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Startups Develop DNA Sample Prep Methods


Two startup companies are entering the DNA sample preparation market, and are working on applications for constructing second-generation sequencing libraries.

Boreal Genomics rolled out its first instrument to early-access customers last year. The system uses the company's Synchronous Coefficient of Drag Alteration technology for electrophoresis-based nucleic acid purification. In late January, the company presented a second instrument, Aurora, which includes certain improvements, at the Lab Automation meeting in Palm Springs, Calif.

Meanwhile, Sage Science is developing an automated preparative system for electrophoresis-based DNA size fractionation and DNA extraction, called Pippin Prep, which it hopes to launch in about a year.

While Boreal is using rotating electric fields to selectively concentrate nucleic acids in a gel and separate them from contaminants, Sage is aiming to automate the standard lab procedure for preparing nucleic acids from an agarose gel.

One application both companies are pursuing is the purification of size-selected DNA fragments for sequencing libraries for the Roche/454, Illumina, and Applied Biosystems SOLiD sequencers.

Boreal Genomics, based in Vancouver, BC, spun out from Andre Marziali's lab at the University of British Columbia. The company is based on technology invented by Marziali, an associate professor at the university, and a colleague. It uses alternating electric fields to move charged molecules in a gel or fluid.

In a collaborative proof-of-concept study, Marziali and his collaborators discovered approximately 200 new organisms by extracting and sequencing DNA from tar sand where other DNA-purification methods had failed.

After removing petroleum from the sample, "we threw the sand and everything else directly onto our instrument, and in one step we got DNA out that was clean enough [for cloning and sequencing]," says Marziali.

Julia Karow

Sequencing Notes

A scientific team led by researchers from the Joint Genome Institute and Stanford University sequenced the complete 730 million-base genome of biofuel candidate Sorghum bicolor. The paper reporting the team's findings was published in Nature.

Scientists at the J. Craig Venter Institute, three branches of the Ludwig Institute for Cancer Research, and New York's Memorial Sloan-Kettering Cancer Center used Roche 454 transcriptome sequencing to look for translocations in a highly rearranged breast cancer cell line. In the process, they identified seven new genomic rearrangements — five truncations and two chimeric proteins — believed to affect at least nine genes. The study was published in PNAS.


7 days
Length of a trial in which the jury unanimously decided that the Applied Biosystems SOLiD sequencer does not infringe an Illumina patent

Funded Grants

$234,000/FY 2008
Robust Methods for the Efficient Analysis and Integration of DNA Sequence Data
Grantee: Andrew Allen, Duke University
Began: Sep. 26, 2008; Ends: Jun. 30, 2011
Allen was funded by the National Institute of Mental Health to "develop a novel class of sequence-based haplotype sharing statistics that exploit the implications of DNA sequence evolution in testing for variant/disease association," according to the abstract. He will also "develop a statistical framework that allows for the unified analysis of DNA sequence and genotype data."

$230,250/FY 2008
Targeted CRT sequencing of 1000 genes in KPD patients
Grantee: Michael Metzker, Baylor College of Medicine
Began: Aug. 1, 2008; Ends: May 31, 2010
NHGRI awarded Metzker this grant to "evaluate the feasibility of our next-generation, cyclic reversible termination (CRT) sequencing approach by targeting 1,000 candidate genes on high-density oligonucleotide chips," the abstract says. Candidate genes will be chosen based on the ones most likely to help elucidate the mechanisms behind diabetes.

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