Long-range PCR amplification-based targeted enrichment & next generation sequencing: A cost-effective testing strategy for lysosomal storage disorders

• Published in: Indian journal of medical research (New Delhi, India : 1994) Vol. 157; no. 6; pp. 577 - 590
• Main Authors: Vanaja, Maria, Nurul Jain, Jamal, Dalal, Ashwin, Ranganath, Prajnya
• Format: Journal Article
• Language: English
• Published: India Wolters Kluwer India Pvt. Ltd 01-06-2023; Medknow Publications and Media Pvt. Ltd; Scientific Scholar
• Subjects: Diagnosis; DNA sequencing; Economic aspects; Genetic testing; Metabolism, Inborn errors of; Methods; Molecular diagnostic techniques; Nucleotide sequencing; Polymerase chain reaction; India; Long-range polymerase chain reaction-based targeted amplification - lysosomal storage disorders - molecular genetic testing
• ISSN: 0971-5916
• DOI: 10.4103/ijmr.IJMR_2707_20

Background & objectives: Lysosomal storage disorders (LSDs) are genetic metabolic disorders which result from deficiency of lysosomal enzymes or defects in other lysosomal components. Molecular genetic testing of LSDs is required for diagnostic confirmation when lysosomal enzyme assays are not available or not feasible to perform, and for the identification of the disease causing genetic variants. The aim of this study was to develop a cost-effective, readily customizable and scalable molecular genetic testing strategy for LSDs.
Methods: A testing method was designed based on the in-house creation of selective amplicons through long range PCR amplification for targeted capture and enrichment of different LSD genes of interest, followed by next generation sequencing of pooled samples.
Results: In the first phase of the study, standardization and validation of the study protocol were done using 28 samples of affected probands and/or carrier parents (group A) with previously identified variants in seven genes, and in the second phase of the study, 30 samples of enzymatically confirmed or biopsy-proven patients with LSDs and/or their carrier parents who had not undergone any prior mutation analysis (group B) were tested and the sequence variants identified in them through the study method were validated by targeted Sanger sequencing.
Interpretation & conclusions: This testing approach was found to be reliable, easily customizable and cost-effective for the molecular genetic evaluation of LSDs. The same strategy may be applicable, especially in resource poor settings, for developing cost-effective multigene panel tests for other conditions with genetic heterogeneity.