Long-range PCR amplification-based targeted enrichment & next generation sequencing: A cost-effective testing strategy for lysosomal storage disorders

Background & objectives

Lysosomal storage disorders (LSDs) are genetic metabolic disorders which result from deficiency of lysosomal enzymes or defects in other lysosomal components. Molecular genetic testing of LSDs is required for diagnostic confirmation when lysosomal enzyme assays are not available or not feasible to perform, and for the identification of the disease causing genetic variants. The aim of this study was to develop a cost-effective, readily customizable and scalable molecular genetic testing strategy for LSDs.

Methods

A testing method was designed based on the in-house creation of selective amplicons through long range PCR amplification for targeted capture and enrichment of different LSD genes of interest, followed by next generation sequencing of pooled samples.

Results

In the first phase of the study, standardization and validation of the study protocol were done using 28 samples of affected probands and/or carrier parents (group A) with previously identified variants in seven genes, and in the second phase of the study, 30 samples of enzymatically confirmed or biopsy-proven patients with LSDs and/or their carrier parents who had not undergone any prior mutation analysis (group B) were tested and the sequence variants identified in them through the study method were validated by targeted Sanger sequencing.

Interpretation & conclusions

This testing approach was found to be reliable, easily customizable and cost-effective for the molecular genetic evaluation of LSDs. The same strategy may be applicable, especially in resource poor settings, for developing cost-effective multigene panel tests for other conditions with genetic heterogeneity.

Sialidosis type II: Expansion of phenotypic spectrum and identification of a common mutation in seven patients

Sialidosis, an autosomal recessive disorder, is characterized by progressive lysosomal storage of sialylated glycopeptides and oligosaccharides. It occurs as a result of biallelic mutations in the NEU1 gene. Sialidosis is traditionally classified as a milder, late-onset type I and a severe early-onset type II disease. The presence of a cherry-red spot is a well-established ophthalmological clue to the disorder. We present a clinical-radiological report of seven unrelated patients with molecularly confirmed sialidosis type II. To the best of our knowledge, This is the largest reported series of patients with Sialidosis type II. A novel, previously unreported ophthalmic phenotype of bulls-eye maculopathy, is described. All seven phenotypically heterogeneous patients had the same pathogenic variant (c.679G > A; p.Gly227Arg) at a homozygous level in the NEU1 gene. We propose that this is a common mutation in north Indians for this rare disorder. We also observed an overlap of symptoms and a continuum of phenotypes in type I and II Sialidosis.

Clinical and Genetic Analysis of Fibrodysplasia Ossificans Progressiva: A Case Report and Literature Review

Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disorder characterized by congenital malformation of the great toes and disabling heterotopic ossification in specific anatomic locations with a world wide prevalence of 1 in 2 million population. Nearly 90% of patients with FOP are misdiagnosed and mismanaged. We present a case of a four-year-old boy brought by his parents with the complaints of stiffness of right shoulder, neck and multiple swellings over the upper back noted over the past 4 months. On examination bilateral symmetrical hallux valgus with microdactyly of great toes and multiple bony hard swellings on both the scapulae were noted. Skeletal survey revealed all the classical features of FOP. Mutation of the ACVR1gene on genetic analysis confirmed the diagnosis of FOP. Invasive surgical procedures including biopsy and manipulations for stiff joints were avoided as they strikingly end up in rapid progression of FOP. Congenital hallux valgus with short great toe in a child should be considered as an early diagnostic tool for FOP even before the onset of mass lesions. Genetic analysis for mutation of ACVR1gene is confirmatory. Prevention of injury, medical management of acute painful flare-ups and rehabilitation are the mainstay of treatment.

Association of VEGF +405G>C polymorphism with endometriosis

The present study was designed to explore the association between the SNP +405G>C of the VEGF gene with the risk of endometriosis, and endometriosis associated with adenomyosis and chocolate cysts. Following extraction of genomic DNA, genotyping of the +405 G>C polymorphisms of the VEGF gene was performed by PCR - RFLP analysis. The genotype (X2 =21.713, 2 df, P = < 0.0001) and allele (X2 =10.697, 1 df, P = 0.0011) frequencies of endometriosis patients were significantly different from those of the control women. The genotype and allele frequencies significantly differed in all the clinical subgroups of endometriosis patients. The significant differences in allele frequencies were the result of an increased proportion of homozygote GG genotype carriers. No significant difference was observed between the clinical subgroups with respect to the genotype and allele frequencies of the VEGF +405G>C polymorphism. These findings suggest that the VEGF +405 G>C polymorphism is associated with the risk of endometriosis, and endometriosis associated with adenomyosis and chocolate cysts.

Genetic contribution of the interferon gamma dinucleotide-repeat polymorphism in South Indian women with endometriosis

AIM

To investigate whether the interferon-gamma (IFNG) gene dinucleotide (CA)-repeat polymorphism is responsible in part for genetic susceptibility to endometriosis in South Indian women.

METHODS

Following extraction of genomic DNA, genotyping of interferon-gamma CA-repeat polymorphism was performed using genescan technology.

RESULTS

The global IFNG allele frequencies in all patients with endometriosis were significantly different from those in the control women (chi(2) = 37.062; 6 degrees of freedom; P < or = 0.0001). Significant difference was observed in global allele frequencies between the control women and each clinical subgroup of patients with endometriosis except for patients suffering from endometriosis associated with adenomyosis. The difference was due to an increase in a12 (112 bp) allele in the patients with endometriosis and each clinical subgroup of patients with endometriosis. The distribution of the IFNG a12 genotypes was significantly different between patients with endometriosis and the control women. (chi(2) = 10.635; 2 degrees of freedom; P = 0.0049). A significant difference in the IFNG a12 genotypes was found only among the three clinical subgroups.

CONCLUSION

These results suggest that the IFNG gene CA-repeat polymorphism is associated with susceptibility to endometriosis in South Indian women.