1. Analytical Validation of BRAF Mutation Testing from Circulating Free DNA Using the Amplification Refractory Mutation Testing System 
Kyaw L. Aung, Emma Donald, Gillian Ellison, Sarah Bujac, Lynn Fletcher, Mireille Cantarini, Ged Brady, Maria Orr, Glen Clack, Malcolm Ranson, Caroline Dive, Andrew Hughes 
The Journal of Molecular Diagnostics 
Volume 16, Issue 3, Pages (May 2014)
DOI: /j.jmoldx
Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

2. Figure 1
Determining the optimal ΔCq cutoff for BRAF mutation calling in cfDNA using a training data set. The boxplots summarize the distribution of mean ΔCq values for 23 serum and 27 plasma samples in which BRAF mutation was detected in cfDNA and the results were concordant with tumor mutation status. Extending the ΔCq cutoff from 7.5 (cutoff used for FFPE tumor DNA shown by dotted lines) to cfDNA-specific ΔCq cutoff of 10 (solid lines) would improve the BRAF mutation pick-up rate in both serum and plasma. By using both cutoffs, there was only one discordant case in which BRAF mutation was detected in both serum and plasma, but not in tumor (an isolated dot below the FFPE tumor cutoff line). Extending the ΔCq cutoff to above 10 would have introduced one extra discordant result in serum (an isolated dot above the cfDNA-specific cutoff line).
The Journal of Molecular Diagnostics  , DOI: ( /j.jmoldx )
Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions