Population Genetics Technology has launched a competition inviting researchers to submit research proposals for population genetics studies that take advantage of the company's technology for doing large-scale pooled targeted sequencing studies.
Frank Massam, the company's chief commercial officer, told In Sequence that the competition will "showcase the ability of our technologies to make such studies feasible," as well as support laboratories that may not be able to afford to analyze the "thousands of samples" required for solid associations.
He added that he expects the majority of applications to come from clinical academic labs that want to analyze several thousand human samples. However, he said, the company has increasingly seen interest from labs doing ag-bio-related studies and microbial sequencing.
Potential applicants for the Populus 2012 award should submit a proposal by Nov. 30 and the company plans to announce a winner in January. Massam said the decision will not be based on the size or cost of the project, but rather its scientific merit. Population Genetics plans to make just one award, but Massam said that could change after seeing the proposals. Additionally, he said the company is considering offering the award on an annual basis.
The company has three different propriety technologies that it uses to prepare large numbers of samples for sequencing — GenomePooling, Reflex, and VeriTag.
Its GenomePooling technique is used to select multiple regions scattered throughout the genome, Massam said. "We'll take thousands of whole genomes, fragment them, then tag the fragments with a unique identifier," he said. After that, the regions of interest are extracted, and then the pooled DNA is sequenced.
The company validated its GenomePooling technology earlier this year in a pilot study analyzing pediatric acute lymphocytic leukemia samples. The company tested the GenomePooling technology across 28 genomic regions from 50 samples, including 40 patient samples and 10 cell lines, demonstrating that it could detect variants in mixed tumor tissue.
The pilot was done as part of a collaboration Population Genetics has with the IntReALL consortium — a group of 23 research teams studying pediatric acute lymphocytic leukemia relapse cases — to identify and validate biomarkers for disease risk and treatment efficacy. Massam said that clinicians are now recruiting patients for the next phase of the study, which will start in a few months.
The Reflex technology is similar to GenomePooling, except that it analyzes longer contiguous segments of DNA — around 10 kilobases to 15 kilobases long. That enables researchers to look at "an entire gene, or one long contiguous haplotype across multiple samples simultaneously," Massam said.
Finally, the company has a technology, known as VeriTag, which can be used in combination with these other two methods. VeriTag can help improve the accuracy of variant calling and distinguish between rare variants and sequencing errors.
The company published the method last year in Nucleic Acids Research and has used it in collaboration with academic groups and pharmaceutical companies in several population genetic studies, including a study investigating genetic predisposition to Alzheimer's disease (IS 5/10/2011).
The UK-based firm specializes in sample-prep and pooling methods and contracts out the actual sequencing. Massam said that the methods are platform-agnostic and can be used with any sequencing platform the customer wants. Illumina is the most common sequencing platform, he said, but for applications where long reads are required, customers request Roche's 454, and there are increasingly requests for Ion Torrent runs.
Massam said the firm has no plans to purchase a next-gen sequencing instrument of its own. "Sequencing is an established commodity now, so we just outsource the best available for the project being considered," he said.
The company contracts sequencing out to several different providers, including local universities. "We have a staple of service providers for each of the different platforms," he said.
Currently, most of the company's customers are researchers who have already done genome-wide association studies to identify candidate regions that they want to examine more closely with next-gen sequencing, Massam said.
The vast majority of the company's projects are focused on human samples, but Massam said that since Syngenta participated in its $5.7 million financing round a year ago (IS 10/18/2011), it has started looking into applications for ag-bio, such as trait improvement and genome characterization studies.
As part of Syngenta's investment, the companies are collaborating on the use of Population Genetics' technology in plant breeding studies, work that Massam said is still ongoing.
The firm last year also inked a deal with contract research organization Quintiles to apply its technology within clinical trials (CSN 5/17/2011).