The molecular landscape of oculocutaneous albinism in India and its therapeutic implications.

Oculocutaneous albinism is an inherited disorder of melanin biosynthesis, characterized by absent or reduced pigmentation of the skin, hair, and eyes. Molecular alterations of genes that cause non-syndromic albinism in Asian Indians are poorly characterized. This information would be useful for developing therapies for this disorder. We analyzed 164 persons with non-syndromic albinism, belonging to unrelated families from all parts of India, for molecular changes in the causative genes. Subjects with white hair, white skin, and red iris had their tyrosinase gene sequenced and were also tested by MLPA for deletions/duplications. Subjects with negative results or with darker skin, golden/brown or darker hair had sequencing of TYR, P, TYRP1, SLC45A2 and GPR143 genes. Pathogenic variants in TYR (OCA1) were observed in 139 (84.7%) patients, in the P gene (OCA2) in 20 (12.2%), in TYRP1 (OCA3) in two (1.2%), in SLC45A2 (OCA 4) in one (0.61%), and in GPR143 (X-linked ocular albinism) in two (1.2%) patients. Of 278 alleles with variants in TYR, 179 (64.3%) alleles had (p.R278*) alteration, suggesting the possibility of therapy with a stop codon readthrough molecule. We report 20 patients with 13 disease associated variants in the P gene and 18 novel pathogenic variants in TYR, P, TYRP1, SLC45A2 and GPR143 genes. The data are compared with those reported from India, Pakistan and rest of the world. The therapeutic options in albinism are briefly described, opening this field for future therapies.

Next-Generation Sequencing in Unexplained Intellectual Disability.

OBJECTIVES: To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. METHODS: This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. RESULTS: The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. CONCLUSIONS: There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.

Eyes See what the Mind Knows: Clues to Pattern Recognition in Single Enzyme Deficiency-Related Peroxisomal Disorders.

Peroxisomal disorders are a heterogeneous group of inborn errors of metabolism that result in impaired function of the peroxisome. Within this, single enzyme deficiencies are known to cause a constellation of symptoms not very different from the peroxisome biogenesis defects. Thus, there is a need to identify features that differentiate the two. We present 3 molecularly confirmed families: 1 with Acyl CoA oxidase deficiency and 2 with D-bifunctional protein deficiency. The clinical, biochemical, and radiological features of these patients have been discussed. We attempt to highlight the overlap in facial features as well as strikingly similar MRI findings of cerebellar atrophy and white matter hyperintensities. This unique clinical profile will not only help in reaching a quick diagnosis, but in this era of variants of uncertain significance, it will prove as supporting evidence. Finally, we expand the genotypic spectrum with a description of 3 homozygous novel mutations (HSD17B4: c.670C>T, c.1807T>C; ACOX1: 1.03-kb exonic deletion) and discuss the role of protein modeling its establishing pathogenicity.

Prenatal diagnosis of steroid 21-hydroxylase-deficient congenital adrenal hyperplasia: Experience from a tertiary care centre in India.

BACKGROUND & OBJECTIVES: Congenital adrenal hyperplasia (CAH) is an autosomal recessive disorder with a wide range of clinical manifestations. The disease is attributed to mutations in CYP21A2 gene encoding 21-hydroxylase enzyme. In view of severe phenotype in salt-losing cases, issues related to genital ambiguity in girls and precocity in boys, most families opt for prenatal testing and termination of affected foetus. CAH can be diagnosed in utero through direct molecular analysis of CYP21A2 gene, using DNA extracted from foetal tissues or cells obtained from chorionic villus sampling or amniocentesis. The objective of this study was to evaluate the feasibility and accuracy of prenatal diagnosis (PND) using sequencing and multiplex ligation probe amplification (MLPA) methods in families at risk for CAH. METHODS: Fifteen pregnant women at risk of having an affected offspring with CAH were included in this study. Ten families had previous affected children with salt-wasting/simple virilising form of CAH and five families did not have live children but had a high index of suspicion for CAH in previous children based on history or records. Mutation analysis was carried out by Sanger sequencing and MLPA method. RESULTS: Seven different mutations were identified in 15 families. Deletions and I2g mutation were the most common. Of the 15 foetuses analyzed, nine were unaffected while six were affected. Unaffected foetuses were delivered, they were clinically normal and their genotype was found to be concordant to the prenatal report. All except two families reported in the second trimester. None of the couples opted for prenatal treatment. INTERPRETATION & CONCLUSIONS: Our preliminary findings show that PND by direct mutation analysis along with MLPA is a feasible strategy that can be offered to families at risk.

