File data is Comparison of WES with CNV-seq results.

Here, we developed a novel pipeline for whole exome sequencing (WES) analysis, designated as next-generation WES (ngWES). Being a composite bioinformatics analysis approach, ngWES is capable of the detection of single nucleotide variation (SNV), insertion and deletion (INDEL) and copy number variation (CNV) within a single test and requiring no changes in laboratory technology or workflow. In this study, 21 samples from patients with known CNV test results were applied as a training set to verify the feasibility and effectiveness of the ngWES. Additionally, 600 subjects with suspected Mendelian disorders who underwent genetic screening were included to further explore the diagnostic capacity of ngWES. All these CNVs and SNVs/INDELs detected by ngWES were further validated by other methods. Notably, all these analyses demonstrated that ngWES could efficiently call SNV/INDEL and CNV in a single test and yield higher diagnostic rates, compared to conventional diagnostic methods WES, CNV-seq or WES combined with CNV-seq, but with same time or cost as WES library preparation. Thus ngWES is expected to be a universal screening strategy for all the suspected genetic patients.