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Improved Genomic Target Selection Using IDT Oligos

Published: Friday, September 28, 2012
Last Updated: Thursday, September 27, 2012
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IDT’s DECODED newsletter highlights developments in Foundation Medicine’s NGS tumor assay using individually synthesized capture probes.

Integrated DNA Technologies (IDT), provides scientists at Foundation Medicine with individually synthesized 5’-biotinylated Ultramer™ Oligonucleotide capture probes which have proved superior to array-synthesized oligonucleotides for genomic target capture.

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 analyzed 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.”

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