The Genomic Landscape of Wilson Disease in a Pan India Disease Cohort and Population-Scale Data.

Background: Wilson's disease (WD) results from pathogenic ATP7B gene variations, causing copper accumulation mainly in the liver, brain, and kidneys.

Objectives: In India, despite studies on ATP7B variants, WD often goes undiagnosed, with the prevalence, carrier rate, and mutation spectrum remaining unknown.

Methods: A multicenter study examined genetic variations in WD among individuals of Indian origin via whole exome sequencing.

Clinico-Radiological and Genotypic Spectrum of Nuclear Mitochondriopathies.

Mitochondrial disorders are a diverse group of diseases caused by mutations in genes encoded by either nuclear or mitochondrial DNA. In a group of patients with nuclear mitochondriopathies, the authors analysed the clinico-radiological and genotypic spectrum. The study included 25 patients with a genetic diagnosis of nuclear mitochondrial cytopathy who were seen over a 5 y period.

Understanding the variant landscape, and genetic epidemiology of Multiple Endocrine Neoplasia in India.

Purpose: Multiple Endocrine Neoplasia (MEN) is a group of familial cancer syndromes that encompasses several types of endocrine tumors differentiated by genetic mutations in RET, MEN1 and CDKN1B genes. Accurate diagnosis of MEN subtypes can thus be performed through genetic testing. However, MEN variants remain largely understudied in Indian populations.

Spectrum of rare and common mitochondrial DNA variations from 1029 whole genomes of self-declared healthy individuals from India.

Mitochondrial disorders are a class of heterogeneous disorders caused by genetic variations in the mitochondrial genome (mtDNA) as well as the nuclear genome. The spectrum of mtDNA variants remains unexplored in the Indian population. In the present study, we have cataloged 2689 high confidence single nucleotide variants, small insertions and deletions in mtDNA in 1029 healthy Indian individuals.

EEG based functional connectivity in resting and emotional states may identify major depressive disorder using machine learning.

Objective: Disrupted brain network connectivity underlies major depressive disorder (MDD). Altered EEG based Functional connectivity (FC) with Emotional stimuli in major depressive disorder (MDD) in addition to resting state FC may help in improving the diagnostic accuracy of machine learning classification models. We explored the potential of EEG-based FC during resting state and emotional processing, for diagnosing MDD using machine learning approach.

Landscape of pharmacogenetic variants associated with non-insulin antidiabetic drugs in the Indian population.

Introduction: Genetic variants contribute to differential responses to non-insulin antidiabetic drugs (NIADs), and consequently to variable plasma glucose control. Optimal control of plasma glucose is paramount to minimizing type 2 diabetes-related long-term complications. India's distinct genetic architecture and its exploding burden of type 2 diabetes warrants a population-specific survey of NIAD-associated pharmacogenetic (PGx) variants.

The genomic landscape of variation in the Indian population.

The gene is highly polymorphic, causing large interindividual variability in the metabolism of several clinically important drugs. The authors investigated the diversity and distribution of alleles in Indians using whole genome sequences (N = 1518). Functional consequences were assessed using pathogenicity scores and molecular dynamics simulations.

Genetic landscape of human neutrophil antigen variants in India from population-scale genomes.

Antibodies against human neutrophil antigens (HNAs) play a significant role in various clinical conditions such as neonatal alloimmune neutropenia, transfusion-related acute lung injury, and other nonhemolytic transfusion reactions. This study aims to identify the genotype and allele frequencies of HNAs in the healthy Indian population. Ten genetic variants in four human genes encoding alleles of HNAs class I-V approved by the International Society of Blood Transfusion-Granulocyte Immunobiology Working Party were used in the analysis.

1029 genomes of self-declared healthy individuals from India reveal prevalent and clinically relevant cardiac ion channelopathy variants.

Background: The prevalence and genetic spectrum of cardiac channelopathies exhibit population-specific differences. We aimed to understand the spectrum of cardiac channelopathy-associated variations in India, which is characterised by a genetically diverse population and is largely understudied in the context of these disorders.

