Functional Genomic Fingerprinting (FGF)
The human genome consists of tiny functional and vast non-functional regions. The functional portion of the genome comprises of regulatory regions and protein-coding regions called exons (colored vertical lines). The non -functional portion essentially lies within genes as introns and between genes as intergenic non-coding regions (the entire black horizontal line). A small number of functional noncoding RNAs have been previously described however
Disease-causing Mutations typically occur within the protein-coding regions that represent just over 1% of the genome. A technique that can specifically compare only the most relevant functional regions between normal and diseased genomes has been lacking. Genome International has developed a novel technique called “Functional Genomic Fingerprinting (FGF)” that can achieve this selective examination of only the functional regions of the genome.
FGF is a scalable technique capable of selectively amplifying and screening any genomic functional region such as the exons that are bordered by splice signals, or regions surrounding the regulatory elements (e.g., promoters and polyA sites) within a genome. FGF multiplex amplifies a defined subset of exons from diseased and normal genomes such that these can be compared to identify any mutational differences between them. FGF carries out a minimal number of steps to compare the exonic regions at a genome-scale. It is thus a powerful alternative to current exome-capture techniques in the market.
FGF in brief is carried out using a set of unique fixed and -random (FR) primer combination. FR primers specifically amplify only the exonic regions in the genome, thus excluding the remaining 99% of the (non-functional) genome. The gel image above shows that incorporating more randomized segments in the primer set amplifies more exons from the human genome (Lane 1 through Lane 5). In FGF, the exonic sequences from diseased and normal genomes are compared and the differences in length can be used to identify the sequence defects in the diseased genome.
[Refer to publication for more details: Senapathy P, Bhasi A, Mattox J, Dhandapany PS, Sadayappan S., Targeted genome-wide enrichment of functional regions. PLoS One. 2010, 5(6):e11138.]