Fig. 2: Transcriptomic characterization.

A Variant allele frequencies of Single Nucleotide Polymorphisms (SNPs) carried in BRCA1 by Family 1 – Patient 2 (F1-P2). Seven SNPs were detected in the duplicated region, all with an allelic ratio of approximately 33% in genomic DNA and approximately 50% in RNA-seq, indicating that only one set of duplicated exons was transcribed. Two SNPs were detected downstream of duplicated exons, with allelic ratios of approximately 50% in genomic DNA and approximately 100% in RNA-seq, indicating that only one allele of the end of the gene is transcribed. B Coding DNA (cDNA) Sanger sequencing showing back-splicing between BRCA1 exon 20 and exon 2. C BRCA1 strand-specific short-read RNA sequencing (RNA-seq) in Family 1 – Patient 2 (F1-P2) and 12 merged controls. Depth of coverage scales are indicated on the left. D Fusion reads involving BRCA1 in long-read direct RNA sequencing (RNA-seq). Represented on rearranged breakpoint 1 (BP1). The two reads aligning on the forward strand of the rearranged region are shown at the top: both started in NBR1 antisense transcript first exon (red) and included BRCA1 exonic sequences (blue). Twenty-one reads aligned on the reverse strand of the rearranged region are shown at the bottom. They all started in BRCA1 (blue) and continued with full NBR1 gene (red) with various alternative splicing. Figures 2-C and 2-D were prepared from BAM file visualization in IGV software²⁶.