Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort

Abstract

Mutations in the DMD gene, encoding the dystrophin protein, are responsible for the dystrophinopathies Duchenne Muscular Dystrophy (DMD), Becker Muscular Dystrophy (BMD), and X-linked Dilated Cardiomyopathy (XLDC). Mutation analysis has traditionally been challenging, due to the large gene size (79 exons over 2.2 Mb of genomic DNA). We report a very large aggregate data set comprised of DMD mutations detected in samples from patients enrolled in the United Dystrophinopathy Project, a multicenter research consortium, and in referral samples submitted for mutation analysis with a diagnosis of dystrophinopathy. We report 1,111 mutations in the DMD gene, including 891 mutations with associated phenotypes. These results encompass 506 point mutations (including 294 nonsense mutations) and significantly expand the number of mutations associated with the dystrophinopathies, highlighting the utility of modern diagnostic techniques. Our data supports the uniform hypermutability of CGA>TGA mutations, establishes the frequency of polymorphic muscle (Dp427m) protein isoforms and reveals unique genomic haplotypes associated with "private" mutations. We note that 60% of these patients would be predicted to benefit from skipping of a single DMD exon using antisense oligonucleotide therapy, and 62% would be predicted to benefit from an inclusive multiexonskipping approach directed toward exons 45 through 55.

Figure 1

Exon distribution of nonsense, splice and small insertion/deletion (indel) mutations by exon in unrelated kindreds. Exons containing CpG codons are marked by asterisks (exon 70 contains three CpG codons).

Figure 2

Dystrophin amino acid polymorphisms and nsSNP haplotypes. (A) Position of non-synonymous variants based on the NM_004006.1 coding region is shown with exon number, spectrin repeat domain (R1 though R24), one-letter amino acid code, minor allele frequency and PolyPhen prediction indicated. (B) Protein haplotype structure for the nsSNPs from 698 fully resequenced patients sorted and scaled by haplotype frequency. Major and minor alleles are shaded by light and dark grey, respectively. The Dp427m5 nsSNP haplotype variant is identical to NM_004006.1 CDS and the four amino acid differences (p.G882D, p.R1745H, p.K2366Q and pQ2937R) observed in the other eight major haplotypes (Dp427m1-m8) are shown to the right of each nsSNP haplotype.

Figure 3

Suppression of truncating mutations by mono-exon skipping. The number of patients that can have their truncating mutation bypassed by single exon skipping is shown for each exon. The mutations found in each exon category are listed in Supp. Table S6.