ABSTRACT
BACKGROUND: Current clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India. RESULTS: 903 smMIPs were designed to target exon and exon-intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood. CONCLUSION: We developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.
Subject(s)
DNA Copy Number Variations , Genetic Testing , High-Throughput Nucleotide Sequencing , Lysosomal Storage Diseases , Humans , Lysosomal Storage Diseases/genetics , Lysosomal Storage Diseases/diagnosis , India , DNA Copy Number Variations/genetics , Genetic Testing/methods , High-Throughput Nucleotide Sequencing/methods , Polymorphism, Single Nucleotide/genetics , Female , Male , Molecular Probes/geneticsABSTRACT
Lipoprotein glomerulopathy (LPG) is a rare condition of renal lipidosis characterized by lipoprotein thrombi in glomeruli, an abnormal plasma lipoprotein profile, and a marked increase in serum apolipoprotein E (apo E) levels. It is a monogenic disorder with autosomal dominant inheritance and the average age of presentation is 32 years (4-69 years). It is rare in children. The presentation can be nephrotic syndrome, hematuria, or progressive renal failure. Here we report the first described case of LPG in an Indian 7.5-year-old boy who presented with steroid-resistant nephrotic syndrome with normal renal function. A renal biopsy was suggestive of lipoprotein glomerulopathy. The detection of a pathogenic variant in apo E, Kyoto type, by exome sequencing, confirmed the diagnosis of lipoprotein glomerulopathy. Complete response was achieved with Angiotensin-converting Enzyme inhibitor and fenofibrates.
