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Abstract 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.

Abstract Fabry disease (FD) is a treatable X linked lysosomal storage disorder with a wide phenotypic spectrum. There is a scarcity of published data on the burden of FD in India. This study evaluates the clinical and molecular spectrum of Indian patients with FD. In this multicentric study involving 10 tertiary referral centers in India, we analyzed the clinical course and genotype of 54 patients from 37 families. Family screening identified 19 new patients (35%) from 12 index cases. Then, 33 GLA gene variants were identified in 49/54 (90.7%) which included 11 novel and 22 known pathogenic variants. Of the 54 patients in our cohort, 40 patients had “classical” and 10 patients had a “nonclassical” presentation. The symptoms and signs included kidney dysfunction in 38/54 (70.3%), neuropathic pain in 34/54 (62.9%), left ventricular hypertrophy in 22/49 (44.8%) and stroke in 5/54 (9.2%). Female heterozygotes were 10/54 (18.5%) of whom 2 were index cases. There was a significant delay in reaching the diagnosis of 11.7 years. Enzyme replacement therapy was initiated in 28/54 (51.8%) patients with significant improvement of neuropathic pain and gastrointestinal symptoms. This study highlights the clinical presentation and mutational spectrum of FD in India and suggests that family screening and screening of high‐risk groups (hypertrophic cardiomyopathy, idiopathic chronic renal failure and cryptogenic stroke) could be the most cost‐effective strategies for early identification of FD.

Introduction: Association of serum folate, Vitamin B6 and B12 deficiencies with hyperhomocysteinemia are well-documented. Several studies on Indian population, address the association of hyperhomocysteinemia with numerous diseases, but populationspecific baseline levels of homocysteine in healthy population have not been elucidated till date. Aim: To establish Indian-population specific reference ranges for total plasma homocysteine in healthy adults in accordance to variation in dietary factors, serum B12 and folate status. The study also aimed to assess the contribution of cofactors in modulating homocysteine levels, and to evaluate the impact of higher homocysteine levels on the oxidative DNA damage. Materials and Methods: In this retrospective study, 151 apparently healthy non-diabetic, non-hypertensive individuals with normal thyroid, renal and cardiac function were recruited. Vitamin B12, Folate, and Homocysteine assays were performed on ADVIA Centaur® XP Immunoassay system. Plasma 8-oxo2deoxyguanosine levels were estimated by using commercially available ELISA kit. Student’s t-test, ANOVA, Spearman rank correlation was used to establish the associations between variables. The p45 yr, n=93) and gender. In both the age groups, homocysteine and 8-oxo-2deoxyguanosine levels were found to be elevated in men (p=0.003) while no gender-specific differences were observed in the levels of folate and B12. Post-menopausal women had higher oxidative DNA damage as compared to the pre-menopausal women. Positive correlation was observed between total plasma homocysteine and plasma 8-oxo-2deoxyguanosine (r=0.35, p=0.03). An inverse correlation was observed between plasma B12 levels and total plasma homocysteine in men (r=-0.24, p=0.02) while no such correlation was observed in women (r=0.22, p=0.10). No significant correlation was observed between plasma folate levels and total plasma homocysteine in both genders (male: r=-0.10, p=0.33; female: r=-0.23, p=0.09). Non-vegetarians had higher plasma B12 levels (p

Ring chromosome 20 is a rare chromosomal abnormality characterized mainly by refractory epileptic seizures, cognitive and behavioral problems, and absence of definite dysmorphic features. We report a 5-year-old boy with refractory epilepsy and minimal dysmorphic features who first presented with mild developmental delay at 11 months of age. The karyotype of the child was 46,XY,r(20)(p13q13.3). Till date there are 69 cases of ring chromosome 20 reported in the literature, including mosaics and supernumerary ring chromosomes. To our knowledge, this is the first case of ring chromosome 20 with refractory epilepsy reported from the south Indian population.

Hyperammonemia and hyperlactatemia in neonates and young children with non-specific biochemical markers poses a diagnostic challenge. An accurate diagnosis is essential for effective management. We present three infants from unrelated families, one with infantile and two with neonatal hyperammonemic encephalopathy, hypoglycaemia, and hyperlactatemia. The underlying cause was confirmed following whole exome sequencing as biochemical markers were not conclusive of a definite diagnosis. The combination of hyperammonemic encephalopathy, hyperlactatemia and hypoglycemia in neonates and infants should prompt physicians to suspect Carbonic anhydrase VA deficiency. Majority of these children can have a favourable long-term outcome with symptomatic treatment. [ABSTRACT FROM AUTHOR]

