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
Applications developed by the Ion Torrent community are focusing
both on solutions that lie upstream and downstream of DNA
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