Identification and characterization of 30 novel pathogenic variations in 69 unrelated Indian patients with Mucolipidosis Type II and Type III.

Mucolipidosis (ML) (OMIM 607840 & 607838) is a rare autosomal recessive inherited disorder that occurs due to the deficiency of golgi enzyme uridine diphosphate (UDP)- N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase) responsible for tagging mannose-6-phosphate for proper trafficking of lysosomal enzymes to lysosomes. Variants in GlcNAc-phosphotransferase (GNPTAB (α, ß subunits) and GNPTG (γ subunits) are known to result in impaired targeting of lysosomal enzymes leading to Mucolipidosis (ML) Type II or Type III. We analyzed 69 Indian families of MLII/III for clinical features and molecular spectrum and performed in silico analysis for novel variants. We identified 38 pathogenic variants in GNPTAB and 5 pathogenic variants in GNPTG genes including missense, frame shift, deletion, duplication and splice site variations. A total of 26 novel variants were identified in GNPTAB and 4 in GNPTG gene. In silico studies using mutation prediction software like SIFT, Polyphen2 and protein structure analysis further confirmed the pathogenic nature of the novel sequence variants detected in our study. Except for a common variant c.3503_3504delTC in early onset MLII, we could not establish any other significant genotype and phenotype correlation. This is one of the largest studies reported till date on Mucolipidosis II/III in order to identify mutation spectrum and any recurrent mutations specific to the Indian ethnic population. The mutational spectrum information in Indian patients will be useful in better genetic counselling, carrier detection and prenatal diagnosis for patients with ML II/III.

Identification and characterization of 20 novel pathogenic variants in 60 unrelated Indian patients with mucopolysaccharidoses type I and type II.

Mucopolysaccharidoses (MPS), a subgroup of lysosomal storage disorders, are caused due to deficiency of specific lysosomal enzyme involved in catabolism of glycosaminoglycans. To date more than 200 pathogenic variants in the alpha-l-iduronidase (IDUA) for MPS I and ∼500 pathogenic variants in the iduronate-2-sulphatase (IDS) for MPS II have been reported worldwide. The mutation spectrum of MPS type I and MPS type II disorders in Indian population is not characterized yet. In this study, we carried out clinical, biochemical, molecular and in silico analyses to establish the mutation spectrum of MPS I and MPS II in the Indian population. We conducted molecular analysis for 60 MPS-affected patients [MPS I (n = 30) (Hurler syndrome = 17, Hurler-Scheie syndrome = 13), and MPS II (n = 30) (severe = 18, attenuated = 12)] and identified a total of 44 [MPS I (n = 22) and MPS II (n = 22)] different pathogenic variants comprising missense, nonsense, frameshift, gross deletions and splice site variants. A total of 20 [MPS I (n = 14), and MPS II (n = 6)] novel pathogenic sequence variants were identified in our patient cohort. We found that 32% of pathogenic variants detected in IDUA were recurrent and 25% in MPS II. This is the first study revealing the mutation spectrum of MPS I and MPS II patients in the Indian population.

Recurrent and novel GLB1 mutations in India.

GM1 gangliosidosis is a lysosomal storage disorder caused by mutations in the GLB1 gene, leading to the deficiency of the enzyme ß-d-galactosidase. In this study, we report molecular findings in 50 Asian Indian families with GM1 gangliosidosis. We sequenced all the exons and flanking intronic sequences of GLB1 gene. We identified 33 different mutations (20 novel and 13 previously reported). The novel mutations include 12 missense (p.M1?, p.E129Q, p.G134R, p.L236P, p.G262E, p.L297F, p.Y331C, p.G414V, p.K493N, p.L514P, p.P597L, p.T600I), four splicing (c.246-2A>G, c.397-2A>G, c.552+1G>T, c.956-2A>G), three indels (p.R22Qfs*8, p.L24Cfs*47, p.I489Qfs*4) and one nonsense mutation (p.Q452*). Most common mutations identified in this study were c.75+2InsT (14%) and p.L337P (10%). Known mutations accounted for 67% of allele frequency in our cohort of patients, suggesting that these mutations in GLB1 are recurrent across different populations. Twenty three mutations were localized in the TIM barrel domain, ß-domain 1 and ß-domain 2. In silico sequence and structure analysis of GLB1 reveal that all the novel mutations affect the function and structure of the protein. We hereby report on the largest series of patients with GM1 gangliosidosis and the first from India.

