Novel platform for sequencing rat genome coding regions
NIEHS researchers have established a novel platform to conduct whole exome sequencing (WES) in the rat, an animal model widely used in toxicology and pharmacology research. The tool developed in this study and the resulting data will help scientists better understand the rat genome and improve human translational research and environmental hazard evaluation.
WES offers an efficient approach to detect disease-related DNA mutations by sequencing the protein-coding regions of the genome. Using an in silico probe design approach, the authors targeted a probe set that is highly specific and sensitive to the rat genome, improving the currently limited rat WES tools.
The probe set achieved high accuracy and reliability in the exome sequencing of DNA samples from the normal rat liver and chemically induced rat tumor cell lines. The data identified common DNA variants registered in the rat genome variant database. Highly relevant cancer-related gene mutations captured from the tumor cell lines matched those archived in the human cancer database. On the new platform, the performance of formalin-fixed, paraffin-embedded (FFPE) tissue, routinely available from clinical settings, was comparable to that of paired fresh frozen samples, the standard source for DNA sequencing. It confirmed the feasibility of using FFPE samples for WES. (QX)
Citation: Foley JF, Phadke DP, Hardy O, Hardy S, Miller V, Madan A, Howard K, Kruse K, Lord C, Ramaiahgari S, Solomon GG, Shah RR, Pandiri AR, Herbert RA, Sills RC, Alex Merrick B. 2018. Whole exome sequencing in the rat. BMC Genomics 19(1):487.