D.P.12 Whole exome sequencing and RNAseq in a Duchenne-like female with no dystrophin mutations: Search for dystrophin gene modifiers

• Published in: Neuromuscular disorders : NMD Vol. 22; no. 9; p. 811
• Main Authors: Brioschi, S, Bovolenta, M, Neri, M, Scotton, C, Castrignanò, T, Pesole, G, Bertini, E, Dallapiccola, B, Kotelnikova, E, Gualandi, F, Ferlini, A
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01-10-2012
• Subjects: Biopsy; Chromatin; Computer programs; Data processing; Dystrophin; Extracellular matrix; Gene expression; Heredity; Mosaics; Multidimensional scaling; Muscles; Muscular dystrophy; Mutation; Neurology; neuromuscular system; RNA; Sarcolemma; Single-nucleotide polymorphism
• ISSN: 0960-8966; 1873-2364
• DOI: 10.1016/j.nmd.2012.06.032

Abstract We identified a Duchenne-like female clinically evaluated as a severely affected symptomatic DMD carrier. Carrier status was confirmed by evidence of mosaic pattern of dystrophin expression on muscle biopsy; nevertheless, extensive analysis by MLPA, sequencing, CGH-array and RNA profiling failed to identify any mutation within DMD gene. We performed whole exome sequencing by means of an Illumina GAIIe sequencer in order to identify genetic modifiers that could contribute to the symptomatic phenotype in this female. A total of 23,776 SNPs passed filtering for quality parameters. We further selected variations present in a list of 883 candidate genes belonging to the dystrophin expression regulation network and, applying a dominant model of inheritance for the modifying genes, we considered only heterozygous variations including SNPs already present in the dbSNP database. This allowed us to retain 902 SNPs. We performed RNAseq analysis on her muscle biopsy to restrict the panel of SNPs and integrated exome and transcriptome results to provide critical/confirmatory information about the SNPs identified. Eight out of the 20 SNPs selected in UTR regions were validated by RNAseq data. For non-synonymous variations, 205 out of the 219 SNPs were mapped in genes expressed in muscle and 61 were validated by RNAseq. In total we validated 69 exploratory SNPs. These SNPs are located within genes involved in the sarcolemma and extracellular matrix, cell signalling and, interestingly, chromatin modification. The 69 SNPs are in course of validation in two groups of females: symptomatic (17) and non-symptomatic (18) DMD carriers. Results will be statistically analysed using both multidimensional scaling and discriminate analysis in order to identify those variations able to discriminate between the two phenotypic groups.