Glutaric Acidemia Type 1-Clinico-Molecular Profile and Novel Mutations in GCDH Gene in Indian Patients.

Glutaric acidemia I (GA I, #231670) is one of the treatable, autosomal recessively inherited metabolic disorders. Macrocephaly, acute encephalitis-like crises, dystonia and characteristic frontotemporal atrophy are the hallmarks of this disease. In this communication, we present the clinical, biochemical and molecular profile of seventeen GA I patients from 15 unrelated families from India and report seven novel mutations in GCDH gene (c.281G>A (p.Arg94Gln), c.401A>G (p.Asp134Gly), c.662T>C (p.Leu221Pro), c.881G>C (p.Arg294Pro), c.1173dupG (p.Asn392Glufs*5), c.1238A>G (p.Tyr413Cys) and c.1241A>C (p.Glu414Ala)). Out of these, c.662T>C (p.Leu221Pro) in exon 8 and c.281G>A (p.Arg94Gln) allele in exon 4 were low excretor alleles, whereas c.1241A>C (p.Glu414Ala), c.1173dupG and c.1207C>T (p.His403Tyr) in exon 11 were high excretor alleles. We conclude that c.1204C>T (p.Arg402Trp) is probably the most common mutant allele. Exons 11 and 8 are the hot spot regions of GCDH gene in Indian patients with GA I. An early diagnosis and timely intervention can improve the underlying prognosis. Molecular confirmation is helpful in providing genetic counselling and prenatal diagnosis in subsequent pregnancy.

Study of NAT2 gene polymorphisms in an Indian population: association with plasma isoniazid concentration in a cohort of tuberculosis patients.

BACKGROUND AND OBJECTIVES: Polymorphisms of the N-acetyltransferase 2 gene (NAT2) vary remarkably between populations of different ethnic origin. The NAT2 gene determines the individual's acetylator status to metabolize drugs and xenobiotics, influencing their toxicity and efficacy profiles. This study investigates the frequencies of the most commonly studied NAT2 polymorphisms in a southwestern Indian population and compares these with those reported in other Indian and world populations. The association of these polymorphisms with plasma isoniazid concentrations in a cohort of tuberculosis patients has also been investigated. METHODS: NAT2 genotyping of 201 subjects was carried out by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis and DNA sequencing. Acetylation phenotypes were predicted from NAT2 genotypes. The association of NAT2 genotypes with plasma isoniazid concentrations was determined by measuring the plasma levels in tuberculosis patients at different time points using reverse-phase high-performance liquid chromatography (HPLC). RESULTS: The predominant alleles found in this study population were NAT2*5B and NAT2*6A, while NAT2*5B/*6A and NAT2*6A/*6A were the most frequent genotypes; the frequency varied widely from other reported studies in the Indian population. The distribution of slow, intermediate, and fast acetylators was 55%, 32%, and 13%, respectively. We observed relatively higher plasma concentrations of isoniazid in our patients than those reported in other similar studies, and they correlated well with the NAT2 genotypes. CONCLUSION: The results suggested high variation in the frequencies of NAT2 alleles and genotypes within Indian populations, which influence plasma isoniazid concentrations. Further studies of the relationship between NAT2 genotypes and adverse drug events are required to make genotyping a helpful tool for optimizing the isoniazid therapeutic response and minimizing adverse drug reactions, particularly in countries with a high burden of tuberculosis.

A novel 9-bp insertion detected in steroid 21-hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods.

BACKGROUND: Steroid 21-hydroxylase deficiency is the most common cause of congenital adrenal hyperplasia (CAH). Detection of underlying mutations in CYP21A2 gene encoding steroid 21-hydroxylase enzyme is helpful both for confirmation of diagnosis and management of CAH patients. Here we report a novel 9-bp insertion in CYP21A2 gene and its structural and functional consequences on P450c21 protein by molecular modeling and molecular dynamics simulations methods. METHODS: A 30-day-old child was referred to our laboratory for molecular diagnosis of CAH. Sequencing of the entire CYP21A2 gene revealed a novel insertion (duplication) of 9-bp in exon 2 of one allele and a well-known mutation I172N in exon 4 of other allele. Molecular modeling and simulation studies were carried out to understand the plausible structural and functional implications caused by the novel mutation. RESULTS: Insertion of the nine bases in exon 2 resulted in addition of three valine residues at codon 71 of the P450c21 protein. Molecular dynamics simulations revealed that the mutant exhibits a faster unfolding kinetics and an overall destabilization of the structure due to the triple valine insertion was also observed. CONCLUSION: The novel 9-bp insertion in exon 2 of CYP21A2 genesignificantly lowers the structural stability of P450c21 thereby leading to the probable loss of its function.

