Era of personalised medicine awaits

By Fergus Walsh
BBC News medical correspondent

BBC medical correspondent Fergus Walsh talks through how you sequence a human genome

A revolution in genome screening has been promised by a biotech company in the US.

Complete Genomics, says it will sequence one thousand complete genomes between June 2009 and the end of the year and one million over five years.

I visited the company, based in Silicon Valley near San Francisco, and saw, first hand, the potential significance of mass gene mapping.

Silicon Valley in California is a key centre for genetics, bio-tech research and computer technology - all of which are key for genome mapping.

Several companies are predicting a dramatic increase in the speed of gene sequencing.

The future that we all envisage is the day when every infant has their genome sequenced at birth and we utilise that information to optimise health throughout their life Andrew Wooton X PRIZE foundation

If Complete Genomics can deliver on its promise - and it has yet to build all the infrastructure it needs - it would be an extraordinary achievement.

So far only around 20 people have had their entire genetic code mapped.

This is due to two factors: cost and complexity.

The first draft of the human genome was published nearly a decade ago.

It involved the work of hundreds of scientists in six countries and took a decade to produce.

The price tag was more than $2bn.

Since then the cost has been reduced to a few hundred thousand dollars, and the time taken to a few months - but it is still a massive undertaking.

'Language of life'

Little wonder, because the genome is a person's entire genetic code contained in chromosomes inside the nucleus of virtually every cell in the body.

It is made up of six billion letters, or three billion base pairs of DNA, half of which come from each parent.

These are arranged in a double helix, whose elegant structure was first described by Crick and Watson in 1953. At the time, their discovery barely made headlines.

We don't understand much about the genome yet despite all the years we've been studying it Professor Steven Brenner University of California, Berkeley

The publication of the first draft of the human genome in 2000 was quite different.

In a dual Washington and London press conference, President Bill Clinton said: "We are beginning to learn the language in which God created Life".

Talking of the medical implications of genome mapping he added: "It is now conceivable that our children's children will know the term cancer only as a constellation of stars".

In Downing Street, Prime Minister Tony Blair said the achievement hailed "a revolution in medical science whose implications far surpass even the discovery of antibiotics, the first great technological triumph of the 21st century".

So what is a genome and were Blair and Clinton's comments in any sense justified?

Start of the process

The genome is nothing less than the blueprint for making a human which scientists are only just beginning to decipher.

It is a chemical alphabet of just four letters: A, T, G and C.

Dr Reid says genomics will be for the 21st century what IT was for the 20th

Genes are sections of DNA which tell cells how to function and decide things like the colour of our eyes.

In everyone's genome there are millions of minute variations called SNPs.

Most are harmless, but some make us more or less susceptible to disease.

Since 2000 scientists have made significant progress in discovering genetic links to disease.

Virtually every week there are new scientific papers which add to our knowledge.

But most of this research is based on analysing sections of DNA, not the entire genome.

Complete Genomics says all that is about to change.

Advances in nanotechnology have allowed it to miniaturise the components needed for genome sequencing.

It is able to fit the coding instructions for an entire genome - six billion characters long - onto three small rectangular silicon plates just a few centimetres across.

Speeding up

Advances in biotechnology have enabled the sequencing process to be accelerated, and improved computing power has enabled dramatic increases in the speed of gene mapping.

Complete Genomics has published its first genome, in what is called a proof of concept trial, and now plans to scale up its sequencing programme.

The knowledge to be gained from one genome, in isolation, is limited.

The latest technology is being deployed

But if you were able to compare huge numbers of genomes then patterns should emerge.

Dr Clifford Reid, CEO of Complete Genomics said: "As soon as we can sequence thousands of genomes then we can understand for the first time, the genetic basis of disease that will enable us to develop new diagnostics for the detection of disease and new therapeutics for the treatment of disease."

It offers the hope of more personalised medicine; tailored treatments to suit individual patients.

Also it should lead to greater understanding of the balance between genetics and environmental risk - to what extent illness is the result of faulty genes inherited from our parents, or due to our lifestyle.

There are several serious single gene disorders, like cystic fibrosis, huntington's disease, and some forms of breast cancer.

But most conditions are a complex combination of multi genetic factors and environment.

Furthermore, the language of the genome - the six billion As, Ts Cs, and Gs - is still largely a mystery - we do not yet really know what most of the code means.

Much to learn

Steven Brenner, professor of biology at University of California, Berkeley, said: "We don't understand much about the genome yet despite all the years we've been studying it, although new technologies are enabling us to learn about it faster and faster.

"At best we understand what 1% of the genome does, but even within that 1%, where we see variations between individuals, in most cases we can't reliably say what the impact of that variation is."

But such is the excitement and promise of mass gene mapping that it has prompted the creation of medicine's richest prize.

Some $10m is on offer to the first company that can sequence 100 genomes in ten days, for $10,000 or less each.

The money for the Archon X PRIZE comes from a Canadian industrialist Stuart Blesson who made his fortune in diamond mining.

Andrew Wooton, from the X PRIZE foundation, says its goal is to bring about radical breakthroughs for the benefits of humanity.

He said: "The future that we all envisage is the day when every infant has their genome sequenced at birth and we utilise that information to optimise health throughout their life and enable customised personalised medicine."

That would raise issues of privacy and discrimination. What would happen if insurance companies or employers got to look at the genomes of individuals?

The beginning of the genome generation, with all its promise and potential problems, may soon be with us.