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The government’s Genome India initiative on Tuesday (February 27) announced the successful sequencing of 10,000 whole genomes of healthy persons from across the country, creating a genetic map of the population. Researchers from 20 science institutes across the country helped in collecting the blood samples, sequencing the genome, developing a methodology, and storing the data.
With each sequence requiring 80 GB storage space, the huge dataset of 8 petabytes will be stored at the Indian Biological Data Centre in Faridabad. This dataset will be made available to researchers as “digital public good.” The data can be utilised to develop new diagnostics, targeted therapies, identify new rare diseases, and cure existing ones.
The Genome India project was approved by the government in 2020 with the aim of creating a comprehensive catalogue of genetic variations found in the Indian population. A map of genetic diversity is essential for understanding the history of our evolution, discovering the genetic basis for various diseases, and creating therapies of the future. This cannot be done using data available in existing international databases, as Indian genomes are likely to be different from that of other populations.
Researchers who analysed 5,750 of the genome sequences have already identified 135 million genetic variants found in India.
This map will also create a unique resource. This is because our population of 1.4 billion consists of more than 4,600 distinct groups. With endogamy — marrying within the same community — common in India, the various groups have maintained their distinct genetic makeup. This can help compare and contrast the impact of genetic variations on physical health. Union Science minister Dr Jitendra Singh described India as the “largest genetic lab in the world.”
The human genome is essentially a biological instruction manual that we inherit from our parents. It is a tome written with just four letters, A,C,G, and T — the four bases that come together to create everyone’s unique genetic makeup. There are around 3 billion pairs of bases in the complete human genome. This contains all the information needed to create your physical form and maintain it throughout life. From your height, colour of the eyes, the genetic diseases you get or those you are at a higher risk for, everything is determined by the genetic makeup.
To sequence the genome, researchers first extract the information from the blood. With a complete sequence of 3 billion pairs being extremely hard to handle, scientists cut it up into small pieces and tag them — like you would when you disassemble furniture. The A,C, G, T code of these smaller chunks are written down by a DNA sequencer and then the complete sequence is put together.
One, it can help identify the genetic basis or genetic risk factors for various diseases.
Prof K Thangaraj, who leads the project and is a senior scientist at the Centre for Cellular and Molecular Biology in Hyderabad, cited the example of a mutation, MYBPC3, which leads to cardiac arrest at a young age. It is found in 4.5% of the Indian population but is rare globally. Another mutation called LAMB3 causes a lethal skin condition. It is found in nearly 4% of the population near Madurai, but it is not seen in global databases.
Two, it can help in targeted treatments, especially for rare diseases that usually arise from genetic anomalies. “An Indian genome database will have a significant impact on treatments for genetic diseases. It can help develop new therapies that can cure these diseases,” said Department of Biotechnology (DBT) Secretary Dr Rajesh Gokhale.
Take for example the under-development mRNA vaccine to prevent relapse of pancreatic cancer, which is based on a genetic mutation that allowed a small group of pancreatic cancer patients beat the odds. The mutation allowed their immune system to identify the cancer cells and attack them.
It can also help in identifying resistance-indicating variants — for example, genes that might make certain medicines or anaesthetics ineffective in certain populations. An example from India is a set of a Vaishya community from South India, who lack the gene for properly processing common anaesthetics. For this group, use of such anaesthetics can result in death.
How long did the project take?
The first whole human genome was sequenced with the collaboration of an international team. It took 13 years and $3 billion, and was completed in 2003. India announced its first complete human genome in 2009. “The technology has come a long way. Now, it takes only about five days to sequence an entire human genome and perform all the quality checks. In fact, we were able to sequence the entire 10,000 genomes in a matter of three to four months,” said Dr Gokhale.
A majority of the time was spent on collecting patient samples and their health history. The samples were collected from the remotest parts of the country, covering various tribal populations as well. In all, 99 distinct population groups were covered by the project. The collection was delayed multiple times due to the Covid-19 pandemic.
“This is a significant milestone. We now have a baseline map of the country,” said Dr Gokhale.
