Researchers from France have reported the development and validation of a Roche Nimblegen CGH multiplex, microarray-based research method.
The researchers are investigating DNA copy number changes associated with genetic disorders.
The Roche Nimblegen CGH multiplex, microarray-based research method was developed to detect genomic deletions and duplications at high resolution.
The findings, published in the 5 August issue of the journal 'Human Mutation', identified highly precise, exon-level variants in DNA samples from affected individuals and carriers of a range of human diseases including muscular dystrophies and cystic fibrosis.
Current techniques used to identify mutations associated with muscular dystrophies and cystic fibrosis, which include a range of point mutations and copy number deletions and duplications, rely on PCR-based targeted approaches such as semi-quantitative fluorescent PCR (QF-PCR) and multiplex ligation-dependent probe amplification (MLPA).
However, these techniques are time-consuming, labour-intensive, exhibit a significant false negative rate, and are often limited to a small number of exonic regions.
To overcome these limitations, the authors of this study, led by Jamel Chelly from the Institut Cochin, Universite Paris Descartes, and a research team from Inserm and Hopital Cochin, Paris, used the Roche Nimblegen multiplex CGH technology to design and build custom, targeted CGH arrays which interrogated 158 exons from a set of eight genes associated with Duchenne and Becker muscular dystrophy, cystic fibrosis, and sarcoglycanopathies.
To achieve higher throughput analysis, the team utilised Roche Nimblegen's 4 x 72K array format, which allows the simultaneous analysis of four independent sample pairs on a single microarray slide.
Using this method, Chelly and the team accurately detected copy number abnormalities in the DMD, SGs, and CFTR genes down to about 1.5 kb resolution in 50 samples from hemizygous affected individuals and heterozygous carrier females.
In addition, even heterozygous deletions and duplications of only one exon, as well as mosaic deletions were detected by this CGH approach.
Future enhancements to the technique include the simultaneous analysis of 12 independent sample pairs at higher resolution using Roche Nimblegen's 12 x 135K CGH arrays (135,000 probes per array versus the current 72,000).
Roche Nimblegen anticipates the 12 x 135K CGH arrays to be commercially available in the autumn of 2008.
