Efficient identification of novel mutations in patients with limb girdle muscular dystrophy

Abstract

Limb girdle muscular dystrophy type 2 (LGMD2) is a genetically heterogeneous autosomal recessive disorder caused by mutations in 15 known genes. DNA sequencing of all candidate genes can be expensive and laborious, whereas a selective sequencing approach often fails to provide a molecular diagnosis. We aimed to efficiently identify pathogenic mutations via homozygosity mapping in a population in which the genetics of LGMD2 has not been well characterized. Thirteen consanguineous families containing a proband with LGMD2 were recruited from Saudi Arabia, and for 11 of these families, selected individuals were genotyped at 10,204 single nucleotide polymorphisms. Linkage analysis excluded all but one or two known genes in ten of 11 genotyped families, and haplotype comparisons between families allowed further reduction in the number of candidate genes that were screened. Mutations were identified by DNA sequencing in all 13 families, including five novel mutations in four genes, by sequencing at most two genes per family. One family was reclassified as having a different myopathy based on genetic and clinical data after linkage analysis excluded all known LGMD2 genes. LGMD2 subtypes A and B were notably absent from our sample of patients, indicating that the distribution of LGMD2 mutations in Saudi Arabian families may be different than in other populations. Our data demonstrate that homozygosity mapping in consanguineous pedigrees offers a more efficient means of discovering mutations that cause heterogeneous disorders than comprehensive sequencing of known candidate genes.Electronic supplementary materialThe online version of this article (doi:10.1007/s10048-010-0250-9) contains supplementary material, which is available to authorized users.

Molecular diagnosis of hereditary inclusion body myopathy by linkage analysis and identification of a novel splice site mutation in GNE

“…We report a family with five siblings affected with HIBM2, which we diagnosed primarily by linkage analysis and identification of mutations in GNE . Recently, we used a similar approach to achieve a molecular diagnosis for a family with multiminicore disease, another rare myopathy that can be mistaken for LGMD [ 24 ]. The exclusion in our linkage scan of almost all known myopathy genes [ 25 ], despite fourteen regions showing linkage at a LOD score of approximately 1.4, confirms the value of linkage analysis as a diagnostic tool even in families not informative enough to generate suggestive or significant LOD scores.…”

Map of autosomal recessive genetic disorders in Saudi Arabia: Concepts and future directions

“…In fact, the recent progress in gene mapping in Saudi Arabia is largely attributed to this method [Alkuraya, 2010]. It has been shown to be helpful in reaching a genetic diagnosis in extremely rare autosomal recessive conditions such as skin fragility disorders and hereditary hyperekplexia due to defects in the desmoplakin [Al-Owain et al, 2011b] and the b subunit of the glycine receptor , respectively; as well as in genetic diseases of autosomal recessive inheritance with locus heterogeneity such as retinitis pigmentosa [Aldahmesh et al, 2009c], Bardet Biedel syndrome [Abu Safieh et al, 2010], limb girdle muscular dystrophy [Boyden et al, 2010], peroxisomal disorders [Shaheen et al, 2011a], neuronal ceroid lipofuscinosis [Aldahmesh et al, 2009b]. Alkuraya [2010] also showed that autozygosity mapping may represent a less expensive option than the traditional approach for some of autosomal recessive genetic conditions which pose a diagnostic dilemma.…”

Homozygous nonsense mutation inSGCAis a common cause of limb-girdle muscular dystrophy in Assiut, Egypt

“…DNA samples from affected individuals in families known or suspected to be consanguineous (1267‐1269, 1271‐1275, 1277, 1280, 1284, 1357, 1358, 1360‐1363) were selected for genotyping at 10,204 single nucleotide polymorphisms (SNPs) using the GeneChip Human Mapping 10K 2.0 Array (Affymetrix), and homozygosity mapping was performed as previously described …”