Categorization of 77 dystrophin exons into 5 groups by a decision tree using indexes of splicing regulatory factors as decision markers

Using a computer-based machine learning system, we first constructed a decision tree separating 77 authentic from 14 known cryptic exons using 25 indexes of splicing regulatory factors as decision markers. We evaluated the classification accuracy of a novel cryptic exon (exon 11a) identified in this study. However, the tree mislabeled exon 11a as a true exon. Therefore, we re-constructed the decision tree to separate all 15 cryptic exons. The revised decision tree categorized the 77 authentic exons into five groups. Furthermore, all nine disease-associated novel exons were successfully categorized as exons, validating the decision tree. One group, consisting of 30 exons, was characterized by a high density of exonic splicing enhancer sequences. This suggests that AOs targeting splicing enhancer sequences would efficiently induce skipping of exons belonging to this group.The decision tree categorized the 77 authentic exons into five groups. Our classification may help to establish the strategy for exon skipping therapy for Duchenne muscular dystrophy.Duchenne muscular dystrophy (DMD), a fatal muscle-wasting disease, is the most common inherited muscle disease, affecting one in every 3500 male births. DMD is characterized by dystrophin deficiency caused by mutations in the dystrophin gene, the largest human gene that spans over 2500 kb on the X-chromosome. For the treatment of DMD, antisense oligonucleotides (AOs) against splicing regulatory sequences have been proposed to produce in-frame dystrophin mRNA from the out-of-frame mRNA by inducing exon skipping during splicing [1]. The newly generated in-frame dystrophin mRNA is expected to produce semi-functional, internally deleted dystrophin protein. Currently, induction of exon skipping with AOs is considered one of the most promising treatments for DMD [2,3].The dystrophin gene encodes a 14-kb mRNA consisting of 79 exons and is characterized by its huge intron size; the largest, intron 44, is 248 kb long. In addition