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Sequencing at ‘Biblical Proportions’


The University of Queensland’s Sean Grimmond gets the first peek at Ion Torrent’s new technology.

By Fiona Wylie

August 2, 2011 | BRISBANE, AUSTRALIA—Sean Grimmond, director of the Queensland Centre for Medical Genomics at the Institute for Molecular Biosciences in Brisbane, was the first lab in Australia to obtain (pre-market) the Personal Genome Machine (PGM) from Ion Torrent.

Unlike second-generation sequencing platforms, Ion Torrent’s technology foregoes optics, lasers, and cameras to quantitatively measures changes in pH generated by hydrogen ions released during nucleotide incorporation. “Relative to how much of a particular base is added, you get a quantitative difference in the amount of hydrogen ions released,” says Grimmond. Those pH spikes are translated into base calls and nucleotide sequence within a matter of seconds. The PGM is essentially a sophisticated pH meter. The chip inside comprises millions of tiny wells for the samples sitting on millions of tiny electrodes. The PGM offers several advantages says Grimmond. “The data file sizes are small, and the way it actually analyzes and measures the nucleotide incorporation is quick. Generating reads of about 120 bases takes less than two hours.”

Moreover, he says, “Converting changes in pH directly into a base call means much smaller files sizes” than other 2nd-gen platforms. “You really could run those machines pretty well all year without emptying the hard drives, whereas we run the SOLiD machine twice and then we have to move data to make more room.”

Scaling Up

The early PGM machines come with a “314” chip, containing about 1.2 million wells and matching electrodes. A newer “316” chip (6-8 million wells) is about to be released, and within a year Ion Torrent is planning to release the “318” chip which will comprise some 25 million wells (Ion Torrent says it is aiming for read lengths of 400 bases). Each new chip offers a theoretical tenfold increase in sequence throughput.

“Using the exact same machine and sequencing platform, you can go from generating 1 million base reads to 25 million reads, and with that many wells, we are getting into the 1-gigabasepair range of data in around two hours,” says Grimmond.

The SOLiD instruments generate about 100 Gb over two weeks and are still Grimmond’s preferred choice for sequencing human genomes. “But for smaller and more tractable sequencing applications such as the transcriptome or microRNAs, or candidate DNA mutation analysis, or microbial genomes, the PGM is ideal,” he says.

Grimmond leads Australia’s effort as part of the International Cancer Genome Consortium (ICGC). In the ICGC program, the PGMs are validating patient mutations initially detected using SOLiD instruments and to address questions of clinical significance. “For example, we can now do very deep sequencing on samples from the tumor margins using primers that will detect every mutation found in the parent cancer, and in this way more closely define the risk of metastases—this is particularly critical in the case of pancreatic cancer,” says Grimmond.

The PGMs are also helping to validate every DNA variant found in the cancer genomes. “We can cut some corners to pick up some of those variants, but for the novel ones we really need validate around 200 mutations per individual. Ion Torrent allows us to automate our primers, hone in on the regions that we think will have mutations, PCR them up and sequence them all on the chip and then move on to the next one quickly and easily,” says Grimmond.

“If they can make a silicon chip that determines DNA sequences the size they are now and sell it for ~$200, and you can generate enough long reads, it would be very easy to make a bigger chip that could generate a human genome in two hours,” says Grimmond. “The detection system needed is virtually already built—they just have to work out how to get the molecular biology down to fit in with the more and more sophisticated chips.”

Grimmond predicts, “we will be reaching data sizes of ‘Biblical’ proportions in the near future—then you really might start seeing one on every bench.”  

This story originally ran in Australian Life Sciences, and also appeared in the 2011 July-August issue of Bio-IT World.
 
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