Rare Genetic Disorders (RGDs) are clinical conditions with underlying genetic origins. Though RGDs are of low prevalence and individually rare, collectively they affect a considerable number of people in a highly populous country like India. The diagnosis of RGDs is challenging due to the lack of awareness and the genetic heterogeneity and variety of overlapping symptoms they present with, as well as the unavailability of accurate genetic tests. Where available, the cost of associated diagnostic and medical tests is beyond the reach of most people in our country.
Palliative treatment (where available) relies on obtaining a correct diagnosis of the disorder as early as possible. We are working towards developing diagnostic kits for RGDs that are cost effective, suitable for carrier and newborn screening, and specific for disease associated genetic mutations common among the Indian population.
Team
Gayatri R Iyer, Harvinder Kour Khera, Iliyas Rashid
Runa Hamid, Shivranjani C Moharir
Activities:
- Developing diagnostic kits for Rare Genetic Disorders
- Development of digital PCR-based diagnostic assay for Spinal Muscular Atrophy (SMA)
- Developing a rare genetic diseases database - GenTIGS
- Metabolite profiling for diagnosis of monoamine neurometabolic disorders in Indian cohort
- Development of MS-PCR kits for genomic imprinting disorders
The actual proportion of human genetic diseases caused due to copy number variations is unknown. With the advent of molecular techniques and whole genome sequencing-based approaches, the underlying cause of several genetic disorders can be unfolded. We are working towards identifying Indian population specific mutations and developing indigenous diagnostic tools and kits for population level screening. Initially, the target disorder is spinal muscular atrophy (SMA), with goals to later expand to other RGDs. The survival motor neuron genes (SMN1 and SMN2) are the causative genes for SMA with copy number variations and gene conversion events eventually leading to a degeneration of motor neurons.
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex, semi-quantitative method for diagnostic testing of genetic disorders. The method is suitable for the identification of deletions or duplications over a broad range, from SNPs to chromosomal aneuploidies, given a suitable set of probes covering the entire target region. By coupling MLPA amplified probes with sequencing, one can include many hundreds of probes in a single reaction. The incorporation of an Next Generation Sequencing (NGS)-based detection approach would make the diagnostic strategy suitable for population level and carrier screening as multiplexing large number of samples for many disorders in a single assay would cut down the cost.
Investigators: Shivranjani C Moharir
Collaborators:
CSIR – Centre for Cellular and Molecular Biology (CSIR – CCMB), Hyderabad
Recent diagnostic advancements have shifted towards molecular testing, allowing for quick and accurate detection of homozygous SMN1 deletions. Alongside identifying SMN1 mutations, determining the copy number of SMN2 is essential, as SMN2 serves as a disease modifier. Quantitative assessment of SMN1 and SMN2 using multiplex ligation-dependent probe amplification (MLPA) is considered the gold standard for SMA genetic testing. However, other methods such as quantitative PCR and next-generation sequencing are also available.
The number of SMN2 copies correlates inversely with the severity of the symptoms. Knowledge of SMN2 copy numbers is crucial for the diagnosis as well as clinical trials. Digital PCR (dPCR), with its high sensitivity and accuracy, is a reliable method for quantifying SMN1 and SMN2 copy numbers over a wide range, providing valuable clinical insights. Under this project, we aim to demonstrate the feasibility and clinical relevance of a cost-effective dPCR-based assay to determine the mutations in SMN1 as well as the copy number of the SMN2 gene.
Investigators: Shivranjani C Moharir. Harvinder Kour Khera
We are developing a repository for clinical data on RGDs in the form of a database that can collate and store information of such diseases in the Indian context and focus on the genomic causes and mutations specific to the Indian population. The database would include a wide variety of information related to RGDs from sources such as OMIM and Orphanet and will include local prevalence, affected genes, pathogenic variants, gene regulatory factors, the role of non-coding RNAs, along with patient information. Clinical data (primary source) will be sourced from our partner hospitals and research organizations. Gene annotations and sequences, reports and information on local trends will be obtained from online databases such as Ensembl and NCBI-gene databases (secondary sources) to perform a comparative analysis. The datasets will be managed and stored using a relational database management system (RDBMS).
