Dr Phil Stephens leads the team responsible for Foundation Medicine’s next generation sequencing (NGS) assay for comprehensive sequencing of clinical tumor specimens from FFPE samples and core needle biopsies. Samples are analysed for the entire coding sequence of 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer. Analysis of a subset of these genes revealed that Ultramer Oligonucleotides provide a more uniform coverage than array-derived RNA baits, with reduced GC bias and are much more cost-effective on a per-reaction basis. The researchers are particularly excited to have been able to reduce hybridization times using proprietary techniques, to 2.5 hr instead of the standard 24-72 hr, while maintaining high target coverage, and intend to continue evolving their technologies with advances in NGS.
Dr Mirna Jarosz, who previously led the team with Dr Stephens, commented, “We are in a sweet spot between large-scale whole genome sequencing and extremely targeted ‘hotspot’ sequencing, and this is where the IDT Ultramer Oligonucleotides are particularly useful to us.”
You can read more about Foundation Medicine’s cutting edge research in the latest issue of the IDT quarterly newsletter, DECODED. For more information about the complete IDT product portfolio, and to sign up to receive DECODED, visit www.idtdna.com. For real-time news and updates, follow us on Twitter @idtdna.