Transgenomic, Inc has completed a preliminary study with a leading pharmaceutical company that validates the use of its licensed COLD-PCR technology to detect colorectal tumour-associated KRAS mutations that determine efficacy of recently developed therapies. These were detected in plasma samples in which the mutation levels were too low for detection by standard DNA analysis methodologies such as Sanger sequencing.

The study, which was performed by Transgenomic’s Pharmacogenomics Services Laboratory in Omaha, NE and the company’s Molecular Biology research team in Gaithersburg, MD, consisted of testing DNA extracted from colorectal tumour-matched plasma samples. Screening with standard Sanger sequencing of the plasma samples resulted in only 70 per cent concordance between matched plasma and tumour due to missing KRAS codon 12 and 13 mutations.

The samples were enriched by Transgenomic’s COLD-PCR mutation enrichment technology before analysis with the SURVEYOR SCAN KRAS assay. COLD-PCR preferentially amplifies genomic DNA mutations in comparison to normal, wild-type sequences. This powerful enrichment and screening method can detect matched-tumour KRAS mutations in serum mutation levels at less than 0.1% of total wild-type DNA.

This resulted in the accurate detection of all KRAS codon 12 and KRAS codon 13 mutations with full discrimination against wild-type or normal samples tested concurrently. Due to the extent of the enrichment process, all of these KRAS containing plasma samples could subsequently be verified by DNA sequencing.

It was confirmed by the study’s pharmaceutical partner that there was a 100% concordance between Transgenomic’s mutation results and the matched tumor KRAS genotypes.

“We believe that the developments in COLD-PCR that we are pursuing at Transgenomic will open the way for detecting tumour mutations in surrogate tissues and body fluids such as serum, plasma and urine rather than by tumour biopsy,” said Craig Tuttle, CEO of Transgenomic. “This study is a very promising start of the process of validating this technology in a clinically oriented setting. We intend to participate in further studies such as this with the aim of developing COLDPCR serum assays for key gene mutations that are biomarkers for early tumour detection, tumour therapy efficacy, emergence of drug resistance biomarkers and relapse.”

COLD-PCR was discovered in the laboratory of Dr. Mike Makrigiorgos at the Dana Farber Cancer Institute. It has been exclusively licensed by Transgenomic for all Sanger Sequencing and mitochondrial DNA applications. Furthermore, it can be coupled with Transgenomic’s proprietary DNA mutation detection technologies to further improve its sensitivity.

Transgenomic is a global biotechnology company specializing in high sensitivity genetic variation and mutation analysis, providing products and services in DNA mutation detection and discovery for clinical research, clinical molecular diagnostics and pharmacogenomics analyses.