Monday, April 18, 2016

NGS concordance with single gene tests... Perfect? Does perfect work for you?

Penn has just published a large scale study by Hiemenz et al. on the concordance of gene calls in tumor tissue made by NGS versus calls made by single gene methods.

In an open-access article at PLoS One, the authors summarize:
For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests {with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection.}
But wait, there's more:
NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.
Article online here.  Subscription coverage at Genomeweb, here.