Results: We utilised the IndiGenomes dataset comprising 1029 whole genomes from self-declared healthy individuals as a template to filter variants in 36 genes known to cause cardiac channelopathies.

Landscape of Variability in Chemosensory Genes Associated With Dietary Preferences in Indian Population: Analysis of 1029 Indian Genomes.

Perception and preferences for food and beverages determine dietary behaviour and health outcomes. Inherent differences in chemosensory genes, ethnicity, geo-climatic conditions, and sociocultural practices are other determinants. We aimed to study the variation landscape of chemosensory genes involved in perception of taste, texture, odour, temperature and burning sensations through analysis of 1,029 genomes of the IndiGen project and diverse continental populations.

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum.

India confines more than 17% of the world's population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets.

Pharmacogenomic landscape of Indian population using whole genomes.

Ethnic differences in pharmacogenomic (PGx) variants have been well documented in literature and could significantly impact variability in response and adverse events to therapeutics. India is a large country with diverse ethnic populations of distinct genetic architecture. India's national genome sequencing initiative (IndiGen) provides a unique opportunity to explore the landscape of PGx variants using population-scale whole genome sequences.

An insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project.

Actively retrotransposing primate-specific repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their InDels. Here, we report the genomic landscape of InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.

Clinical, immunological and genomic characteristics of children with X-linked agammaglobulinemia from Kerala, South India.

X-linked agammaglobulinemia (XLA) is an X-linked recessive primary immunodeficiency disorder caused due to a pathogenic variant in the Bruton tyrosine (BTK) gene with an incidence of 1:379,000 live births and 1:190,000 male births. Patients affected with XLA present with recurrent infections of the gastrointestinal and respiratory tracts. Here we report the first case series of 17 XLA patients of 10 South Indian families with a wide spectrum of clinical and genetic features.

Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes.

Background: Autoinflammatory disorders are the group of inherited inflammatory disorders caused due to the genetic defect in the genes that regulates innate immune systems. These have been clinically characterized based on the duration and occurrence of unprovoked fever, skin rash, and patient's ancestry. There are several autoinflammatory disorders that are found to be prevalent in a specific population and whose disease genetic epidemiology within the population has been well understood.

Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes.

Numerous drugs are being widely prescribed for COVID-19 treatment without any direct evidence for the drug safety/efficacy in patients across diverse ethnic populations. We analyzed whole genomes of 1029 Indian individuals (IndiGen) to understand the extent of drug-gene (pharmacogenetic), drug-drug and drug-drug-gene interactions associated with COVID-19 therapy in the Indian population. We identified 30 clinically significant pharmacogenetic variants and 73 predicted deleterious pharmacogenetic variants.

Baseline cell proliferation rates and response to UV differ in lymphoblastoid cell lines derived from healthy individuals of extreme constitution types.

Differences in human phenotypes and susceptibility to complex diseases are an outcome of genetic and environmental interactions. This is evident in diseases that progress through a common set of intermediate patho-endophenotypes. Precision medicine aims to delineate molecular players for individualized and early interventions.

IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes.

With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the 'IndiGen' program.

Spectrum of clinical features and genetic variants in mevalonate kinase (MVK) gene of South Indian families suffering from Hyperimmunoglobulin D Syndrome.

Hyper-IgD syndrome (HIDS, OMIM #260920) is a rare autosomal recessive autoinflammatory disorder caused by pathogenic variants in the mevalonate kinase (MVK) gene. HIDS has an incidence of 1:50,000 to 1:5,000, and is thought to be prevalent mainly in northern Europe. Here, we report a case series of HIDS from India, which includes ten patients from six families who presented with a wide spectrum of clinical features such as recurrent fever, oral ulcers, rash, arthritis, recurrent diarrhea, hepatosplenomegaly, and high immunoglobulin levels.

Frequency of primary mutations of Leber's hereditary optic neuropathy patients in North Indian population.

Purpose: Leber's hereditary optic neuropathy (LHON) is an inherited optic neuropathy characterized by subacute painless vision loss. The majority of LHON is caused due to one of the three primary mutations in the mitochondrial DNA (m.G3460A, m.