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Genome sequencing by a Bangalore lab will help early detection and in patient-specific treatment options

Genome sequencing is not just a fad in Bangalore’s biotech industry. It is all set to achieve a major breakthrough in the treatment of oral cancer. Bangalore-based Ganit Labs has made steady progress in sequencing genomes of oral cancer patients. This will facilitate early detection and even help doctors suggest tailor-made treatment options.

WHY ORAL CANCER?
Dr Binay Panda, head of Ganit Labs, said, “As far as incidence and mortality rate of oral cancer goes, India is ahead of Japan and US. Nearly 25-30 per cent of the total cancer patients among males in India are affected by head and neck cancer.”

Oral cancer is categorised by the lab, located in the Institute of Bioinformatics and Applied Biotechnology (IBAB) Centre in Electronics City, under head-and-neck cancer.

Currently, the identification of oral cancer is largely done on the basis of checking the medical history of patients, physical examination of the oral cavity and through pathological tests. “Sometimes a cell might not appear abnormal under a microscope but might harbour genetic changes that could lead to it turning into a tumour cell. If we know what and where to look at, one could do focused experiments but unfortunately we don’t. Hence, unbiased sequencing of the cancer genome would get us to the root and might help in identifying the potential reason behind the disease,” Dr Panda said.

HOW IS SEQUENCING DONE?
The oral cancer study is being done in collaboration with Mazumdar Shaw Cancer Centre of Narayana Hrudayalaya. Dr Panda said, “Genome is the collection of genes and other non-coding parts that is made up of individual nucleotides A, T, G and C arranged in different combinations. If you compare the genomes of different samples of cancer patients with those of normal individuals, the pattern in which A, T, G and C are arranged is different. Once we know where the changes are, we correlate that with the disease. Once samples are collected, they are processed in the laboratory to extract DNA, which is sequenced.”

The team at Ganit Labs is mainly sequencing the genomes in the backdrop of a person’s changing habits. “You cannot stop cancer if you are inheriting the changes. But if the disease is linked to a particular habit, we need to know what are those exact changes in the genomes to which a particular habit is linked with,” says Dr Panda. This apart, the sequencing may also reveal the effect of a particular drug on patients. “If you are administering the same drug to two patients, one might respond well while another might not. Sequencing might shed light on which genetic changes are responsible for the action of a particular drug. Out of the samples we have sequenced, we have identified specific genetic signatures that we are analysing,” Dr Panda said.

DEPENDENCE ON WEST
“Though the biotech industry in the state is vibrant, the lack of equipment and skilled researchers have retarded progress. We rely upon equipment from the West for our studies. Some equipment require huge investments running into several crores of rupees. The problem is that development of these equipment requires multi-discipline knowledge, which we lack here. If any Indian firm takes up manufacturing these sequencing equipment, they may become affordable and eventually prompt many more to take up projects in the subject,” explained  another researcher.

Further, the falling number of researchers has also crippled the process of research. “Sequencing is not just about bioscience but incorporates several other fields such as computers and biochemistry. A computer engineer need not back off saying it is just bioscience domain as he too has a role to play in sequencing experiments. But unlike other fields, results in biotechnology are very slow. One needs to be patient,” explained Dr Panda. Currently, his team is working with more than 10 researchers.

SEQUENCING AMARANTH LEAVES
Recently, the lab had sequenced the genome of the neem plant for the first time in the world. Another team at the Institute is trying sequence genomes of the local variant of Amaranth leaves (harive soppu). Prof N Yathindra, director of IBAB Centre, told Bangalore Mirror, “The plant is rich in lysine, a type of essential amino acid. The human body can synthesise a few forms of amino acids but not essential ones. They need to be supplied through our food. Lysine is one such amino acid. It helps digestion and metabolism. We are trying to sequence the genome of this plant for better utilisation of this amino acid.”

The institute also has plans of taking up studies into male infertility.