Daunting challenges ahead for genetics: J. Craig Venter

We're almost 10 years on from the joint announcement by J. Craig Venter and Francis Collins that the first human genome has been sequenced, and the science and technology of genomics has improved at breathtaking speed.

Yet today's genetics researchers still face tremendous challenges in pushing the field ahead, says Venter, writing in a special edition of Nature.

"The challenges facing researchers today are at least as daunting as those my colleagues and I faced a decade ago," he wrote.

One of great advances is the increase in speed and decrease in cost of producing a complete genome.

The publicly-funded Human Genome Project cost upwards of $US3 billion and took years to complete in a massive worldwide effort.

Just a decade later we have genome sequencing technology arriving on the market that can sequence a human genome for less than $US6,000 in just one day.

However, Venter warns that this speed comes at the cost of data quality. New sequencing technology performs very short reads - of around 100 base pairs at a time - compared to earlier, slower, technology that read from 500 to 900 base pairs per read.

The challenge then becomes stringing each of these tiny fragments together in the correct order to make up the entire genome.

Venter warns that the current practice of using an existing genome as a 'reference' to help align the individual reads risks giving a distorted view of any single genome

He stresses that data quality needs to be improved if we're to progress genomics to the point of understanding the link between genes and disease.

"Improving data quality is crucial, because if a human genome cannot be independently assembled then the sequence data cannot be sorted into the two sets of parental chromosomes, or haplotypes. This process - haplotype phasing - will become one of the most useful tools in genomic medicine," he wrote.

This is the objective of another global genomics effort, the International HapMap Project.

Venter also warns that the pace discoveries in genomics risks outpacing our understanding of the other end of the spectrum: phenotypes.

"Phenotypes - the next hurdle - present a much greater challenge than genotypes because of the complexity of human biological and clinical information."

Even if we had the detailed information about genotypes and phenotypes we wouldn't have the computational power to link it all together.

Venter recommends we build an 'exascale' supercomputer, which would run 1,000 times faster than today's fastest supercomputers.

The genomics revolution is only beginning, but Venter expect it to progress dramatically in the next decade, to the point where we don't just have a single genome for each individual, but multiple genomes covering all aspects of our bodies and internal flora.

"The genome revolution is only just beginning," says Venter.