Serum leptin levels in obese Indian children relation to clinical and biochemical parameters.

OBJECTIVE: To evaluate serum leptin levels in obese Indian children and its correlation to anthropometric and biochemical parameters. DESIGN: Cohort study. SETTING: Referral tertiary hospital. METHODOLOGY: Leptin levels were measured in 36 children (26 boys, age 1.5 to 15 years) and 37 adults (21 men, age 25 to 69 years) with obesity and 29 normal weight controls (15 children and 14 adults). RESULTS: Leptin levels were higher than controls in obese children (19.4 +/- 6.4 ng/mL against 5.4 +/- 1.7 ng/mL, p = 0.0001) and obese adults (18.9 +/- 6.4 ng/mL against 7.8 +/- 5.6 ng/mL, p = 0.0001). Leptin levels were higher than males in obese girls (23.5 +/- 1.7 ng/mL against 18.0 +/-7.6 ng/mL, p = 0.040) and women (21.3 +/- 4.4 ng/mL against 15.8 +/- 7.4 ng/mL). Leptin levels correlated with body mass index, waist circumference and waist to-hip ratio. A positive correlation was observed between serum leptin and cholesterol, triglycerides and LDL-cholesterol. No correlation was seen with fasting blood glucose and HDL-cholesterol. CONCLUSIONS: Leptin levels correlate significantly with anthropometric and laboratory parameters in obese children. There is a need for further studies on the role of leptin in childhood obesity and metabolic syndrome.

Prevalence of the triple X syndrome in phenotypically normal women with premature ovarian failure and its association with autoimmune thyroid disorders.

OBJECTIVE: To determine the prevalence of triple X females among patients with premature ovarian failure and to describe the clinical features of the syndrome. DESIGN: Case report. SETTING: Tertiary care hospital. PATIENT(S): Fifty-two consecutive patients with secondary amenorrhea due to premature ovarian failure and no clinical stigmata of Turner's syndrome. MAIN OUTCOME MEASURE(S): Triple X syndrome and clinical features, as assessed by karyotype analysis using Giemsa trypsin banding of metaphase chromosomes. RESULT(S): Two of the 52 patients with premature ovarian failure had triple X syndrome. Both cases had associated autoimmune thyroid disorder. One of the women with triple X syndrome had two pregnancies that were complicated by premature birth, idiopathic thrombocytopenia, neonatal death, and occipital encephalocoele. CONCLUSION(S): Among patients with premature ovarian failure, 3.8% have triple X syndrome. The syndrome may be associated with autoimmune thyroid disorder and poor pregnancy outcome due to congenital malformation.

Rapid prenatal karyotyping using foetal blood obtained by cordocentesis.

BACKGROUND: Prenatal karyotyping using foetal blood samples obtained by cordocentesis is a useful method of detecting abnormal chromosomes in the foetus. METHODS: Cordocentesis was performed in 187 cases for prenatal karyotyping between January 1995 and September 2000. Pregnant women were between 18 and 38 weeks of gestation and their ages ranged from 18 to 40 years. The common indications were ultrasonographic abnormalities (47.6%), history of previous Down syndrome (13.3%), advanced maternal age (11.7%), low maternal serum alpha foetoprotein levels (10.7%), previous child with malformation (10.7%), previous child with trisomy (chromosome 13/18) (2.6%), parent a balanced translocation carrier (1.6%) and high maternal serum alpha foetoprotein levels (1.6%). RESULTS: Analysis of 137 successful cultures showed 8 (5.2%) karyotype abnormalities. The remaining samples could not be reported due to the presence of maternal contamination of the sample (12.3%), inadequate sample (6.4%) or culture failure (9.8%). In those with an abnormal karyotype, obstetric management could be altered appropriately. CONCLUSION: In foetuses at high risk of a chromosomal aberration, a rapidly obtained karyotype is helpful in obstetric management.