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

Figure 3

Targeted adaptive nanopore sequencing reveals the L1 insertion to be ~5.6 kb in size. (a) Integrative Genomics Viewer (IGV) view of the aligned nanopore sequencing reads over exons 2-4 of RP1 gene (NM_006269.2). The location of the L1 insertion in exon 4 is indicated (arrowhead). Misaligned (soft-clipped) bases are shown to visualise sequencing reads that cover the L1 insert only partially. Misaligned bases to the left of the arrowhead show the 3 end of the L1 insert ending with a pA track, whereas misaligned bases to the right of the arrowhead indicate the 5 end of the L1 insert. Below is a schematic representation of transcript NM_006269.2 showing coding exons (blue boxes), noncoding exons (grey boxes), introns (grey lines), and exon numbers (below the exons). GRCh38 was used as the reference. (b) A schematic representation of the sequence structure of the L1 insertion, comprised of parts of various LINE-1 subfamily members in both orientations, according to the Dfam database (https://www.dfam.org/) (top panel). Simple repeat sequences are indicated in grey. A schematic representation of sequence alignment of the L1 insertion (RP1_L1) with a LINE-1 sequence (GenBank: GU477636.1) (bottom panel). (c) 5 and 3 breakpoints of the L1 insertion site (green background), showing the RP1-derived target site duplication (TSD) (blue background) and the RP1 sequence around the insertion site (purple background).

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