THE multi-centric programme at the Centre for Biochemical Technology (CBT) on 'Functional Genomics' happens to be a comprehensive and reasonably funded one and the best formulated among the 27 projects supported under the Indian Human Genome Initiative o f the Department of Biotechnology (DBT) since the programme got under way in 1997. 'Functional Genomics' refers to the area of genomics that is concerned with the use of genomic sequence data to identify genes and the association of functions, including diseases and genetic disorders, to specific genes and their variations (polymorphisms) among populations.
This programme was established in 1998 involving molecular biologists, immunologists and bio-organic chemists with medical scientists from various medical institutions and hospitals. The collaboration with hospitals provides ready access to biological sa mples to carry out "functional analysis" of genome sequence. In particular, the determining of genomic sequence variations (polymorphisms) in both coding and non-coding regions of genes and its statistical correlation with characteristics (phenotype) pre sented clinically constitutes an important component of functional genomics, points out Samir Brahmachari, Director of the CBT. This method is called 'functional polymorphism scanning'.
In particular, the CBT project aims at identifying novel mutations in the Indian population in known genetic disorders such as thalassaemia, Down's Syndrome and other mental retardations, Duchenne's Muscular Dystrophy (DMD), Myotonic Dystrophy, Spino Cer ebellar Ataxia (SCA), Huntington's disease, and asthma, and developing novel diagnostics, specific to Indian populations, based on such mutational analysis.
The institutions/hospitals collaborating with the CBT in the functional genomics project include the National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore; the Jawaharlal Nehru Centre (JNC) for Advanced Research, Bangalore; the Neuro sciences Centre of the All India Institute of Medical Sciences (AIIMS), New Delhi; the Manipal Institute of Neurological Disorders, Bangalore; the Department of Medical Genetics of the Ganga Ram Hospital, New Delhi; and Vivekananda Institute of Medical S ciences (VIMS), Calcutta.
With the objective of developing a genetic material resource base, over the last two years a good sample collection facility has been established for various neurological and psychiatric disorders, haemoglobinopathies and asthma. For polymorphism screeni ng, an automated genotyping and sequencing facility has been established. This together with improvements made in the techniques, particularly the development of DNA markers, has brought down the cost per reaction significantly. The accuracy of results c ompares well with highly expensive methods that use imported markers, says Brahmachari.
One of the important programmes of research undertaken as part of the Functional Genomics project of the CBT is the understanding of the molecular basis of neurological disorders. Many neurological disorders have been found to be associated with the expa nsion of certain repetitive sequences involving three nucleotides or three basic units of DNA. According to Satish Jain of the AIIMS, who is collaborating with the CBT on the project, this is the first time that such an extensive genomic study on neurolo gical disorders among the Indian population has been carried out. The majority of neurological orders caused by trinucleotide repeat expansion belong to the class of hereditary ataxias known as spinocerebellar ataxias (SCA), which lead to a generalised f ailure of coordination and balance. The SCA has been used as a model to understand the mechanism of trinucleotide repeat expansion.
According to Satish Jain, there are 13-14 types of mutations that lead to SCA and physicians find it difficult to detect one from the other. It is here that 'Functional Genomics' - which seeks to analyse the mutations in the DNA of patients with known cl inical profiles (phenotype) - helps differentiate one form from the other. An analysis of 42 families showed that type SCA2 was the most prevalent in Indian populations. It was found that there was a length variation of the specific repetitive sequence n ot only between generations but within the generation with the increasing birth order of the offspring. This implies that in susceptible families, the youngest child runs the greatest risk of SCA2. This also indicates the important role of parental age i n the genomic instability of the offspring.
It was also found that the SCA loci in genes in the Indian population under study showed similarity to those of the Caucasian population but were significantly different from those of the Japanese population. The study also showed that as many as 40 per cent of the SCA cases could still not be precisely understood in genetic terms. "Maybe their loci are in many genes and across different chromosomes," says Satish Jain.
Another important area of the functional genomics project of the CBT that the AIIMS is the study of genomic variations associated with heriditary epilepsy where many candidate genes have been identified and the number of epileptic syndromes have been lin ked to different loci on human chromosomes. "In India," says Brahmachari, "we need to form our own database of large families with many members having seizures of similar or different types. This database can be subsequently used to screen for genetic as sociations in clinical applications using appropriate markers."
Another major programme that is under way as part of the CBT project is the association of repetitive nucleotide sequences in bipolar disorder and schizophrenia. This work is carried out in association with Sanjeev Jain of NIMHANS, Bangalore. These are s evere behavioural disorders with a lifetime risk of about one per cent in the population worldwide. Similar to the phenomenon of ataxias, a repeat sequence involving the nucleotide bases C, A and G contained in the coding gene called KCCN3, has been impl icated in these disorders. Polymorphism in this repeat sequence, which causes variation in the gene size, seems to be associated with scizophrenia.
Sanjeev Jain points out that common gene disorders such as asthma and hypertension, which afflict one per cent of the population of India, are increasing rather than becoming extinct. The national human genome programme, he feels, will help identify the genetic cause and therefore the type of treatment required.
While the DBT-supported 'functional genomics' component is based only on institution-hospital linkages, the CBT has been able to forge a triangular linkage on its own by tying up with a pharmaceutical company (Nicholas-Piramal) with the objective of coup ling the pharmaco-genomics component as well. According to Swati Piramal, the company's chief research officer, it has launched a project called 'Genomed' in association with the CBT and Wellspring Hospital, a Mumbai-based private hospital, with an inves tment of Rs.100 crores over a 10-year period. Clinical trials of any gene-based drug that will be evolved are proposed to be carried at Wellspring.
Even in this well-formulated programme of the CBT, it can be noticed that the fourth arm of the desired quadrangular partnerships, namely the involvement of an IT company, is missing despite the market hype and Brahmachari's concerted efforts.