Summary

Our lab focus on developing bioinformatics methods of omics analysis and noncoding RNAs for vision biology and eye diseases. This includes whole genome, exome, transcriptome next-generation sequencing data analysis in identifying molecular targets for ocular cancer and diseases,  the small-RNA seq analysis of human with focus on profiling micro-RNAs and identifying their regulatory role in eye diseases, comparative genome analysis to identify virulence and drug resistance mechanisms in ocular pathogens and structure based approaches of non-synonymous variants (nsSNVs) to understand the molecular mechanisms of the phenotype. As part of the multidisciplinary nature of our field, we work on these projects in close collaboration with wet lab scientists. The following gives a short summary of a few selected projects.

Clinical Exome Analysis Pipeline for Eye Diseases

Develop automated pipelines and infrastructure to detect pathogenic variants from exome data of eye disease patients. The exome sequencing studies primarily aim at the discovery of single nucleotide variants (SNVs), and small insertions and small deletions (INDELs) of coding region that is about 85 % of mutations among all the genetic variations. Exome sequencing method has been widely used to elucidate the genetic causes of many eye diseases, starting from single gene disorders and moving on to more complex genetic eye disorders, including complex traits and cancer. Although the exome sequencing has demonstrated identifying clinical variants, bioinformatics challenges are being faced as the current bottleneck in exome/genome methods shifted from sequence generation to data management and analysis. Using our in-house automated pipeline, we can find almost all variants within the targeted region of the genomes. We apply a series of filters to identify the potential disease-causing variants. We are developing a statistical model to specifically filter eye disease causing variants.

Clinical Exome Analysis Pipeline for Eye Diseases

Comparative genomics of ocular pathogens

Comparative genomics approach of ocular isolates from keratitis patients with different clinical outcomes used to better understand the infection, genome-wide identification of genetic features responsible for multiple virulence and multidrug-resistant (MDR) mechanisms. Microbial keratitis due to either fungus or bacteria is a major cause of blindness in India. The bacterial keratitis, often caused by Pseudomonas aeruginosa and methicillin-resistant staphylococcus aureus (MRSA) at Aravind Eye hospital, Madurai, majority of times in spite of adequate medical management the ulcer does not heal and may require a corneal transplant. P.  aeruginosa can cause a most severe keratitis, carrying a wide array of virulence factors that contribute pathogenesis. Keratitis pathogenesis is a complex process, where in several virulence factors has been implicated including Cell-associated structures such as type IV pili and flagella, slime polysaccharide, proteases such as elastase B (LasB), alkaline protease, protease IV and Pasp and exotoxins. Also, clinical isolates of Pseudomonas often exhibit multiple resistances to antibiotics. On the other hand, studies have shown an increase in the pervasiveness of ocular MRSA infections. Here, comparative genomics through de novo assembly of NGS data of ocular isolates of P. aeruginosa  carrying specific features compare to other strains suggesting that they may be adapted with these features to cause eye infections. We are using same approach to study MRSA ocular pathogens and further studying the link between MDR genotypes and clinical outcome or virulence factors.(Genome Announc. 2014)

Human microRNAs and their regulatory role in eye diseases

Computational strategies to analyze intrinsic relationships among dysregulated miRNA and their target interactions in infection and explore their regulatory role and as potential biomarkers. MicroRNAs are a novel group of non-coding small RNAs that post-transcriptionally control gene expression by promoting either degradation or translational repression of target messenger RNA. They are implicated in a large variety of physiological and pathophysiological processes. Levels of miRNAs in the serum of humans have been shown to be stable, reproducible, consistent amongst healthy individuals and change during pathophysiology, and their presence in ocular fluids allowing them to be of potential value as clinical biomarkers of eye disease. We focus on miRNAs regulatory role from dysregulated human miRNAs identified through small-RNA sequencing in glaucoma, diabetic retinopathy and fungal keratitis (IOVS, 2015). In addition, we are looking at their regulatory role in maintenance of limbal stemness with wet lab scientist.

Structural Bioinformatics of eye disease associated – nsSNVs

Structural Bioinformatics of eye disease associated – nsSNVs

Use structural bioinformatics to investigate functional impact of non-synonymous single nucleotide variants and its association with genetic eye diseases. The advent of NGS identified several new candidate genes for eye diseases. Variations in the same gene can cause very different eye diseases (pleiotropy), on the other hand, single disease can be genetically heterogeneous. Thus, a detailed underlying molecular mechanism is needed to understand this complexity. Non-synonymous single nucleotide variants (nsSNVs) in the coding region of the protein is of critical importance to understand the molecular mechanisms of the disease and to clarify the association between patient-specific variants and disease phenotype. We use simple analytical strategy using protein structure to predict the pathogenicity of nsSNVs and investigate their functional impact that may leads to eye disease phenotypes.

Use structural bioinformatics to investigate functional impact of non-synonymous single nucleotide variants and its association with genetic eye diseases. The advent of NGS identified several new candidate genes for eye diseases. Variations in the same gene can cause very different eye diseases (pleiotropy), on the other hand, single disease can be genetically heterogeneous. Thus, a detailed underlying molecular mechanism is needed to understand this complexity. Non-synonymous single nucleotide variants (nsSNVs) in the coding region of the protein is of critical importance to understand the molecular mechanisms of the disease and to clarify the association between patient-specific variants and disease phenotype. We use simple analytical strategy using protein structure to predict the pathogenicity of nsSNVs and investigate their functional impact that may leads to eye disease phenotypes.

Targeted Analysis Pipeline for Ocular Cancer Panel

Develop targeted analysis pipeline for RB1 gene and other cancer associated genes to identify pathogenic variants for the molecular diagnosis of Retinoblastoma. Accurate identification of pathogenic variants in a reduced time is very important for diagnosis, confirmation, genetic counselling, risk assessment, and carrier screening of Retinoblastoma (RB) patients and their family members. However, genetic analysis of heterogeneous spectrum of variants in RB1 gene and other cancer associated genes is no trivial task and essentially requires comprehensive approach. Target enrichment followed by next-generation sequencing offer a time-efficient and accurate approach for the molecular diagnosis of many eye diseases. However, identifying pathogenic variants, moreover, spectrum variations, is challenging as data analysis requires several bioinformatics tools, data management, pathogenic variant filtering and reporting. Our in-house bioinformatics pipeline can identify heterogeneous spectrum of RB1 gene variants including SNVs, InDels and CNVs for the molecular diagnosis of RB. (BMC Cancer, 2015) We develop the automated targeted analysis pipeline to both germline and somatic variants for ocular cancer gene panel.

Department of Bioinformatics
‚ÄčAravind Medical Research Foundation
No 1, Anna Nagar, Madurai, Tamil Nadu - 625020, India
email : bharanid@gmail.com; bharani@aravind.org
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