BERLIN (GenomeWeb) – Laboratories at 11 institutions in Europe, Canada, and Japan have tested Thermo Fisher Scientific's Oncomine Lung cfDNA assay and found that it can detect low-level mutations in circulating free DNA control samples with high sensitivity and specificity.
Yesterday at the Association for Molecular Pathology AMP Global Congress in Berlin, Claudia Vollbrecht of the Institute of Pathology at Charité University Medicine Berlin presented the results of the study, which was conducted by the OncoNetwork Consortium, a network of researchers organized by Thermo.
Being able to detect low-frequency actionable mutations in lung cancer is important, Vollbrecht explained, but it is difficult because for about a quarter of lung cancer patients, no tissue samples are available. Advanced non-small cell lung cancer patients with the EGFR T790M mutation, for example, can be treated with the tyrosine kinase inhibitor Tagrisso (osimertinib), which was approved by the European Medicines Agency a year ago.
As an alternative to tissue profiling, mutations could be determined in cell-free circulating tumor DNA from the plasma of lung cancer patients, but such DNA is often present at very low concentrations and contains mutations with allele frequencies of 5 percent or less. Such an assay could also be used to noninvasively monitor patients under treatment for the development of minimal residual disease, which she said has already been shown for breast cancer.
To test whether Thermo's Oncomine cfDNA Lung assay fits the bill, the Charité laboratory joined the OncoNetwork consortium to evaluate it with a number of reference standard DNA samples from Horizon Discovery.
The assay, which Thermo launched last summer, looks for 169 hotspot mutations in 35 amplicons from 11 genes, including activating and resistance mutations in EGFR. It uses molecular barcodes to tag each DNA molecule in the sample, so false positive mutations introduced during the amplification process can be distinguished from bona fide mutations in the sample. To reach a detection limit of 0.1 percent, the assay requires 20 nanograms of input cfDNA.
The consortium labs tested the assay on Horizon Dx cfDNA reference standard samples, which contain DNA from human cell lines that is fragmented to an average size of 160 base pairs and thus resembles cfDNA from human plasma. The standard has eight mutations in four genes – EGFR, KRAS, NRAS, and PIK3CA – at allele frequencies of 5 percent, 1 percent, and 0.1 percent, as well as wild type DNA. It was shipped to all 11 participating laboratories, which prepared libraries using the Oncomine assay and the Ion Chef and sequenced each sample twice, using either the Ion PGM or the Ion S5 sequencer, followed by variant calling with the Torrent Server software.
The labs were able to detect all eight mutations at the three allele frequencies, with an average sensitivity of 94.8 percent and an average specificity of 99.8 percent. Importantly, at 0.1 percent allele frequency, all labs were able to detect the EGFR T790M mutation, which serves as the marker for Tagrisso sensitivity.
Vollbrecht said that her lab has not yet compared the assay to other methods, for example digital PCR, but plans to do so. She said that because of the high cost of the assay, her lab does not currently run the Oncomine Lung cfDNA assay on all lung cancer samples but initially uses a colon and lung cancer panel, which is designed for FFPE samples, and applies the Oncomine assay as a secondary test.