ESR1 mutation detection in FFPE and Plasma DNA of breast cancer patients using Crystal Digital PCR® and Nio®+.

To detect and quantify the most frequent ESR1 mutations in a single test, a highly multiplexed cdPCR assay was developed: the ESR1 12-plex assay. FFPE DNA and Plasma cfDNA samples from breast cancer patients were analysed using this assay on the Nio®+ system and the results were compared to previously obtained cdPCR results from Centre Eugène Marquis.

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Highlights

• The all-in-one Nio®+ and its associated microfluidic consumable, the Ruby Chip, are suitable with dPCR high-order multiplexing approach such as color combination while significantly reducing the hands-on-time to results.
• The ESR1 12-plex assay, based on a color combination approach, was successfully applied for monitoring 10 ESR1 mutations and 1 AKT1 mutation simultaneously in a single test. This hyper-plexing approach enables fast and robust data analysis using the Nio®+ system: just one threshold per fluorescent channel to be set and the Nio® Analyzer Advanced Population Editor will identify and quantify all targets.
• This highly multiplexed assay is compatible with clinical samples (plasma & FFPE DNA) and showed a very good result concordance and MAF correlation with a previous cdPCR study performed with sequential lower multiplexed assays.