A web-based platform will be developed by incorporating analytical and statistical tools for clinical data analysis and interpretive output. Interactive search and query features will be built in. Apart from providing information on patient care services, the analytical platform will facilitate pedigree analysis from patient to family and population level using clinical data, a novelty of this database. Custom programs are in place for automated data extraction and presentation via the user-friendly front-end of the GenTIGS web interface. The browser enables viewing and interactive searching of all the collected information on RGDs and their relevant gene(s) (PubMed and GeneID links), along with structural and functional gene information (from NCBI-GeneDB and OMIM). We are currently working on incorporating a pipeline at the back end to analyse genome and exome level population data to identify pathogenic variants.
Investigators: Iliyas Rashid, Shivranjani C Moharir
Inherited monoamine Neurometabolic disorders (mNMDs) are a group of fifteen rare genetic disorders (RGDs) caused by genetic defects in genes involved in monoamine neurotransmitter metabolism. These include genes for enzymes, cofactors, and membrane transporters of monoamine neurotransmitters (Dopamine, Serotonin, Epinephrine, and Norepinephrine pathway). Defective functioning of these proteins leads to toxic accumulations of metabolites or lack of metabolites leading to progressive neurological deterioration with an onset in the neonatal stage or early childhood. Misdiagnosis of these disorders poses a significant challenge because there is an overlap of clinical features with other neurological disorders like encephalopathy, cerebral palsy, primary movement disorders, etc. The diagnosis of these disorders is routinely made through analysis of neurotransmitters in cerebrospinal fluid by doing lumbar puncture. Collectively, the rarity, complexity, absence of definitive biomarkers, and progressive nature of these disorders pose a significant challenge for accurate diagnosis.
To address these challenges the project has been initiated to develop a dry blood spot based rapid and cost-effective biochemical diagnostic test based on tandem mass spectrometry. This will enable the detection of reduced or heightened metabolites of monoamine neurotransmitters in blood with high sensitivity. This method will have a predictive value for the diagnosis of mNMDs. Such a method offers advantages over the invasive method of lumbar puncture generally used for diagnosis. The developed methodology can aid in the simultaneous quantification of all the neurotransmitter metabolites present in blood plasma and can potentially serve as a multiplex diagnostic assay for mNMD disorders. The development of this method is currently in progress.
Investigator: Runa Hamid
Collaborator:
Indira Gandhi Institute of Child Health (IGICH), Bengaluru
Despite the advances and application of different genomic technologies over 5 decades, the etiopathology of more than 25% of rare genetic disorders associated with intellectual disability (ID), abnormal growth and behavior is unclear emphasizing the need for exploring novel and newer mechanisms of diagnosis.
One such group of disorders is disorders of genomic imprinting. About 150+ genes in the mammalian genome are exclusively expressed from either parent depending on the parent of origin. This is achieved by the epigenetic mechanism of DNA methylation and is known as genomic imprinting.
Methylation-specific polymerase chain reaction (MS-PCR) is a simple, rapid, cost-effective, low labor and equipment-intensive modality that can be easily deployed even in remote locations with robust performance. Isolated genomic DNA is first given a sodium bisulphite treatment that deaminates the unmethylated cytosines to uracil. The converted DNA sample now has differentiated methylated and unmethylated alleles in a single tube which can be amplified with the help of allele-specific primers A pilot study of 102 clinically suspected cases mentioned above showed about 28% to be confirmed as one of four known imprinting disorders by a simple methylation-based test indicating these disorders are not as rare as cited to be but require a timely referral and correct diagnostic modality to offer genetic counselling, plan prenatal diagnosis and facilitate appropriate management.
Investigator: Gayatri Iyer