Applied Biosystems offers commentary about discovery of increased genetic variation in human genome

This month in PLoS Biology (vol. 5, issue 10), researchers published results from the sequencing of the first human diploid genome; all the DNA from both sets of chromosomes. This landmark sequencing study has shed light on how scientists will carry out future analyses of human genomes. The study revealed that there is as much as five times more genetic variation between two individuals than was previously estimated. To understand how that variation contributes to disease or individual response to treatment for disease, researchers will need to identify the amount, kind, and specific location of variations within the genome.

At the Genome, Medicine and the Environment meeting, a three-day gathering of many of the world’s leading genomics researchers, Kevin McKernan, PhD, one of the inventors of the SOLiD™ System, Applied Biosystems’ next-generation DNA sequencing platform, today said that this discovery will fundamentally change the way people approach and conduct genomics-related research. As a result, life scientists using next-generation sequencing technologies to pursue the study of complex genomes will require systems capable of addressing this increased genetic variation.

The majority of genetic differences between individuals are represented by single base changes, or single nucleotide polymorphisms (SNPs), which are scattered throughout the approximately 3 billion bases of the human genome. In the PLoS Biology study, researchers identified more than 1.2 million previously unknown genetic variants, including SNPs and structural variants. Dr McKernan believes that high throughput, scalability, and accuracy of emerging genetic analysis technologies will be the ultimate success factors for associating this increased genetic variation with how individuals respond to treatments for disease.

“This finding is a calling for us to raise the bar, to usher in the next-generation life sciences era, in which highly sophisticated technologies will be required to fulfil the promise of next-generation sequencing,” said Dr McKernan, a senior director for Applied Biosystems’ molecular and cell biology division. “To unlock the hidden knowledge in complex genomes, researchers will need ultra-high throughput platforms capable of producing highly accurate sequence data and the ability to scale those systems to support future studies of increasing complexity.”

Next-generation sequencing platforms capable of ultra-high throughput will become more common for the study of complex genomes because as the technologies mature, the cost of analysis will continue to decrease. As part of its continued development of next-generation sequencing technology, Applied Biosystems, an Applera Corporation business, today announced that the SOLiD System is currently the industry’s highest throughput next-generation sequencing platform. In Applied Biosystems’ development laboratories, the SOLiD System has generated sequence data that has exceeded 4 gigabases (GB). This sequence data has been shared with some of the company’s early access customers and collaborators. This output of sequence per run surpasses the number of bases that comprise the entire human genome, which makes this system effective for carrying out whole human genome studies.

Applied Biosystems achieved this advanced throughput by enriching the beads on the system. Beads are an integral part of the SOLiD System’s open-slide format architecture, enabling the platform to be scaled to support a higher density of sequence per slide. The combination of the open-slide format, bead enrichment, and software algorithms provide the infrastructure for allowing it to scale to even higher throughput, without significant changes to the platform’s current hardware or software. Applied Biosystems’ development team reports that, over the past 15 months, the SOLiD System has doubled its throughput every three months. Dr McKernan and the development team believe the system’s architecture may support even higher levels of throughput that will facilitate the study of complex genomes.

Along with the scalable bead technology, mate-paired library preparation is a method that enables highly accurate mapping and sequence assembly. This combination, which is unique to the SOLiD System, helps researchers to cost effectively identify specific genomic regions where structural variations are located. This is significant because a key finding of the individual human genome study revealed that structural variation accounts for almost 74% of the variant DNA sequence in the human genome.

A key to understanding structural variation is the ability to visualise structural rearrangements, such as gene copy number variations, single base duplications, inversions, insertions, and deletions. The SOLiD System is currently generating read lengths of 35 base pairs – a 30% increase from six months ago – which increases the accuracy of locating where both single base and structural variation occurs.

Increased read lengths provide researchers using the SOLiD System a raw base accuracy greater than 99.94% due to two-base encoding, a mechanism that discriminates random or systematic errors from true SNPs. This represents a five-fold better performance than any data currently published to date on alternative next-generation platforms. Applied Biosystems believes that in order to understand the role of genetics in health and disease, researchers will need a robust next-generation sequencing system that can identify the location of structural variation in genomes.

“We recognise the paradigm shift created by the PLoS Biology study and believe that technical advancements made to the SOLiD platform uniquely position it to address the increased genetic variation in the human genome,” said Dr McKernan. “We expect that the advancements to the throughput, accuracy, and scalability of the SOLiD System will enable researchers to make more meaningful associations between genetic variation and medical conditions. This is expected to be crucial in the emerging era of personalised medicine.”

Applied Biosystems is a global leader in the development and commercialisation of instrument-based systems, consumables, software, and services for the life-science market and is the recognised market leader in the commercialisation of DNA sequencing platforms.

In the study that reported the first sequencing of an individual’s diploid genome, researchers used Applied Biosystems’ 3730xl DNA Analyzers and BigDye^® Terminator chemistry to sequence the DNA. By having a diploid genome, the researchers were able to compare DNA from both sets of chromosomes, which revealed the amount of genetic variation. This was the same DNA sequencing platform that helped scientists to sequence the first human genome, a composite genome of several individuals.

In developing the SOLiD System, Applied Biosystems continues its leadership in DNA sequencing by commercialising a technology that helps scientists to better understand and treat disease based on genomic information. Applied Biosystems will officially announce the commercial availability of the SOLiD System later this month.