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Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy.

Authors
  • Yamashita, Yoshihiro
  • Matsuura, Tohru
  • Shinmi, Jun
  • Amakusa, Yoshinobu
  • Masuda, Akio
  • Ito, Mikako
  • Kinoshita, Masanobu
  • Furuya, Hirokazu
  • Abe, Koji
  • Ibi, Tohru
  • Sahashi, Ko
  • Sahashi, Koo
  • Ohno, Kinji
Type
Published Article
Journal
Journal of Human Genetics
Publisher
Springer Nature
Publication Date
Jun 01, 2012
Volume
57
Issue
6
Pages
368–374
Identifiers
DOI: 10.1038/jhg.2012.37
PMID: 22513715
Source
Medline
License
Unknown

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.

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