An Effort to Identify Genetic Determinants in Siblings With Wilson Disease Manifesting Striking Clinical Heterogeneity: An Exome Profiling Study of Two Indian Families.

BACKGROUND: Wilson disease (WD) is a rare autosomal recessive disorder of copper metabolism caused due to mutations in the copper transporter ATP7B. There is often a striking variability of clinical manifestations among patients with ATP7B mutations, including in siblings. This phenomenon may be caused by individual differences in copper accumulation in hepatocytes and intolerance to copper toxicity as governed by genetic variations in copper metabolism genes acting as modifier loci to the disease. OBJECTIVE: To elucidate the genetic basis of striking clinical heterogeneity among two siblings of two families with WD. METHODS: The disease diagnosis and subsequent clinical examinations were performed by expert clinicians. The younger siblings in both families presented with early neurological manifestations at a younger age than their older siblings. Interestingly, only the younger siblings were reported to have had hepatic manifestations. Exome sequencing of all the four individuals was performed to understand their heterogeneous phenotypic outcomes. RESULTS: Genetic screening revealed no difference in the ATP7B variant spectrum between the siblings of each family. However, the siblings of both the families were found to harbor mutually exclusive pathogenic variants in suspected modifier genes implicated in copper metabolism and/or other neurological and hepatic disorders having overlapping symptoms with WD, viz., CFTR, PPARG, ABCB11, ATP7A, CYP2D6, mTOR, TOR1A, and CP, which can potentially explain their differential clinical phenotypes. CONCLUSION: Clinical heterogeneity between siblings with WD with the same ATP7B mutation profile may be attributed to the presence of different pathogenic variants in potential modifier genes.

Identification of TNF-α as Major Susceptible Risk Locus for Vitiligo: A Systematic Review and Meta-Analysis Study in the Asian Population.

INTRODUCTION: Vitiligo is a common depigmentation disorder characterized by defined white patches on the skin and affecting around 0.5% to 2% of the general population. Genetic association studies have identified several pre-disposing genes and single nucleotide polymorphisms (SNPs) for vitiligo pathogenesis; nonetheless, the reports are often conflicting and rarely conclusive. This comprehensive meta-analysis study was designed to evaluate the effect of the risk variants on vitiligo aetiology and covariate stratified vitiligo risk in the Asian population, considering all the studies published so far. METHODS: We followed a systematic and comprehensive search to identify the relevant vitiligo-related candidate gene association studies in PubMed using specific keywords. After data extraction, we calculated, for the variants involved, the study-level unadjusted odds ratio, standard errors, and 95% confidence intervals by using logistic regression with additive, dominant effect, and recessive models using R software package (R, 3.4.2) "metafor." Subgroup analysis was performed using logistic regression (generalized linear model; "glm") of disease status on subgroup-specific genotype counts. For a better understanding of the likely biological function of vitiligo-associated variant obtained through the meta-analysis, in silico functional analyses, through standard publicly available web tools, were also conducted. RESULTS: Thirty-one vitiligo-associated case-control studies on eleven SNPs were analysed in our study. In the fixed-effect meta-analysis, one variant upstream of TNF-α gene: rs1800629 was found to be associated with vitiligo risk in the additive (p = 4.26E-06), dominant (p = 1.65E-7), and recessive (p = 0.000453) models. After Benjamini-Hochberg false discovery rate (FDR) correction, rs1800629/TNF-α was found to be significant at 5% FDR in the dominant (padj = 1.82E-6) and recessive models (padj = 0.0049). In silico characterization revealed the prioritized variant to be regulatory in nature and thus having potential to contribute towards vitiligo pathogenesis. CONCLUSION: Our study constitutes the first comprehensive meta-analysis of candidate gene-based association studies reported in the whole of the Asian population, followed by an in silico analysis of the vitiligo-associated variant. According to the findings of our study, TNF-α single nucleotide variant rs1800629G>A has a risk association, potentially contributing to vitiligo pathogenesis in the Asian population.

A comprehensive meta-analysis and prioritization study to identify vitiligo associated coding and non-coding SNV candidates using web-based bioinformatics tools.