GALNS mutations in Indian patients with mucopolysaccharidosis IVA.

Mucopolysaccharidosis IV A (Morquio syndrome A, MPS IVA) is a lysosomal storage disease caused by the deficiency of N-acetylgalactosamine-6-sulfatase (GALNS). The mutation spectrum in this condition is yet to be determined in Indians. We aimed to analyze the mutations in the GALNS gene in Asian Indians with MPS IVA. All the exons and the adjacent intronic regions of the gene were amplified and sequenced in sixty-eight unrelated Indian families. We identified 136 mutant alleles comprising of 40 different mutations. We report twenty-two novel mutations that comprise of seventeen missense (p.Asn32Thr, p.Leu36Arg, p.Pro52Leu, p.Pro77Ser, p.Cys79Arg, p.His142Pro, p.Tyr191Asp, p.Asn204Thr, p.Gly188Ser, p.Phe216Ser, p.Trp230Cys, p.Ala291Ser, p.Gly317Arg, p.His329Pro, p.Arg386Ser, p.Glu450Gly, p.Cys501Ser), three splice-site variants (c.120+1G>C, c.1003-3C>G, c.1139+1G>A), one nonsense mutation (p.Gln414*) and one frameshift mutation (p.Pro420Leufs*440). Eighteen mutations have been reported earlier. Among these p.Ser287Leu (8.82%), p.Phe216Ser (7.35%), p.Asn32Thr (6.61%) and p.Ala291Ser (5.88%) were the most frequent mutations in Indian patients but were rare in the mutational profiles reported in other populations. These results indicate that the Indian patients may have a distinct mutation spectrum compared to those of other populations. Mutant alleles in exon 1, 7 and 8 accounted for 44.8% of the mutations, and sequencing of these exons initially may be a cost-effective approach in Asian Indian patients. This is the largest study on molecular analysis of patients with MPS IVA reported in the literature, and the first report from India.

Polydactyly and genes.

Pediatricians deal with cases with the congenital malformations and malformation syndromes interest many of them. A lot of information about genes involved in development is available now. Genetics of hand development and genes involved in polydactyly syndromes is discussed in this article as a prototype to know about genetics of malformations: how it is studied and what is known. Genetic and chromosomal defects are often associated with congenital malformations. Polydactyly is one of the commonly seen malformations and genetic defects of many malformation syndromes associated with polydactyly are known. The role of genetic defect in polydactyly syndromes and the correlation between genotypes and phenotypes is discussed in this review article.

Ring chromosome 13 in an infant with ambiguous genitalia.

Ring chromosome is a rare chromosomal abnormality. We report a case of ring chromosome 13 associated with ambiguous genitalia. Karyotype is the important investigation in the evaluation of a case with ambiguous genitalia and chromosomal analysis should not be limited to only presence of X and Y chromosomes.

Clinical utility of fetal autopsy and comparison with prenatal ultrasound findings.