In the current study, we report three cases of Asparagine Synthetase (ASNS) Deficiency from two consanguineous families. Family 1 had two early neonatal deaths due to a novel mutation in the ASNS gene c.788C > T (p.S263F) and both the children presented with microcephaly and one of them had severe intracranial haemorrhage. The proband from the second family was homozygous for c.146G > A (p.R49Q) and manifested myoclonic seizures, developmental delay, coarse hair and diffuse cortical atrophy. Molecular docking studies of both the mutations revealed alteration in the ligand binding site. Till date, 26 mutations were reported in ASNS gene in 29 affected children indicating high degree of genetic heterogeneity and high mortality. Although asparagine depletion is not of diagnostic utility, multiple linear regression model suggested that asparagine levels vary to the extent of 20.6% based on glutamine and aspartate levels and ASNS deficiency results in depletion of asparagine synthesis. ASNS deficiency should be suspected in any neonate with microcephaly and epileptic encephalopathy. • Three cases of ASNS Deficiency were reported from two consanguineous Indian families • Family 1 with ASNS c.788 C>T (p.S263F) mutation had two early neonatal deaths • Manifested with microcephaly and severe intracranial haemorrhage • Family 2 with ASNS c.146G>A (R49Q) mutation showed diffuse cortical atrophy • Till date, 26 ASNS mutations were reported in 29 affected children [ABSTRACT FROM AUTHOR]

Here, we report SLC25A13 c.1610_1612delinsAT mutation from India in a 13-year old boy who presented with recurrent episodes of delirium and hyperammonemia. This is the second case with this mutation; the first case was of Pakistani origin. The boy responded to diet modification, sodium benzoate and arginine supplementation. Furthermore, we have aimed to establish genotype-phenotype correlation of 79 cases of citrin deficiency (46 males and 33 females) reported in 24 studies from all over the world. Inverse association was observed between age of onset and jaundice ( r  = −0.73). Late age of onset was associated with delirium ( r  = 0.61), aggressive behaviour ( r  = 0.67), altered sensorium ( r  = 0.67) and tremors ( r  = 0.65). The most common mutations associated with citrin deficiency were c.851_854del4, IVS16ins3kb, 1638-1660dup with a frequency of 42.41%, 16.46% and 6.33%, respectively. The c.851_854del4 mutation showed positive association with alpha feto protein ( r  = 0.40), ammonia ( r  = 0.50) and tyrosine ( r  = 0.40) while showing inverse association with threonine ( r  = −0.55). The IVS16ins3kb mutation was associated with high total ( r  = 0.65) and conjugated bilirubin ( r  = 0.54) along with high aspartate transaminase ( r  = 0.49) while citrulline levels are lower ( r  = −0.36). To conclude, all cases of intrahepatic cholestasis and neuropsychiatric abnormalities should be evaluated for citrin deficiency. However, the ethnic group-specific mutation frequencies should be considered in implementing screening. [ABSTRACT FROM AUTHOR]

The Forkhead box N1 ( FOXN1 ) is a transcriptional factor regulating the development, differentiation and function of thymic epithelial cells; maintaining T-lineage progenitors in bone marrow; promoting terminal differentiation of epithelial cells of hair follicles. Mutation in FOXN1 was reported to cause a rare disorder characterized by rudimentary thymus gland, T-cell immunodeficiency, congenital alopecia and nail dystrophy within an Italian community. This is the first report of FOXN1 p.R255X mutation from India, outside this endogamous Italian community. Out of the two affected children, only one was alive during the genetic evaluation and had all the clinical manifestations such as alopecia totalis and nail dystrophy. The proband was homozygous for FOXN1 p.R255X Italian founder mutation. The carrier status of both the parents was established. Immunological study of the proband revealed total absence of T-cells confirming T-cell immunodeficiency. Prenatal diagnosis during third pregnancy revealed absence of FOXN1 mutation. To conclude, this is the first report of FOXN1 mutation from India highlighting that diseases once confined to certain geographical areas are spreading across the globe probably due to human migrations. [ABSTRACT FROM AUTHOR]

Objective: To estimate total plasma homocysteine levels in Indian newborns by modifying the existing SBD-F based High performance liquid chromotography (HPLC) method in order to enable analysis in newborn heel-prick samples and assess the prevalence of hyperhomocysteinemia in Indian newborns who are exclusively breast-fed.Methods: Reverse-phase HPLC with fluorescence detection for plasma homocysteine estimation and statistical analysis using student t-test.Results: SBD-F based HPLC method was modified and Bland and Altman analysis was carried out to assess agreement between original and modified methods. The correlation co-efficient was 0.994. The limits of agreement (-5.9, 6.3) were small enough to apply new method in place of the old for heel-prick sample analysis. Total plasma homocysteine analysis was carried out on heel-prick samples of 607 randomly selected newborns (331 males and 276 females). The mean plasma homocysteine estimated by this method in Indian newborns was 6.99 (95% CI: 6.48-7.49) with no appreciable gender effect (P=0.74). Elevated homocysteine levels were observed in 31 males and 21 females.Conclusions: Modified HPLC method is validated and can be used for homocysteine analysis on newborn heel-prick samples. Using this method, the prevalence of hyperhomocysteinemia in Indian newborns is 8.6%. [ABSTRACT FROM AUTHOR]

