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
The Birth Defects Registry of India-Chennai (BDRI-C) was created in 2001 to monitor birth defects and provide timely referrals. Using established guidelines to evaluate surveillance systems, we examined the following attributes of BDRI-C to help strengthen the registry: simplicity, flexibility, data quality, representativeness, acceptability, timeliness, and stability. We reviewed BDRI-C documents, including reporting forms; interviewed key informants; and calculated data completeness, coverage, and reporting time. BDRI-C captured 14% of the births in Chennai April 2013 - March 2014. About 7% of institutions in Chennai registered in BDRI-C, and of those registered, 37% provided data in 2013. Median reporting time was 44 days after birth in 2013. BDRI-C is a useful, simple, flexible, and timely passive birth defects surveillance system; however, improvements can be made to ensure BDRI-C is representative of Chennai, data processing and quality checks are on-going, and the system is acceptable for member institutions and stable.