OBJECTIVES: To present a comprehensive analysis of autopsy findings in 206 fetuses referred to our genetic center and to assess the clinical utility of fetal autopsy in reaching a final diagnosis, which is essential for counseling regarding the risk of recurrence. We also compared the autopsy findings with prenatal ultrasound findings to evaluate the potential benefit of fetal autopsy in fetuses terminated after prenatal diagnosis of malformations. STUDY DESIGN: Retrospective review of patient records in a tertiary referral genetic center in North India during 5-year period (April 2000-March 2005). This includes 206 fetuses, 138 terminated after detecting an anomaly in ultrasonogram and 68 spontaneous fetal losses. In all cases, fetal autopsy was carried out and complimented by radiography, karyotype wherever possible and histopathological examination wherever necessary. In fetuses with prenatally diagnosed malformations, ultrasound findings were compared with autopsy findings. RESULTS: Fetal autopsy was able to provide a definite final diagnosis in 59% (122/206) cases. Fetal autopsy confirmed the ultrasound findings in all cases but two. Moreover, autopsy provided additional findings in 77 cases and of these, 24 cases had a significant change of recurrence risk. CONCLUSION: This study confirms the utility of fetal autopsy in identifying the cause of fetal loss, which will help in the genetic counseling of the couple. In cases with prenatally diagnosed anomalies, the new information from fetal autopsy changes the predicted probability of recurrence in 18% cases. Even though the prenatal ultrasonogram reasonably predicts the malformations, fetal autopsy gives significant additional malformations in one-third of the cases and is essential for genetic counseling.

Asphyxiating thoracic dystrophy with facial dysmorphism.

Here it is reported a male newborn baby with features of asphyxiating thoracic dystrophy (ATD) with facial dysmorphism. The disproportionate rhizomelic short stature, narrow thorax, long fibulae, wide metaphysis and trident acetabule are consistent with diagnosis of ATD. In addition the baby had facial dysmorphism and broad thumbs and great toes similar to Oto-palato-digital syndrome type II (OPD II). The association of these features with ATD is not reported till date.

TNFR2 gene polymorphism in coronary artery disease.

BACKGROUND: Recently atherosclerosis and coronary artery disease (CAD) are considered to be inflammatory diseases. The genetic polymorphism in inflammatory markers has been well studied and found to be associated with development of CAD. AIM: To study the association of biallelic polymorphism at position 196 in exon 6 of tumor necrosis factor 2 (TNFR2) gene and coronary artery disease. SETTINGS AND DESIGN: The study design was a prospective case control study conducted at a tertiary referral center mainly catering to the north Indian population. MATERIALS AND METHODS: One hundred and fifty angiographically proven patients with coronary artery disease and one hundred and fifty age matched controls were genotyped for TNFR2 gene by polymerase chain reaction followed by analysis of restriction fragment length polymorphism. STATISTICAL ANALYSIS: Genotype frequencies were compared in patients and controls by Chi-square test. Binary logistic regression analysis was used to examine the relationship between genotypes and disease, incorporating other variables into the model. RESULTS: The incidence of CAD in those with MM genotype was 65% and in those with RM genotype was 42%. Genotype frequency shows significant association of MM genotype with development of CAD (P < 0.001; odds ratio-2.585; 95% confidence interval 1.533-4.359). The association of TNFR2 genotype with CAD persisted on logistic regression analysis. CONCLUSION: MM genotype of TNFR2 gene is associated with development of CAD and RM genotype appears to be protective.

T1 and M1 polymorphism in glutathione S-transferase gene and coronary artery disease in North Indian population.

BACKGROUND: DNA damage has been found to play an important role in atherosclerosis and coronary artery disease. Genetic polymorphisms of the genes coding for enzymes involved in the metabolism of genotoxins result in different phenotypes with respect to their ability to detoxify these agents. In the present study the contribution of the polymorphism in the glutathione S-transferase gene to the development of coronary artery disease has been investigated. METHODS: One hundred and ninety seven angiographically proven patients with coronary artery disease and one hundred and ninety eight age-matched controls were genotyped for glutathione S- transferase polymorphism by polymerase chain reaction. Genotype frequencies were compared in patients and controls by Chi-square test. Binary logistic regression was used to examine the relationship between genotype and disease, incorporating other variables into the model. RESULTS: GSTT1 null genotype was significantly decreased in patients with coronary artery disease. No significant association was found with GSTM1 genotypes. No such association was seen with smokers. CONCLUSION: Null genotype of GSTT1 is protective against coronary artery disease in our population.