'Multi-omics' is changing the way TB and cancer are diagnosed and treated in India

'Multi-omics' is changing the way TB and cancer are diagnosed and treated in India


Over the past decade, the use of genomics in India has undergone a significant transformation, so much so that the diagnosis, management, and treatment of many diseases — including tuberculosis, cancer, and diseases caused by antimicrobial resistance — are on the verge of a revolution.

More recently, in January 2024, the Department of Biotechnology said it had Full sequencing Under the 'Genome India' project, 10,000 genomes will be collected from 99 ethnic groups. This national initiative aims to develop a reference genome for Indian people, which will help in designing genome-wide and disease-specific 'genetic chips' for low-cost diagnosis and research.

Earlier, in October 2020, the Council of Scientific and Industrial Research (CSIR) had reportedly completed the sequencing Genomes of 1,008 individuals Campaigns representing various ethnic groups were conducted for six months in India. This effort 'Indigen' – To create a pilot dataset through which researchers can analyze the epidemiology of genetic diseases and help develop cost-effective testing approaches, optimize treatments, and minimize adverse events.

Other, more disease-specific consortia have also emerged across the country and efforts are underway to create new datasets to address individual health problems, ranging from the chronic scourge of tuberculosis to cancer, rare genetic disorders in children and even antimicrobial resistance. Researchers have been able to extract more value from these using artificial intelligence and machine learning, and develop a ‘multi-omics’ approach to tackling diseases by combining their contents with other comprehensive datasets on proteins (proteomics), gene expression in cells (transcriptomics) and chemical changes that control gene expression (epigenomics).

Tuberculosis

A recent consortium talks about tuberculosis, a disease that continues to pose significant challenges for its elimination in India and around the world. The Indian Tuberculosis Genomic Surveillance Consortium (InTGS) comprises 10 Report India sites covering eight states for tuberculosis, with the goal of sequencing approximately 32,000 tuberculosis clinical strains from active patients and developing a centralized biological repository of clinical diseases. Mycobacterium tuberculosis Tension in India.

According to Vinay Nandikoori, Director, CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, other key objectives with respect to tuberculosis include mapping the genetic diversity of pulmonary and extrapulmonary isolates of tuberculosis bacteria from newly reported active cases in India, associated treatment outcomes and correlation of mutations with drug resistance patterns. The ultimate goal of the project is to validate the identified mutations to develop a sequence-based method for determining drug resistance and combine epidemiological data with the results of whole-genome sequencing to develop a working solution.

Scientists from leading research institutes have divided the various parts of the project as follows. In the first phase, scientists from Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry; National Institute for Research in Tuberculosis, Bhagawan Mahaveer Medical Research Centre, Hyderabad; Byramjee Jeejeebhoy Government Medical College, Pune; and PD Hinduja Hospital, Mumbai will collect clinical samples including metadata of patients. Next, scientists from the New Delhi-based International Centre for Genetic Engineering and Biotechnology will isolate genetic material from the samples and establish a strain repository. In the third phase, scientists from CCMB and National Institute of Biomedical Genomics, Kalyani will conduct whole genome sequencing. In the fourth and final phase, a team from National Institute of Immunology, New Delhi will conduct RNA sequencing data analysis and develop AI and ML models to predict drug resistance and take cognizance of metadata to detect resistance patterns, according to Dr. Nandikoori.

“This is a very, very, very big project,” he said. The starting point is to create baseline data – a relatively neglected task in India compared to many other countries.

Rare genetic disorder

India has also launched a pan-country mission for paediatric rare genetic disorders (PRaGeD), which have become a common public health concern despite their rarity. Mission PRaGeD plans to create awareness, perform genetic diagnosis, discover and characterise new genes or variants, provide counselling and develop new therapies for rare genetic diseases affecting India's children.

The mission will incorporate IndiGen data into its in-house bioinformatic pipelines that will be used to analyse the parts of the genome that code for proteins (the exome). CSIR-Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, plans to enroll patients with rare genetic disorders and their families in collaboration with 15 centres across India.

