The impact of IT on next-generation DNA sequencing

Ever wonder if you have a genetic disposition to a certain disease, or why a medicine works for your friend, but not for you? The answer might come sooner than you think. In the past couple of months, several significant breakthroughs in DNA sequencing technology have been made, giving hope to the researchers that a $1000 genome is just around the corner.

Since the completion of the Human Genome Project in 2003, which took over a decade and cost over $300 million, the idea of personalised medicine and using genetic testing for medical procedures has become much more of a reality. Decoding a whole human genome is far too costly, and so, several companies are in a race to develop the next-generation DNA sequencer that will drive down the costs of sequencing a person’s genome to $1000, and to win the $10 million Archon X Prize – awarded to the company that successfully sequences 100 human genomes in 10 days for $10,000 per genome.

In February 2008, Illumina claimed to sequence a human genome in four weeks for $100,000, only to be outdone five weeks later by its competitor, Applied Biosystems (ABI), which announced the sequencing of a whole human genome for less than $60,000. ABI also mentioned that its next-generation DNA sequencer is capable of generating up to nine gigabases per run, which is the highest throughput reported to date. Also in February 2008, Pacific Biosciences (PacBio) presented a revolutionary technology that within five years could produce a three-minute raw sequence, and a complete, high-quality sequence in 15 minutes — all for under $1000. PacBio plans to introduce a sequencing machine in 2010, but an instrument capable of performing the $1000 whole genome sequencing will not be available until 2013.

The rapid advancement of next-generation DNA sequencers has been possible due to vast improvements in computer technology, specifically in speed and size. But is this enough? These new systems produce enormous amounts of data – one run could generate close to one terabyte of data – and bioinformatics and data management tools have to play catch-up to handle the analysis and storage of this data.

Data management and storage will always be an issue for the life science and medical research industries, and is something that vendors will constantly have to improve to appease the research world. Luckily, there is hope for software vendors. Researchers will only begin to warm to the idea that next-generation technologies produce better data, and will provide time and cost savings, if there are adequate software applications to analyse the data.

To support software development, ABI has supplied the bioinformatics and software vendor communities with sample data sets, data file formats and data conversion tools. Other sequencing system providers should do the same if they want to provide their customers with the relevant software applications they need for next-generation sequencing projects. Software vendors should collaborate with the next-generation DNA sequencer providers, bioinformatics experts, and genomic researchers to develop research-specific — eg, whole genome sequencing, gene expression, microRNA discovery, microbial sequencing and genetic variation detection — software applications.

The $1000 genome has the potential to bring the genomic age to the physician’s office. At this price tag, DNA sequencing may become common for certain medical procedures — such as testing for cancer and developing treatments specifically for the patient — and one day, routine decoding at birth could provide parents with a genetic instruction guide to their children’s future ailments. But this concept of genome sequencing as a standard medical procedure raises several privacy issues, as there is nothing more personal than your genetic code.

Who should have access to this information and how easily attainable would this data be for others? For example, should only the patient and physician share this knowledge or should health insurance companies be privy to this valuable genome report? Technology vendors will have to work with the healthcare and medical industries to figure out the answers to these questions and then develop the appropriate security protocols. Healthcare and life science IT vendors should utilise the expertise of other industries, such as the banking and credit card industry, that also require high levels of security in their day-to-day workflow to aid in the development of software to ensure patient privacy.

Thus far, the race to the $1000 genome is neck and neck. Currently, the lack of software and sufficient data storage are major obstacles that next-generation sequence providers are attempting to hurdle. Technology vendors can help them cross the finish line faster by providing robust data management and storage systems and working with the healthcare and life science industries to develop relevant software applications. The research and medical communities are anxiously watching this race to the finish. Who will win the coveted $10 million Archon X Prize? Who will dominate this multi-billion dollar market?