By Julia Karow
Life Technologies last week launched a competition for users of its SOLiD system, offering a $1 million prize to the first user who succeeds in sequencing the genome and transcriptome of a single cancer cell.
The competition is part of Life Tech's $7 million "Grand Challenges" prize program, launched late last year, which also includes three programs to improve technical aspects of the Ion Torrent PGM and three that have not yet been announced (IS 12/14/2010).
"We really feel that there is a need for single cell work," said Michael Rhodes, senior product manager for genetic systems at Life Tech. "We know that in the cancer field, there is a lot of interest in working in single cells or small groups of cells."
Contestants will have to isolate a single cancer cell from a liquid or solid human cancer and sequence at least 85 percent of its genome and 80 percent of its transcriptome, using the SOLiD 4 or 5500 series SOLiD.
Participants will also have to validate their data experimentally, using the bulk of the cancer, for example by showing that the cell they captured actually came from the cancer; that they have called a "reasonable proportion" of the SNPs, both homozygous and heterozygous; and that the RNA balance measured matches that present in the cell originally. Participants are asked to submit a validation plan when they enter the competition.
Life Tech would like contestants to use its LifeScope software, which it developed for the 5500 series SOLiD, to map the reads and do some of the initial data analysis, although the company realizes that researchers may need to develop some of their own algorithms for further analysis.
To claim the prize, contestants also need to publish their findings in "a major journal," according to Rhodes. They also need to sign any intellectual property developed as part of the challenge over to Life Tech.
Unlike the three challenges Life Tech has launched for the Ion Torrent PGM, this one is not focused on improving the SOLiD platform itself but on sample preparation and analysis methods. It will build on published work on single-cell analyses using the SOLiD system (IS 7/13/2010).
Some of the biggest challenges of the latest contest will be to separate DNA and RNA from the same cell and to amplify the entire genome, according to Rhodes.
Life Tech does not necessarily expect a winner to emerge soon. "It could take several years," Rhodes said. After a year, the company plans to review the competition and to raise the bar if the technology has already moved on beyond the current specifications.
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