Rapid advances in gene sequencing using Ion Torrent PGM sequencer
21 Feb 2011
Life Technologies Corporation has announced that just six weeks following the launch of the Ion Torrent PGM sequencer, independent researchers have presented data generated with the system at the annual Advances in Genome Biology and Technology (AGBT) conference.
The presentations demonstrated both the simplicity and speed of the Ion Torrent system — to data from delivery in six weeks — as well as how rapidly a user community is forming around the technology.
The vendor community is also embracing Ion semiconductor sequencing technology because the system’s simplicity and affordability is opening the sequencing market to tens of thousands of researchers and clinicians. Companies including Diagenode, CLC bio, Partek Inc., DNASTAR and BioTeam are partnering with Ion Torrent to provide innovative upstream and downstream solutions accessible to all researchers.
“When you democratize something, you can build a community, and that’s what we’re rapidly seeing develop around Ion Torrent, on both the user and the vendor side,” said Dr. Jonathan M. Rothberg, founder of Ion Torrent. “Ion Torrent’s speed, simplicity and scalability are enabling fast results and rapid application development as both of these communities see the advantages of semiconductor based sequencing.”
Ion semiconductor sequencing, which is at the heart of the Ion Personal Genome Machine (PGM) sequencer has already demonstrated a consistent 10x improvement in throughput every six months during the system’s development, and continued increases along that trajectory promise to radically transform DNA sequencing for all scientists.
Data generated on the Ion Torrent PGM sequencer and presented at AGBT focused on the sequencing of amplicons, microbial genomes and barcoded samples.
Applications developed by the Ion Torrent community are focusing both on solutions that lie upstream and downstream of DNA sequencing.
Upstream solutions: amplicon and genome sequencing
“The potential speed and simplicity of the system we hope will allow us to analyze multiple samples in an efficient manner,” said Dr. Iafrate. “These features would be essential for incorporating high-throughput sequencing technologies into clinical applications.”
Dr Joe Boland, with SAIC-Frederick Inc., is using the Ion PGM system in conjunction with the Fluidigm Access Array System to perform multiplex amplicon sequencing. He used this combination to rapidly and economically sequence multiple amplicons — up to 48 different bar-coded samples in a single Ion Torrent PGM run — with minimal hands-on time.
For researchers interested in sequencing whole genomes, Life Technologies has partnered with Diagenode who has a long history of providing world-class DNA fragmentation tools. Diagenode’s Bioruptor, which uses a unique system to uniformly process multiple samples, has been extensively validated to quickly generate unbiased genomic fragments suitable in the creation of DNA libraries for the Ion PGM at an entry cost accessible to any laboratory.
Downstream Solutions: data analysis and management
Ion Torrent is also partnering with CLC bio, Partek and DNASTAR, three companies that have a long history of delivering world-class bioinformatics solutions and services.
“I generate and analyze my own data and by using bioinformatics tools from companies like DNASTAR and Partek, I’m able to significantly decrease my time to results and focus on the next experiment rather than struggling through data analysis,” said Dr. Long Le, Clinical Pathology Resident and Molecular Fellow at Massachusetts General Hospital.
Data management can also be a significant hurdle for many scientists, so Life Technologies has partnered with BioTeam, a consulting firm dedicated to helping researchers choose the best platform for their IT, storage and data management needs.
In addition to partnering with leading vendors, Life Technologies has also created the Ion Community, a web-based forum for the scientific community to develop robust solutions that leverage the full potential of Ion semiconductor sequencing. Resources include sample data, protocols, source code, data formats and discussion forums. The Ion PGM sequencer is also the first subject of the Life Grand Challenges $7 million crowd sourcing initiative.
About the Life Grand Challenges Contest
The Life Grand Challenges Contest is a first-of-its-kind crowd sourcing initiative focused on the life sciences tools and technology industry. The goal of the US$7 million competition is to unlock even bigger opportunities the company is witnessing, while accelerating innovation within the life sciences community.
There will be seven individual challenges, each with a $1 million prize. The first three challenges are focused on Ion semiconductor sequencing. The fourth challenge is focused on SOLiD sequencing. The remaining three challenges will be related to Life Technologies products and will be announced later in 2011.
The three Ion challenges, which are to use the Ion Personal Genome Machine, are to:
- produce twice as much sequence data;
- do it twice as fast; and
- do it with twice the accuracy.
The SOLiD challenge is to sequence both the genome and the RNA content of a single cancer cell using the 5500 Series SOLiD Sequencers, effectively doubling the biological readout that is currently achievable by sequencing a single cell.
The judges for the first three Grand Challenges include Dr Rothberg, Dr Sidney Altman, who shared the 1989 Nobel Prize in Chemistry and Professor Sir Aaron Klug, who won the 1982 Nobel Prize in Chemistry.