Pilot study for the detection of mutations associated with lysosomal diseases using Next Generation Sequencing
Julia Lindgren1,*, Åsa Nilsson1, Emma Samuelson1, Birgitta Kjellström1, Jan-Eric Månsson1, Jorge Asin Cayuela1
1Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
Introduction: Lysosomal diseases are a group of inherited metabolic disorders caused by deficiencies in lysosomal enzymes, resulting in the accumulation of different substrates like sphingolipids, oligosaccharides and mucopolysaccharides. Nowadays routine diagnosis is highly demanding in terms of resources and can lead to long response times. Using a Next Generation Sequencing (NGS) panel covering all the known genes involved in lysosomal diseases as a screening tool, would improve time- and cost efficiency of the diagnostic process of this group of diseases.
Objectives: To test the capacity of a commercial NGS-panel to detect pathogenic mutations coupled to lysosomal diseases.
Methods: DNA was extracted from seven patients with lysosomal diseases and one negative control. Pathogenic mutations or deletions were previously detected with Sanger sequencing in all patient samples at diagnosis. Library construction was done using the TruSightTM Rapid Capture Kit and the Exome panel (Illumina®). The kit targets exons of 2761 genes, including 46 genes associated with lysosomal disease. Prepared libraries were sequenced on the MiSeq instrument (Illumina®) at Genomics Core Facility, Sahlgrenska Academy. Variant analysis and annotation was performed at the Bioinformatics Core Facility, Sahlgrenska Academy. Variants within the 46 genes of interest were filtered according to allele frequency, exonic/splice site location and autosomal recessive or X-linked pattern of inheritance.
Results: High quality data was obtained for all eight samples. Results from six out of seven patients showed the expected pathogenic mutations. The seventh patient had a 30 kb deletion that was not detected. In addition, one sample showed a pathogenic mutation that was not found with Sanger sequencing in the original investigation.
Conclusion: The tested panel can be a useful tool for the detection of pathogenic point mutations linked to lysosomal diseases. However, further validation and optimization is required before implementation in clinical routine.
Keywords: Genomics, Inborn error of metabolism, Metabolic disease