Utility of next-generation sequencing in genetic testing and counseling of disorders involving the musculoskeletal system-trends observed from a single genetic unit.

BACKGROUND: Disorders involving the musculoskeletal system are often identified with short stature and a range of orthopedic problems. The clinical and genetic heterogeneity of these diseases along with several characteristic overlaps makes definitive diagnosis difficult for clinicians. Hence, using molecular testing in addition to conventional tests becomes essential for appropriate diagnosis and management. METHODS: Comprehensive clinical examination, detailed pretest and posttest counseling, molecular diagnosis with next-generation sequencing (NGS), genotype-phenotype correlation and Sanger sequencing for targeted variant analysis. RESULTS: This manuscript reports a molecular spectrum of variants in 34 orthopedic cases referred to a single genetic unit attached to a tertiary care hospital. The diagnostic yield of NGS-based tests coupled with genetic counseling and segregation analysis was 79% which included 7 novel variants. In about 53% (i.e. 18/34 cases), molecular testing outcome was actionable since 8 of the 18 underwent prenatal diagnosis, as they were either in their early gestation or had planned a pregnancy subsequent to molecular testing, while ten cases were premaritally/prenatally counseled for the families to take informed decisions as they were in the reproductive age. CONCLUSIONS: The report highlights the importance of NGS-based tests even in a low resource setting as it helps patients, families and healthcare providers in reducing the economic, social and emotional burden of these disorders.

Expanding the clinico-molecular spectrum of Angelman syndrome phenotype with the GABRG3 gene: Evidence from methylation and sequencing studies.

Angelman syndrome (AS) (OMIM#105830) is an imprinting disorder caused due to alterations in the maternal chr 15q11-13 region. Majority of cases can be diagnosed by methylation-specific polymerase chain reaction (MS-PCR) of SNRPN gene and by UBE3A sequencing, however, about 10% of cases with AS phenotype remain undiagnosed. Differential diagnoses of AS can be detected by chromosomal microarray (CMA) and clinical exome sequencing (CES). In this study, 30 cases with AS features were evaluated by MS-PCR, CMA, and CES. SNRPN MS-PCR confirmed AS in eight (26%), CMA and CES diagnosed nine (30%) cases. One case was identified with a novel variant c.1125C > T in GABRG3, located at 15q12 region, which is currently not associated with any syndrome. The GABRG3 gene is also speculated to be imprinted, a MS-PCR assay was designed to confirm its differential parental methylation status. This assay identified another case with altered GABRG3 methylation. The two cases with GABRG3 alteration-sequence change and methylation indicate that GABRG3 may be associated with a subtype of AS or a new related syndrome. Performing GABRG3 MS-PCR and sequencing of a larger group of patients with AS phenotype and normal SNPRN and UBE3A status will help in establishing exact genotype-phenotype correlation.

Familial Acute Necrotizing Encephalopathy: Evidence From Next Generation Sequencing of Digenic Inheritance.

Infection-induced acute encephalopathies (IIAEs) are a group of neurologic disorders caused post infection. They are of 8 types, 6 of which are herpes specific, whereas IIAE3 and IIAE4 can be triggered by infections additional to herpeslike influenza, enterovirus, etc. IIAE3 is also known as acute necrotizing encephalopathy type 1, which is a rare type of encephalopathy that occurs following an infection in infancy or early childhood. Symptoms include fever, cough, congestion, vomiting, and diarrhea followed by seizures, hallucination, ataxia, and abnormal muscle tone, and sometimes it leads to untimely death. Here, we describe a familial case where 3 siblings were clinically diagnosed with acute necrotizing encephalopathy 1. Genetic testing revealed 2 heterozygous variations: RANBP2 c.5249C>G, p.P1750 R, and CPT2 c.365C>T, p.S122F. Variants in RANBP2 and CPT2 have been individually known to be associated with IIAE3 and IIAE4, respectively. Segregation analysis revealed that the RANBP2 variant was inherited from the father and the CPT2 variant from the mother. This case qualifies to be the first of its kind where digenic inheritance (ie, DNA sequence variants in 2 genes are required for the pathogenic phenotypes) appears to cause a lethal class of acute necrotizing encephalopathy.

Purine nucleoside phosphorylase deficiency with a novel PNP gene mutation: a first case report from India.

The authors report a case of purine nucleoside phosphorylase (PNP) deficiency for the first time from India. The case presented with recurrent severe infections, developmental delays, seizures and progressive neurological deterioration. The diagnosis of primary immunodeficiency disorder was delayed in spite of recurrent infection due to predominant neurological symptoms. Sequencing of the PNP gene revealed a novel mutation resulting in a premature stop codon.