Background Glutaric aciduria type I is an autosomal recessive organic acid disorder. The primary defect is the deficiency of Glutaryl-CoA dehydrogenase (EC number 1.3.99.7) enzyme that is involved in the catabolic pathways of the amino acids l -lysine, l -hydroxylysine, and l -tryptophan. It is a treatable neuro-metabolic disorder. Early diagnosis and treatment helps in preventing brain damage. Methods The Glutaryl-CoA dehydrogenase gene ( GCDH ) gene was sequenced to identify disease causing mutations by direct sequencing of all the exons in twelve patients who were biochemically confirmed with GA I. Results We identified eleven mutations of which nine are homozygous mutations, one heterozygous and two synonymous mutations. Among the eleven mutations, four mutations p.Q162R, p.P286S, p.W225X in two families and p.V410M are novel. A milder clinical presentation is observed in those families who are either heterozygous or with a benign synonymous SNP. Multiple sequence alignment (MSA) of GCDH with its homologues revealed that the observed novel mutations are not tolerated by protein structure and function. Conclusions The present study indicates genetic heterogeneity in GCDH gene mutations among South Indian population. Genetic analysis is useful in prenatal diagnosis and prevention. Mutation analysis is a useful tool in the absence of non-availability of enzyme assay in GA I. [ABSTRACT FROM AUTHOR]

Abstract: Beta-ketothiolase deficiency, or mitochondrial acetoacetyl-CoA thiolase (T2) deficiency, is a rare autosomal recessive disorder affecting isoleucine catabolism and ketone body metabolism. A patient from South India presented with acute ketoacidosis at 11months of age. During the acute crisis the C5OH (2-methyl-3-hydroxybutyryl) carnitine and C5:1 (tiglyl) carnitine were elevated and large amounts of 2-methyl-3-hydroxybutyrate, tiglylglycine, and 2-methylacetoacetate were excreted. Brain CT showed bilateral basal ganglia lesions. Potassium ion-activated acetoacetyl-CoA thiolase activity was deficient in the patient’s fibroblasts. The patient is a homozygote for a novel c.578T>G (M193R) mutation. This is the first report of T2 deficiency confirmed by enzyme and molecular analysis from India. [Copyright &y& Elsevier]

(A) FAR1 genotype-phenotype comparison; (B) FAR1 mutation spectrum vs. topology; (C) Proband showing cataract; (D) non-AUG translation initiation sites; (E) MRI brain showing thin corpus Callosum(genu); and (F) FAR1 mutation analysis in parents [Colour figure can be viewed at wileyonlinelibrary.com] gl Honsho et al. proposed the presence of the NADPH and PEX 19 binding domains in the N- and C-termini, respectively.2 These insights and Phyre2 helped in predicting the topology changes associated with I FAR1 i variants. Fatty acyl-CoA reductase 1 (FAR1) deficiency is an autosomal recessive peroxisomal disorder overlaps with rhizomelic chondrodystrophy except for rhizomelia and skeletal dysplasia and presents with intellectual disability, cataracts, growth failure, and seizures.1 Until now, only one study reported FAR1 deficiency in two families with three affected children (two siblings homozygous for c.495 507 delinsT and the third case compound heterozygous for c.787 C>T and c.1094A>G).1 This is the second report on FAR1 deficiency in a 20-month-old female infant exhibiting a similar phenotype. A rare case of fatty acyl-CoA reductase 1 deficiency in an Indian infant manifesting rhizomelic chondrodystrophy phenotype. [Extracted from the article]

