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. 2021 Jan 16;2(2):100023. doi: 10.1016/j.xhgg.2021.100023

Figure 1.

Figure 1

Proband 6 has a de novo insertion resulting in duplication of exon 3 of CDKL5

(A) Ideogram showing location of CDKL5 on chromosome X. Ideogram is from the NCBI Genome Decoration Page.

(B) Gene structure of CDKL5, RS1, and PPEF1, indicating the location of the 6,993 bp insertion in CDKL5 (blue/red/gray bars) and location of the origin of the duplicated PPEF1 intronic sequence (red).

(C) Zoomed-in view of the insertion. The gray box indicates the entire 6,993 nt insertion, which consists of a partial L1HS retrotransposon (blue box), duplicated PPEF1 intronic sequence (red box), and target site duplication (TSD, yellow box) with duplicated exon 3 (3∗). Green boxes indicate RepeatMasker annotation of the proband’s insertion-bearing, contig sequence.

(D) Alignment of CCS reads near exon 3 of CDKL5 in IGV in proband 6 and her parents. Gray reads represent alignment to reference, and multicolor alignments represent unaligned ends of reads. The TSD is indicated by a yellow box. Reads highlighted by the pink box include examples of reads that align to reference upstream of the insertion, contain the TSD, and then have inserted sequence at their 3′ end. Those highlighted in the turquoise box represent inserted sequence, TSD, and reference sequence downstream of the insertion. Note that some reads have hard-clipped bases, which are designated with a black diamond.