Myophosphorylase (PYGM) mutations in Turkish patients with McArdle disease: A next generation sequencing study

McArdle disease, also known as a glycogen storage disease type V (GSDV), is caused by a deficiency in myophosphorylase activity. This study aimed to identify common and other PYGM mutations in Turkish patients with McArdle disease by next generation sequencing (NGS) in order to establish a precise genetic diagnosis, instead of having patients undergo muscle biopsies. Patients and relatives from 33 families with previously diagnosed myophosphorylase deficiency based upon muscle biopsy and enzyme activity measurements were studied (n = 68). The control group consisted of unrelated healthy volunteers with no clinical evidence of myopathy (n = 53). Genomic DNA was extracted from EDTA blood and examined by NGS with an Illumina Miseq system. The DNA sequencing data were analysed using BWA to align the human genome sequence (hg19), SAMtools to manipulate BAM files, GATK to call SNPs and small indels, SnpEff for functional annotation, and VarSifter for variant filtering. By far the most common PYGM mutation identified was p.Met1Val/c.1A>G (patients/families = 18/7). This point mutation abolishes the translation initiating codon resulting in a severe McArdle phenotype and was previously identified in a patient with Turkish ancestry. Other mutations found included p.621Phe_622Iledel/c.1864_1865delCTT (6/4), g.4853_4854delTG (4/3), p.Arg488X/c.1462C>T (3/3), p.665Lys_666Glnfs/c.1998_1999delA (2/1) p.Arg50X/c.148C>T (1), c.1563+7A>G (1), p.Leu491Pro/c.1472T>C (1), and p.169Lys_170Iledel/c.509_510delAGA (1). Compound heterozygosity was identified in 12 patients of which half were heterozygous for the common p.Met1Val mutation. Coverage of the NGS reads was unsatisfactory to detect mutations in 10 other patients. In conclusion, a common point as well as 8 other PYGM mutations was identified in Turkish patients with GSDV. The NGS technique readily allowed the discovery of PYGM mutations upon which a molecular flowchart for the diagnosis of GSDV in Turkish patients was developed.