Characterisation of a LINE-1 Insertion in the RP1 Gene by Targeted Adaptive Nanopore Sequencing in a Family with Retinitis Pigmentosa

Figure 2

Whole exome sequencing identifies an L1 fragment insertion in RP1 of both patients III.1 and III.2. (a) RP1 transcript NM_006269.2 showing coding exons (blue boxes), noncoding exons (grey boxes), introns (grey lines), and exon numbers (below the exons). An Integrative Genomics Viewer (IGV) view, including soft-clipped bases of the sequencing reads, indicates a misalignment (arrowhead, top panel). A schematic representation of the adjacent insertion sites in RP1 exon 4 called by DRAGEN (middle panel). The misaligned 64 bp, called by DRAGEN, aligns with the L1P1_orf2 consensus sequence from the Dfam database (DF0000316, https://www.dfam.org) (bottom panel). GRCh38 was used as the reference. (b) PCR over the predicted 5 and 3 breakpoints (BP) from healthy controls (C1-C3) and two affected patients (III.1, III.2). Specific PCR products of the expected size are indicated (arrowhead). Unspecific PCR products likely caused by L1-specific primers are indicated (asterisk). Lanes: M: marker; N: negative PCR control.

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