The diagnostic performance in this study was evaluated by calculating the mutation detection rate as a percentage of mutations detected for the cohort of 12 patients with 24 known mutations, and by calculating the diagnostic yield as the percentage of patients for which a molecular diagnosis was obtained (for details, see Results).
They are concerned that our findings of an unexpected high percentage of heterogeneity reflect methodical problems of mutation detection rather than tumour biology.
Considering the percentage represented by this variant in patients (26%) and the obtained mutation detection rate (60.5%), this change would represent the 15.7% of all the potential arSTGD associated alleles.
Comparing the validation results with the mutation detection parameters, optimum parameters of phred score = 18 or 19, with the minimum read percentage with non-reference nucleotide of 0.17% and maximum read percentage with non-reference nucleotide of 5% could predict the largest number of "true" mutations (Table 3).
Moreover, if we consider that this value has been obtained through screening on the ABCR400 chip (mutation detection rate = 60.5%) and the high frequency of rare mutations reported in this gene, this percentage could be even higher.
Consequently, the percentage of tumour cells in the analyzed sample as well as the threshold of mutation detection of the currently molecular test appeared to be two essential data to better understand the significance (i.e., prognostic or predictive factor) of the detected mutation.
Weisschuh, N. et al. Mutation Detection in Patients with Retinal Dystrophies Using Targeted Next Generation Sequencing.
In the Cel-1 assay, the PCR products for gRNA1 and gRNA3 were digested with Guide-it™ Mutation Detection Kit (Takara, Japan) or Surveyor® Mutation Detection Kits (Transgenomic, USA).
The detection percentage of the method is ∼70%.
Shiraishi, Y. et al. An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data.
