Fig. 1 | Genetics in Medicine

Fig. 1

From: eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data

Fig. 1

eKLIPse workflow. A four-step process for the detection and quantification of mitochondrial DNA (mtDNA) deletions. (a) eKLIPse workflow diagram. (b) Detailed alignment of the reference sequence (top) to deleted mtDNA region (in red) analyzed by high-throughput sequencing reads. The two repeat flanking regions are indicated in black and only one repeat is retained in the sequence of the deleted molecule. (c) Forward and reverse reads containing the deleted region are aligned to the mtDNA reference leading to two soft-clipping events occurring at positions called forward and reverse soft-clipping positions. (d) Soft-clipped and upstream perfect match sequences are retrieved and realigned using BLASTN. (e) Breakpoint positions are predicted by searching bidirectional BLAST between forward and reverse soft-clipping positions. Unidirectional BLAST and insufficient BLAST number are removed from the analysis. (f) Final outputs of eKLIPse analysis. eKLIPse provides a Circos graphical representation and two descriptive tables summarizing the main findings of each mtDNA deletion (breakpoint nucleotide locations, deletion sizes, mutant loads) and the cumulative deletion percentage related to each mtDNA gene locus.

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