title: Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy.
abstract: Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and TTN exon 45 were unique to DM1. Retrospective analysis revealed that four parameters efficiently detect aberrantly spliced exons: (i) the signal intensity is high; (ii) the ratio of probe sets with reliable signal intensities (that is, detection above background P-value=0.000) is high within a gene; (iii) the splice index (SI) is high; and (iv) SI is deviated from SIs of the other exons that can be estimated by calculating the deviation value (DV). Application of the four parameters gave rise to a sensitivity of 77.8% and a specificity of 95.6% in our data set. We propose that calculation of DV, which is unique to our analysis, is of particular importance in analyzing the exon array data.
authors.affiliation: Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamashita
authors.forename: Tohru
authors.initials: T
authors.lastname: Matsuura
authors.forename: Jun
authors.initials: J
authors.lastname: Shinmi
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Amakusa
authors.forename: Akio
authors.initials: A
authors.lastname: Masuda
authors.forename: Mikako
authors.initials: M
authors.lastname: Ito
authors.forename: Masanobu
authors.initials: M
authors.lastname: Kinoshita
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Furuya
authors.forename: Koji
authors.initials: K
authors.lastname: Abe
authors.forename: Tohru
authors.initials: T
authors.lastname: Ibi
authors.forename: Ko
authors.initials: K
authors.lastname: Sahashi
authors.forename: Koo
authors.initials: K
authors.lastname: Sahashi
authors.forename: Kinji
authors.initials: K
authors.lastname: Ohno
mesh_terms: D017398:Alternative Splicing; D030561:Databases, Nucleic Acid; D005091:Exons; D020869:Gene Expression Profiling; D006801:Humans; D007438:Introns; D058977:Molecular Sequence Annotation; D009223:Myotonic Dystrophy / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012680:Sensitivity and Specificity