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

Abstract

Introduction The genetic causes of limb-girdle muscular dystrophy (LGMD) have been studied in numerous countries, but such investigations have been limited in Egypt. Methods A cohort of 30 families with suspected LGMD from Assiut, Egypt was studied using immunohistochemistry, homozygosity mapping, Sanger sequencing, and whole exome sequencing. Results Six families were confirmed to have pathogenic mutations, 4 in SGCA and 2 in DMD. Of these, 3 families harbored a single nonsense mutation in SGCA, suggesting that this may be a common mutation in Assiut, Egypt originating from a founder effect. Discussion The Assiut region in Egypt appears to share at least several of the common LGMD genes found in other parts of the world. It is notable that 4 of the 6 mutations were ascertained via whole exome sequencing, even though it was the last approach adopted, illustrating the power of this technique for identifying causative mutations for muscular dystrophies.

Molecular diagnosis of muscular diseases in outpatient clinics

“…1 Therefore, genetic testing is increasingly used and can be obtained in a noninvasive manner. Across different countries such as Canada, the United States, China, Korea, Germany, the United Kingdom, Egypt, Poland, Australia, and Japan, gene panel sequencing has a yield varying from 16% to 65%, [2][3][4][5][6][7] depending on subgroups of patients' selection, whereas exome sequencing has a yield in between 13% and 69% [8][9][10][11][12][13][14][15] in different settings. Its superiority over gene panel, in diagnosing common etiologies, remains to be quantified.…”

The sensitivity of exome sequencing in identifying pathogenic mutations for LGMD in the United States

“…The Genomics Platform at the Broad Institute was used to perform whole exome sequencing of DNA samples representing selected subjects from 45 of the 55 families; the full sequencing protocol has been published for LGMD cohorts from other countries 7 , 9 . The Agilent Sure-Select Human All Exon v2.0, 44Mb baited target and the Broad in-solution hybrid selection process were used to target exons in genomic DNA.…”

Identification of a pathogenic mutation in ATP2A1 via in silico analysis of exome data for cryptic aberrant splice sites

“…The output included a list of candidate PANESS, their genomic coordinates, the MAF, the affected gene, the type of splice site created, and a comparison of the canonical extended and essential splice site sequence with the equivalent sequence surrounding the PANESS variant. A VCF file (ExAC r0.3.1) was downloaded from the Exome Aggregation Consortium website (Lek et al, 2016) and used to validate performance of the PANESS pipeline. Human Splicing Finder v.3.0 (HSF) (Desmet et al, 2009) (http://www.umd.be/HSF3/) was used to assess the effect on splicing of selected PANESS variants.…”

“…Next-generation sequencing (NGS) technologies are now routinely used to discover pathogenic mutations underlying rare genetic disorders. Unfortunately, in many cohorts, NGS techniques identify pathogenic mutations in a minority of families (Lee et al, 2014;Yang et al, 2014); for neuromuscular disorders, in general, it has been found to be around 40% (Ankala et al, 2015), as well as for limb-girdle muscular dystrophy in particular (Ghaoui et al, 2015;Reddy et al, 2017Reddy et al, , 2016. The genetic etiologies of the remaining families often prove difficult to ascertain, as they may lie in unsequenced regions (for exomes and targeted sequence panels in particular) or may be cryptic mutations in regions that are already sequenced.…”