Functional characterization of novel variants in SMPD1 in Indian patients with acid sphingomyelinase deficiency.

Pathogenic variations in SMPD1 lead to acid sphingomyelinase deficiency (ASMD), that is, Niemann-Pick disease (NPD) type A and B (NPA, NPB), which is a recessive lysosomal storage disease. The knowledge of variant spectrum in Indian patients is crucial for early and accurate NPD diagnosis and genetic counseling of families. In this study, we recruited 40 unrelated pediatric patients manifesting symptoms of ASMD and subnormal ASM enzyme activity. Variations in SMPD1 were studied using Sanger sequencing for all exons, followed by interpretation of variants based on American College of Medical Genetics and Genomics & Association for Molecular Pathology (ACMG/AMP) criteria. We identified 18 previously unreported variants and 21 known variants, including missense, nonsense, deletions, duplications, and splice site variations with disease-causing potential. Eight missense variants were functionally characterized using in silico molecular dynamic simulation and in vitro transient transfection in HEK293T cells, followed by ASM enzyme assay, immunoblot, and immunofluorescence studies. All the variants showed reduced ASM activity in transfected cells confirming their disease-causing potential. The study provides data for efficient prenatal diagnosis and genetic counseling of families with NPD type A and B.

Multi-gene testing in neurological disorders showed an improved diagnostic yield: data from over 1000 Indian patients.

BACKGROUND: Neurological disorders are clinically heterogeneous group of disorders and are major causes of disability and death. Several of these disorders are caused due to genetic aberration. A precise and confirmatory diagnosis in the patients in a timely manner is essential for appropriate therapeutic and management strategies. Due to the complexity of the clinical presentations across various neurological disorders, arriving at an accurate diagnosis remains a challenge. METHODS: We sequenced 1012 unrelated patients from India with suspected neurological disorders, using TruSight One panel. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS: We were able to detect mutations in 197 genes in 405 (40%) cases and 178 mutations were novel. The highest diagnostic rate was observed among patients with muscular dystrophy (64%) followed by leukodystrophy and ataxia (43%, each). In our cohort, 26% of the patients who received definitive diagnosis were primarily referred with complex neurological phenotypes with no suggestive diagnosis. In terms of mutations types, 62.8% were truncating and in addition, 13.4% were structural variants, which are also likely to cause loss of function. CONCLUSION: In our study, we observed an improved performance of multi-gene panel testing, with an overall diagnostic yield of 40%. Furthermore, we show that NGS (next-generation sequencing)-based testing is comprehensive and can detect all types of variants including structural variants. It can be considered as a single-platform genetic test for neurological disorders that can provide a swift and definitive diagnosis in a cost-effective manner.

Spectrum of SMPD1 mutations in Asian-Indian patients with acid sphingomyelinase (ASM)-deficient Niemann-Pick disease.

Acid sphingomyelinase (ASM)-deficient Niemann-Pick disease is an autosomal recessive lysosomal storage disorder caused by biallelic mutations in the SMPD1 gene. To date, around 185 mutations have been reported in patients with ASM-deficient NPD world-wide, but the mutation spectrum of this disease in India has not yet been reported. The aim of this study was to ascertain the mutation profile in Indian patients with ASM-deficient NPD. We sequenced SMPD1 in 60 unrelated families affected with ASM-deficient NPD. A total of 45 distinct pathogenic sequence variants were found, of which 14 were known and 31 were novel. The variants included 30 missense, 4 nonsense, and 9 frameshift (7 single base deletions and 2 single base insertions) mutations, 1 indel, and 1 intronic duplication. The pathogenicity of the novel mutations was inferred with the help of the mutation prediction software MutationTaster, SIFT, Polyphen-2, PROVEAN, and HANSA. The effects of the identified sequence variants on the protein structure were studied using the structure modeled with the help of the SWISS-MODEL workspace program. The p. (Arg542*) (c.1624C>T) mutation was the most commonly identified mutation, found in 22% (26 out of 120) of the alleles tested, but haplotype analysis for this mutation did not identify a founder effect for the Indian population. To the best of our knowledge, this is the largest study on mutation analysis of patients with ASM-deficient Niemann-Pick disease reported in literature and also the first study on the SMPD1 gene mutation spectrum in India. © 2016 Wiley Periodicals, Inc.

Embryogenesis and types of subcostal hernia--a rare entity.

BACKGROUND/PURPOSE: Four infants with congenital subcostal hernia are reported, as it is a rare entity with only two cases previously reported. Further, there are no reports concerning the complex multisystem subtype. Embryogenesis of the associated anomalies and subcostal hernia and their management are discussed. MATERIALS/METHODS: Clinical features, history, investigations, associated anomalies, and management data of four patients with subcostal hernia were collected and analyzed. RESULTS: The following associated anomalies were detected: renal agenesis (2), musculoskeletal abnormality (3), congenital heart disease (2), müllerian-renal-cervicothoracic somite abnormalities and vertebral-anorectal-cardiac-tracheoesophageal-renal-radial-limb anomalies (1). The subcostal hernias were treated by laparoscopic assisted (3) or laparoscopic herniorrhaphy (1). CONCLUSIONS: Subcostal hernia is a rare entity with varied clinical presentations and presents either as an isolated defect or as a complex multisystem defect. The exact etiology is still unknown. Phenotypic manifestation of the complex defect is probably due to developmental gene defect affecting the coordinated growth of mesoderm around 4th to 10th weeks of fetal life.

Androgen insensitivity syndrome: ten years of our experience.

Abnormalities of secondary sexual differentiation manifest in varying degrees depending upon the severity of the underlying cause. Primary amenorrhea in phenotypic females is caused by several different factors, including hormonal imbalance, nutritional deficiency and sex differentiation abnormalities. Androgen insensitivity syndrome (AIS) accounts for a large proportion of such cases in phenotypic females but genetically male individuals. Over the past 10 years, we have collected data related to androgen insensitivity from more than 150 cases. The research identified several important but neglected facts about this syndrome; including the identification of mutations in 39% of the cases and the establishment of the cause of pathogenesis in 60% of them. The most intriguing facts were uncovered in relation to late presentation of the AIS cases, little awareness among patients and family members, no consensus on the age of performing gonadectomy, and reluctance of the patients to undergo recommended surgery. These issues need immediate attention to improve healthcare and management of AIS cases. This article summarizes our observations about AIS with an aim to spread awareness among patients and clinicians.