Fig. 2

Validation of targeted-seq workflow for the detection of germline and low-frequency variants. A The pedigree of family 1 with abortus presenting dwarfism by ultrasound finding. B Visualization of reads at FGFR3 loci (c.1949A) site by using Integrative Genomics Viewer in three samples of family 1. C Validation of targeted-seq results by Sanger-seq at FGFR3 loci (c.1949A). D The targeted-seq was performed at expected read depth of 10,000x, 15,000x, and 25,000x on Ion Proton. The ratio of read count of each amplicon to total reads count was plotted. P-value was calculated by Kruskal–Wallis test. E The targeted-seq was performed using spike-in DNAs with FGFR3 mutation (c. 1138G > A) at fraction of 2.5%, 5%, and 10% on NextSeq550. The ratio of read count of each amplicon to total reads count was calculated and compared. P-value was calculated by Kruskal–Wallis test. F The allele frequency of 5 SNPs obtained from Ion Proton and NextSeq550 at various spike-in fractions were compared and the correlation was calculated using Pearson’s correlation coefficient