“The aim of the study is to identify new genes for various known as well as unexplained inherited phenotypes (observable traits), but also to help the patient and family in the management of the disease and prenatal diagnosis,” said Ashwin Dalal, group leader and scientist for diagnosis at CDFD. The team will also characterise the new genes or their variants to determine their function or role in the disorder using cell lines and/or model organisms such as mice, fruit flies and zebrafish.

The mission also includes the use of next-generation sequencing, one of the latest tools for managing rare diseases and assessing the likelihood of developing many chronic diseases, especially when conventional tests give negative results. “Implementing newborn genetic testing at the national level can contribute to the management of rare genetic conditions through faster and more accurate diagnosis,” Dr. Dalal said.

cancer

The Indian Cancer Genome Consortium (ICGC-India), which is part of the larger International Cancer Genome Consortium (ICGC) and supported by the Department of Biotechnology, plans to identify genomic abnormalities in various types of cancers in Indian patients and identify population-specific genetic variations that are associated with cancer risk and treatment response. According to Dinesh Gupta, group leader of translational bioinformatics at the New Delhi-based International Centre for Genetic Engineering and Biotechnology, such population-wide genome sequencing projects can help discover new biomarkers, potential new treatment targets and personalised treatment strategies.

Dr Gupta said that several Indian institutions have set up genomic data repositories like ICGC to facilitate cancer research and precision medicine initiatives, which cater to the genetic structure of Indian people. Another example is the Indian Cancer Genome Atlas Project, a non-profit public-private-philanthropic initiative that is trying to create a comprehensive catalogue of genomic alterations in various cancer types prevalent in India. This can help researchers identify new biomarkers and treatment targets. The atlas collects and generates detailed genomics with linked clinical data.

Dr Gupta said genomics is also being incorporated in cancer clinical trials in the country. Indian cancer centres use genomic profiling to categorise patients for clinical trials based on their molecular subtypes, and link potential responders to targeted therapies.

Antimicrobial Resistance

Genomics and metagenomics are proving useful for analysing antimicrobial resistance and understanding the possibility of rapid spread of any antibiotic resistance functions among bacterial species. Some microorganisms, such as the bacteria that cause tuberculosis, grow very slowly even in laboratory conditions, said Bhabatosh Das, associate professor at the Translational Health Science and Technology Institute, Faridabad. “So clinicians prescribe antibiotics without knowing the actual resistance profile of infectious agents.”

He said genome sequencing is very helpful in such cases because it can provide researchers with information about the resistance profile of microorganisms without growing them in the laboratory. “Such information helps clinicians to use antibiotics judiciously.” In tuberculosis, pathogen-specific resistance signatures “should add immense value to antimicrobial-resistance diagnosis and selection of appropriate drug combinations for successful antimicrobial therapy.”

AI, ML, and Multi-omics

Meanwhile, artificial intelligence (AI) and machine learning (ML) algorithms are helping genomics analyse massive datasets. These techniques can help predict a person's risk of developing cancer, develop diagnostic tools for early detection of certain cancers, classify them and develop treatment strategies, Dr Gupta said.

Researchers have also talked about using AI and ML to help analyze genome-sequencing data in cases of rare genetic disorders. An example of sequencing a person's entire exome can yield 5 GB of data and whole genome sequencing can yield 90 GB of data, Dr. Dalal explained: “Analysis of such large-scale sequencing is impossible without the use of computational tools.” Technicians are using AI and ML-based approaches in in-house bioinformatic pipelines as well as part of commercial tools to analyze sequencing data to identify disease-causing variants.

According to Dr. Das, with the rapid expansion of AI, it is now easier to access multi-omics and rapidly analyze big data products, even with only standard computational facilities. He said that multi-omics is an emerging technology in the field of clinical science in India today.

T.V. Padma is a science journalist based in New Delhi.


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