BRCA1/2, ATM, CHEK2 targeted sequencing

Background: The use of Next Generation Sequencing (NGS) to diagnose Mendelian diseases is expanding and technology rapidly moves forward into routine medical genetics experiment. Hence, advances in the development of performance measures are required to achieve higher quality standards. Meanwhile, such performance measures are considered to be designed in context of the application and therefore account for spectrum of clinically relevant variants and their relative importance.Results: We have developed a new computational methodology for bioinformatics quality control in clinical context. Given a single NGS dataset in BAM format and pre-compiled VCF-file of targeted clinically relevant variants it associates this dataset with a single parameter. Leveraging the simple variant calling model under the reversed null hypothesis this approaches allow estimating the probability to miss any variant from the defined spectrum during the variant calling given that NGS dataset. Such performance measure virtually resembles diagnostic sensitivity of given NGS dataset. We have performed thorough examination of the use of EphaGen in the context of BRCA1/2 and CFTR sequencing. For this we performed a series of 14 sequencing runs across a total of 42 unselected blood samples. We have demonstrated pitfalls of the commonly used metrics, namely average coverage depth and coverage uniformity, and how presented here performance measure may be used to overcome these pitfalls.