Genome 'dark horse' comes to the fore

Raw data from chromosome 21

A "dark horse" private company in the US is claiming to have taken a major lead on its rivals in the race to produce a complete gene map of humans.

At the same time, publicly-funded scientists in Germany and Japan have passed another milestone in decoding human chromosome 21.

What we have found so far is approximately 65,000 genes that are marked with high confidence

Nick Tsinoremas, DoubleTwist

The private company DoubleTwist is a relative newcomer in the genome race but claims to have completed the first large-scale computational analysis of the human genome.

It says it did this by analysing publicly-available data using Sun supercomputers and its own gene-hunting software. The company believes it now knows the location of about two-thirds of the genes in the human "book of life".

"What we have found so far is approximately 65,000 genes that are marked with high confidence," Nick Tsinoremas, director of research at Oakland-based DoubleTwist, told reporters.

"We are looking closely at another 40,000 potential genes."

Surprise entry

DoubleTwist's entry into the genome race comes as a surprise to genetic onlookers as it was thought that the battle to complete the human genome first was essentially between the privately-funded Celera Genomics corporation and the publicly-funded Human Genome Project (HGP).

Three weeks ago, Celera's CEO Craig Venter announced that his company had obtained the entire DNA sequence of a human but had not yet assembled it into the correct order. He added that it would only take them a few weeks to complete that task.

We are now standing at the starting point of understanding the molecular mechanism of Down's Syndrome

Professor Yoshi Sakaki

For its part, the HGP released a statement on Monday saying it had started the final phase of deciphering the three billion "base pairs" that make up the human genetic code.

The Project has a rough map of more than 90% of the genes and is now attempting to plug the holes in its data. The HGP expects to have a rough draft of the entire human genetic blueprint done by mid-June.

The decoding of chromosome 21 is a significant achievement for the HGP. It will be published in the journal Nature.

It comes as rumours circulate in the scientific community that an official announcement that the entire human genetic blueprint has been sequenced is just days away.

The announcement could be made at an important gathering of genome scientists on Thursday at Cold Spring Harbour Laboratory, Long Island, US.

Chromosome 21 is the smallest human chromosome comprising less than 1.5% of the entire human genetic code.

Extra copies of the chromosome result in Down's Syndrome, the most frequent cause of mental retardation. It affects one in 700 births.

Professor Yoshi Sakaki, who heads the Human Genome Project at Tokyo University, told the BBC he was particularly pleased to have completed the chromosome 21 work because he himself had Down's Syndrome relatives.

"We are now standing at the starting point of understanding the molecular mechanism of Down's Syndrome," he said. "I hope we can find effective therapies for patients in the coming 10 years."

Scientists say that chromosome 21 has 33,546,361 base pairs of DNA, incorporating 127 genes.