To investigate whether genetic polymorphisms are the underlying causes for aberrations in folate pathway that was reported in autistic children.A total of 138 children diagnosed as autistic based on Diagnostic and Statistical Manual of Mental Disorders, fourth edition criteria and Autism Behavior Checklist scoring and 138 age and sex matched children who are nonautistic were tested for five genetic polymorphisms, that is, cytosolic serine hydroxyl methyl transferase (SHMT1 C1420T), methylene tetrahydrofolate reductase (MTHFR C677T and MTHFR A1298C), methionine synthase reductase (MTRR A66G), methionine synthase (MS A2756G) using PCR-restriction fragment length polymorphism methods. Fisher's exact test and logistic regression analysis were used for statistical analyses.MTHFR 677T-allele frequency was found to be higher in autistic children compared with nonautistic children (16.3 vs. 6.5%) with 2.79-fold increased risk for autism [95% confidence interval (CI): 1.58-4.93]. The frequencies of MTRR 66A allele (12.7 vs. 21.0%) and SHMT 1420T allele (27.9 vs. 45.3%) were lower in autistic group compared with nonautistic group with odds ratios 0.55 (95% CI: 0.35-0.86) and 0.44 (95% CI: 0.31-0.62), respectively, indicating reduced risk. MTHFR 1298C-allele frequency was similar in both the groups (53.3 vs. 53.6%) and hence individually not associated with any risk. However, this allele was found to act additively in the presence of MTHFR 677T allele as evidenced by 8.11-fold (95% CI: 2.84-22.92) risk associated with MTHFR 677CT+TT/1298AC+CC genotypes cumulatively.MTHFR C677T is a risk factor, whereas MTRR A66G and SHMT C1420T polymorphisms reduce risk for autism. MTHFR A1298C acts additively in increasing the risk for autism. [ABSTRACT FROM AUTHOR]

This is the first reported case of prosaposin ( PSAP ) mutation from India manifesting as an acute neuronal Gaucher disease-like condition. A 2-month-old male baby presented with encephalopathy, resistant tonic-clonic seizures, moderate hepatosplenomegaly, hypotonia, and cherry red spot in the retinae. The child had anemia, thrombocytopenia, elevated chitotriosidase, and normal activity of acid sphingomyelinase and low normal activity of β-glucosidase 1 (β-glucocerebrosidase 1, GBA). The child succumbed in the fourth month of life due to persistent respiratory distress and refractory seizures. The clinical phenotype, cherry red spots, elevated chitotriosidase, and lysosomal assays led to the suspicion of Gaucher disease. Exome sequencing revealed a homozygous stop codon mutation in the PSAP gene (c.G1228T, p.Glu410ter). Prenatal diagnosis in the next pregnancy revealed a carrier fetus, who was unaffected postnatally. The diagnosis of specific activator deficiency such as saposin C and saposin D deficiency (in the current study) should be considered and tested for when Gaucher disease is suspected in an infant with partially deficient or near normal GBA activity.

In this study, we report three cases of nonketotic hyperglycinemia (NKHG) diagnosed biochemically and molecularly. Clinical exome analysis in two families revealed two novel mutations in the aminomethyltransferase (AMT) gene, that is, c.14_15insT (p.Ser6LysfsTer22) and c.259-2A > T, both of them adversely affecting the protein. This is the first report of AMT gene mutations in NKHG from India. Prenatal diagnosis in the first family showed an unaffected fetus in the third pregnancy. The role of AMT protein is pivotal for the synthesis of 5,10-methylene tetrahydrofolate, the first metabolite in one-carbon metabolism that regulates DNA synthesis, repair, and methylation.

Background: The rationale of the current study was to test the clinical utility of the folate pathway genetic polymorphisms in predicting the risk for autism spectrum disorders (ASD) and to address the inconsistencies in the association of MTHFR C677T and hyperhomocysteinemia with ASD., Patients and Methods: An artificial neural network (ANN) model was developed from the data of 138 autistic and 138 nonautistic children using GCPII C1561T, SHMT1 C1420T, MTHFR C677T, MTR A2756G, and MTRR A66G as the predictors of autism risk. A neuro fuzzy model was developed to explore the genetic determinants of homocysteine. Meta-analyses were carried out on 1361 ASD children and 6591 nonautistic children to explore the association of MTHFR C677T and homocysteine with the risk for ASD., Results: The ANN model showed 63.8% accuracy in predicting the risk of autism. Hyperhomocysteinemia was observed in autistic children (9.67±4.82 vs. 6.99±3.21 μmol/l). The neuro fuzzy model showed synergistic interactions between MTHFR C677T and MTRR A66G inflating homocysteine levels. The meta-analysis showed MTHFR to be a genetic risk factor for autism in both fixed-effects (odds ratio: 1.47, 95% confidence interval: 1.31-1.65) and random-effects (odds ratio: 1.57, 95% confidence interval: 1.16-2.11) models. The meta-analysis of nine studies showed hyperhomocysteinemia as a significant risk factor for autism in both fixed-effects (P<0.0001) and random-effects (P=0.026) models., Conclusion: Genetic polymorphisms of the folate pathway were moderate predictors of autism risk. MTHFR C677T and hyperhomocysteinemia have been identified as risk factors for autism worldwide. Synergistic interactions between MTHFR C677T and MTRR A66G increase homocysteine.