Vitiligo is a prevalent depigmentation disorder affecting around 1% of the general population. So far, various Genome Wide Association Studies (GWAS) and Candidate Gene Association Studies (CGAS) have identified several single nucleotide variants (SNVs) as a risk factor for vitiligo. Nonetheless, little has been discerned regarding their direct functional significance to the disease pathogenesis. In this study, we did extensive data mining and downstream analysis using several experimentally validated datasets like GTEx Portal and web tools like rSNPBase, RegulomeDB, HaploReg and STRING to prioritize 13 SNVs from a set of 291SNVs that have been previously reported to be associated with vitiligo. We also prioritized their underlying/target genes and tried annotating their functional contribution to vitiligo pathogenesis. Our analysis revealed genes like FGFR10P, SUOX, CDK5RAP1 and RERE that have never been implicated in vitiligo previously to have strong potentials to contribute to the disease pathogenesis. The study is the first of its kind to prioritize and functionally annotate vitiligo-associated GWAS and CGAS SNVs and their underlying/target genes, based on functional data available in the public domain database.

Mapping the TYR gene reveals novel and previously reported variants in Eastern Indian patients highlighting preponderance of the same changes in multiple unrelated ethnicities.

Oculocutaneous albinism (OCA) is a group of congenital autosomal recessive disorders with seven known subtypes (OCA1-OCA7) characterized by loss or absence of pigmentation in the skin, hair, and eyes. OCA1, caused by pathogenic variations in the tyrosinase (TYR) gene, has been documented to be the most prevalent subtype across the world including India. In the present study, we recruited 53 OCA-affected individuals from 45 unrelated families belonging to 20 different marriage groups/ethnicities of 15 different districts of West Bengal. We took a targeted sequencing-based approach to find the causal variations in the TYR gene. We report here identification of two novel potentially pathogenic variations [NM_000372.4:c.614C>T, NP_000363.1:p.(Pro205Leu), and NM_000372.4:c.1036+1=/G>T], one novel synonymous TYR variant [NM_000372.4:c.204=/A>G, NP_000363.1:p.(Gln68=)], two pathogenic variations documented for the first time in Indian OCA cases [NM_000372.4:c.1147G>A, NP_000363.1:p.(Asp383Asn), and NM_000372.4:c.585G>A, NP_000363.1:p.(Trp195*)], along with nine previously reported pathogenic variants in 36 out of 53 (∼68%) patients recruited. We report common haplotype backgrounds for the two most prevalent variations [NM_000372.4:c.124G>A, NM_000372.4:c.832C>T] in cases belonging to different marriage/ethnic groups, suggesting a possible founder effect. To our knowledge, this is the most comprehensive genetic study on OCA1 from India, firmly establishing OCA1 as the commonest form of albinism in this part of the world.

Dopamine ß hydroxylase (DBH) polymorphisms do not contribute towards the clinical course of Wilson's disease in Indian patients.

BACKGROUND: Wilson's disease (WD) is a rare copper metabolism disorder with hepatic and neurological symptoms. Dopamine ß hydroxylase (DBH) encodes a copper-dependent mono-oxygenase that converts dopamine to norepinephrine, thereby regulating the endogenous dopamine content in the neurons. Polymorphisms of DBH have been reported to be associated with several neurological diseases, such as Parkinson's disease, Alzheimer's disease, schizophrenia and attention-deficit hyperactivity disorder, which have overlapping neurological symptoms with WD. The present study aimed to assess the role of DBH polymorphisms on the clinical course of WD. METHODS: In total, 141 WD patients from India were included in the present study. Three polymorphisms of DBH (rs1611115 in the promoter, rs1108580 in exon 2 and rs129882 in 3'-UTR) were screened for their association with the clinical attributes (hepatic and neurological features) and age of onset of WD using a polymerase chain reaction-restriction fragment length polymorphsm method and sequencing approach. The distribution of genotype or allele frequencies was tested using 2 × 2 contingency chi-squared and logistic regression analysis (additive, dominant and recessive model). RESULTS: The genotypic and allelic frequencies of these single nucleotide polymophisms did not vary significantly along with the clinical symptoms (hepatic and neurological) or the age of onset of WD. No significant association was observed when we analyzed our samples with respect to harboring different kinds of ATP7B mutations (nonsense/in-del and missense). CONCLUSIONS: The data obtained in the present study suggest that the selected DBH variants are unlikely to have any significant contribution towards modifying the clinical symptoms of Indian WD patients.

Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using ENCODE data-based web-tools.

Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3'UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several ENCODE-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.

Clinical Profile and Therapeutic Response of Scrub Typhus in Children: A Recent Trend from Eastern India.

OBJECTIVE: The aim of this study was to assess the clinico-laboratory parameters, complications and therapeutic responses in children with scrub typhus in Eastern India. MATERIALS AND METHODS: In this prospective, observational study, all children (age, <12 years) with suspected scrub typhus with a compatible clinical scenario were enrolled consecutively over six months. Cases confirmed by means of a positive IgM serology or a positive Weil-Felix reaction (OXK = 1/80 or above) were administered enteral doxycycline (4.5 mg/kg/day). RESULTS: Out of 94 recruited children, 61 had confirmed scrub typhus (mean age = 6.1 years, M:F = 1.1:1) with or without complications and having a considerably higher incidence of neurological presentation (meningoencephalistis n = 21, 34.4%). The most frequent manifestations included vomiting (n = 39, 63.9%), abdominal pain (n = 33, 54.1%), lymphadenopathy (n = 36, 59%), hepatosplenomegaly (n = 32, 52.5%), pedal edema (n = 32, 52.5%) and eschar formation (n = 30, 49.2%). Low hemoglobin levels, leukocytosis, thrombocytopenia, hypoalbuminemia, hyponatremia, increased liver enzymes and increased C-reactive protein were associated with delayed defervescence (>48 h). CONCLUSION: Scrub meningoencephalitis, with a notably higher incidence, showed favorable therapeutic response. Prompt and empiric doxycycline therapy could be lifesaving.

Profile of Pediatric Idiopathic Inflammatory Myopathies from a Tertiary Care Center of Eastern India.

OBJECTIVES: To report data on Idiopathic inflammatory myopathies (IIM) from eastern India. METHODS: All IIM patients diagnosed over the last 5 y (2011-2016) were included through a retrospective review of records from the hospital and specialty clinic at Institute of Postgraduate Medical Education & Research (I.P.G.M.E.&R.), Kolkata. RESULTS: Out of the 11 IIM patients, 9 had Juvenile dermatomyositis (JDM) and 2 had overlap myositis (OM) [with systemic lupus erythematosus (SLE) and scleroderma]. The overall sex ratio was M: F = 1: 2.6. The mean age at diagnosis was 6.94 y for JDM and 7 y for OM. The mean interval from onset to diagnosis was 5.2 mo. All patients had heliotrope rash and proximal myopathy (n = 11,100%). Other findings included Gottron papule (n = 7; 64%), arthritis (n = 6; 54%), malar rash (n = 5; 45%), dysphagia (n = 4; 36%), nasal intonation (n = 3; 27%), subcutaneous nodule (n = 2; 18%), cutaneous sinus (n = 1; 9%), calcinosis universalis (n = 1; 9%), GI bleed (n = 1; 9%). All patients had raised erythrocyte sedimentation rate (ESR), aspartate aminotransferase (AST), lactate dehydrogenase (LDH) while 10 had raised creatine kinase (CK). Three were anti-nuclear-antibody (ANA) positive. Electromyography (EMG) showed proximal myopathy in most cases (n = 9; 82%). All patients received corticosteroid. Intravenous immunoglobulin (IVIG) was given to 2 patients. Two received hydroxychloroquine. Cyclophosphamide and azathioprine were given in one each. CONCLUSIONS: This study, first reported profile of IIM from eastern India, showed JDM as the commonest form of IIM with a female preponderance. Five children had complete and 2 had partial remission. Two patients of JDM and 1 of OM died. Increased awareness, early referral, prompt diagnosis and treatment might improve the outcome and survival.