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The clean genome crusade

Amrapali Singh

Last month, scientists completed the job of decoding the entire 3.2 billion chemical units of human deoxyribonucleic acid (in layman's terms, DNA) in the correct order, paving the way for geneticists worldwide to plan their own brave new world.

This is the biggest thing to happen for some time in genetics, supplanting the one about Dolly, the famous cloned sheep. It is a kind of culmination of the discovery of the structure of the DNA molecule by Francis Crick and James Watson in 1953. Armed with the information collected about the human genome, geneticists now believe this could be the beginning of the end for congenital human diseases.

One of those at the vanguard of the set who hope to abolish genetic disorders is Sudhir Kumar, an assistant professor at the department of biology, Arizona State University, who heads a $ 1.5 million-project. By comparing known genes in humans and other animals, Kumar and his team of 10 researchers hope to accelerate the understanding of genes and, finally, help address genetic disorders.

The team uses computers and a software program to detect similarities and differences between hundreds of thousands of gene sequences. Kumar developed the software, MEGA (Molecular Evolutionary Genetics Analysis), to study gene sequences the differences in them when he was a student at Pennsylvania State University in 1993. It has become one of the most widely-used tools worldwide by scientists doing gene sequence research. It can be downloaded free of cost from his web site, www.megasoftware.net.

"We have huge amount of data in gene sequences, not just of human but other species too... Thus, while the first working draft of the human genome has been completed, geneticists are actually experiencing a data crisis. The sheer amount of data is difficult to analyze using conventional experimental methods. That is where our work starts," says Kumar, 33.

To shorten the exhaustive process so that scientists can learn the function of the genes, Kumar hopes to locate the genes by following family history

"It's what we call finding the footprints of the gene in the available data of gene sequences. It may give us an insight into what makes different genes have different functions, and how they differ. Identification of these signatures or footprints will take biomedicine closer to understanding the genetic basis of diseases," he says.

"Gene sequences change as a result of mutation. Sometimes changing one critical nucleic acid can turn a gene off or alter its function. This is the basis for many inherited genetic diseases. But for many diseases controlled by large number of genes, like heart diseases, it's difficult to pinpoint the exact gene. But if you have the entire function of gene sequence in front of you, it is easier to chalk out the ones that differ and react with each other and cause heart disease.

Other scientists have identified gene function but not all. We are trying to finish that identification," he says.

Kumar is not new to big news. In 1998, where Kumar was a post-doctoral scholar, he and a fellow researcher at Pennsylvania State University came up with the theory that mammals flourished alongside dinosaurs for 30 to 40 million years, and not after the extinction of the big beasts as was believed.

The theory sent shock waves among the anthropologists and paleontologists around the world. The duo based their controversial conclusion on an analysis of the "molecular clocks" in present-day genes. Later research backed their findings and they were soon ducking the media at every turn.

A resident of New Delhi, Kumar first came to the USA in 1990 for a PhD in population genetics and molecular evolution after completing his dual degrees in electrical engineering and computer science from the Birla Institute of Technology and Sciences, Pilani.

Author of several books on molecular evolution and genetics, Kumar recently became one of the 11 recipients of the prestigious Innovation Awards in Functional Genomics from the Burroughs Wellcome Fund of Research in North Carolina. The award targets a small, distinguished group of high-impact projects that will speed the process of determining what thousands of genes do and how they influence human disease.

Kumar, who prefers the academic world to the corporate, though he knows gene research is one of the most exciting areas of science today and among the most lucrative, believes research freedom lies only in academia.

"I love interacting with students. It is comfortable and what's more, it gives be complete freedom to do any kind of project you want to. I don't think I could have the same freedom if I were to work for a company," he said.

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