Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India.

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.

The Etiological Profile of Global Developmental Delay at a Tertiary Care Hospital in India: An Observational Study.

Background Global developmental delay (GDD) is common and has a significant impact on affected children, families, and society. Understanding its etiology is crucial for management and prevention strategies. However, data on the etiological profile of GDD in developing countries are limited. This study aimed to identify the etiological profile of GDD at a tertiary care hospital in India. Methodology This observational study included children aged three months to five years with a developmental quotient below 70%. Data on demographics, clinical features, relevant investigations, and diagnoses were collected. Etiologies were categorized into prenatal, perinatal, postnatal, and unknown causes. Informed consent was obtained from the parents. Results A total of 52 children, with a median age of 15.5 months, were included in the study, with 69.2% being males. Prenatal causes accounted for half of the cases, with genetic abnormalities (32.7%) and chromosomal abnormalities (7.7%) being prominent. Perinatal causes were the next most common (34.6%), including hypoxic-ischemic encephalopathy (26.7%). Postnatal causes were rare (3.8%). The overall etiological yield was 88.4%, with some cases remaining unidentified. Conclusions Prenatal causes, including genetic and chromosomal abnormalities, are common in GDD. The utilization of genetic testing enhances etiological yield. Hypoxic-ischemic encephalopathy remains a significant factor and highlights the importance of perinatal care in preventing developmental delays. Large multicentric studies are needed for a comprehensive database of etiological profiles.

Proband only exome sequencing in 403 Indian children with neurodevelopmental disorders: Diagnostic yield, utility and challenges in a resource-limited setting.

Whole exome sequencing is recommended as the first tier test for neurodevelopmental disorders (NDDs) with trio being an ideal option for the detection of de novo variants. Cost constraints have led to adoption of sequential testing i.e. proband-only whole exome followed by targeted testing of parents. The reported diagnostic yield for proband exome approach ranges between 31 and 53%. Typically, these study designs have aptly incorporated targeted parental segregation before concluding a genetic diagnosis to be confirmed. The reported estimates however do not accurately reflect the yield of proband only standalone whole -exome, a question commonly posed to the referring clinician in self pay medical systems like India. To assess the utility of standalone proband exome (without follow up targeted parental testing), we retrospectively evaluated 403 cases of neurodevelopmental disorders referred for proband-only whole exome sequencing at Neuberg Centre for Genomic Medicine (NCGM), Ahmedabad during the period of January 2019 and December 2021. A diagnosis was considered confirmed only upon the detection of Pathogenic/Likely Pathogenic variants in concordance with patient's phenotype as well as established inheritance pattern. Targeted parental/familial segregation analysis was recommended as a follow up test where applicable. The diagnostic yield of the proband-only standalone whole exome was 31.5%. Only 20 families submitted samples for follow up targeted testing, and a genetic diagnosis was confirmed in twelve cases increasing the yield to 34.5%. To understand factors leading to poor uptake of sequential parental testing, we focused on cases where an ultra-rare variant was detected in hitherto described de novo dominant neurodevelopmental disorder. A total of 40 novel variants in genes associated with de novo autosomal dominant disorders could not be reclassified as parental segregation was denied. Semi-structured telephonic interviews were conducted upon informed consent to comprehend reasons for denial. Major factors influencing decision making included lack of definitive cure in the detected disorders; especially when couples not planning further conception and financial constraints to fund further targeted testing. Our study thus depicts the utility and challenges of proband-only exome approach and highlights the need for larger studies to understand factors influencing decision making in sequential testing.

Spectrum of Common and Rare Small Molecule Inborn Errors of Metabolism Diagnosed in a Tertiary Care Center of Maharashtra, India.

Introduction Inborn errors of metabolism (IEM) form a large group of genetic diseases involving defects in genes coding for enzymes, receptors, and cofactors in the metabolic pathways of small and large molecules. The present study is the comprehensive data analysis of the tandem mass spectrometry (TMS) and urine metabolic pattern for the diagnosis of IEMs by gas chromatography and mass spectrometry (GC/MS) in samples received for high-risk IEM screening. Methods We conducted a retrospective analysis of children diagnosed with IEMs presenting at the genetic clinic of Mahatma Gandhi Missions (MGM) Medical College, Aurangabad. This article summarizes retrospective data of 40 pediatric cases over a three-year period, diagnosed with small molecule IEM based on the standard testing criteria. Results Out of 40, 17 patients (42.5%) were found to have organic acidemias, four (10%) had fatty acid oxidation defects, six (15%) had disorders of aminoacidopathies, seven (17.5%) had mitochondrial diseases, and three (7.5%) had urea cycle defects. One patient in each group (2.5% each) had carbohydrate metabolism defects, purine metabolic defects, and neurotransmitter metabolic defects. Conclusions This clinico-etiological profile study has thrown light on the clinical features and natural course of many common and rare IEMs, and it may provide clinicians with a deeper understanding of these conditions, allowing for improved early diagnosis and treatment of these diseases. Because of the high degree of consanguinity and marriages in the same community, common as well as many rare inherited metabolic diseases were diagnosed and novel genetic variants were identified.

Targeted Screening for Gaucher Disease in High Suspicion Patients and Clinical Profile of Screen Positives in a Large Pediatric Multispecialty Hospital.

OBJECTIVES:  The proposed screening study was aimed at determining the prevalence of Gaucher disease in a selected high-risk population of patients and describing the clinical profile of diagnosed patients. METHODOLOGY: It was a prospective observational study from January 2020 to September 2022 (two years and eight months) in the genetic clinic of the pediatric department. A total of 22 patients were suspected to be having Gaucher disease based on clinical findings of hepatosplenomegaly with bicytopenia or isolated thrombocytopenia. In these patients, chronic liver disease, portal hypertension, and other hematological conditions were ruled out. Three patients with Gaucher disease applied for enzyme replacement therapy (ERT) support under India Charitable Access Program and one patient received therapy for two months. Clinical findings were compared before and after ERT. Clinical findings were noted in all patients. RESULTS:  Among the 22 patients, nine (40.9%) patients were confirmed to be suffering from Gaucher disease with six based on enzyme assay on dry blood spot and three based on DNA mutation analysis. One patient among the screen positives received ERT for two months and was noted to have an improvement in hemoglobin and platelet count, a reduction in liver size, and better general well-being. CONCLUSION: High-suspicion targeted screening of Gaucher disease in patients with splenomegaly and thrombocytopenia based on a dry blood spot enzyme assay is high yielding, effective strategy in identifying Gaucher disease patients. Clinical features were variable in severity, though a common mutation was found in the majority of patients.