Fig. 3

Precise patients’ SV characterization by NanoVar. a Scatter plots showing the confidence score and breakend read ratio of each SV characterized in patient 1 (top) and patient 2 (bottom). SVs selected for validations are labeled on the plots by their SV id. The red horizontal line indicates the confidence score threshold used for filtering. b Table displaying the details of SVs selected for validation for patient 1 and patient 2. The in silico PCR size refers to the expected size of the PCR amplicon without the SV. c Gel electrophoresis images of PCR products corresponding to each of the SVs in table b, amplified from the genomic DNA of patients 1 and 2, normal donors (normal A and normal B) and cell lines (HCT116 and MCF10A). Sample names in red (left image lane 1, right image lane 2) indicate the sample where the SV was initially detected. d Schematic illustrating a 409-bp deletion (SV 1-2) in the intronic region of the gene BPGM in patient 1, supported by 3GS nanopore reads (top), 2GS Illumina reads (middle), and 1GS Sanger sequencing chromatogram (bottom). Blue and red arrows represent the primer locations used for PCR amplification. For each nanopore read, base substitutions and base insertions are represented by red and orange markers respectively. Base deletions are represented by gaps. All nanopore reads have at least 90% alignment identity. Illumina paired-end short reads are represented by pink (forward) and blue (reverse) small rectangles, and the read coverages are displayed in gray above all the reads. The red dotted line on the sequencing chromatogram marks the precise breakpoint of the deletion at single nucleotide resolution