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Gencove Bets On Low-Pass Whole-Genome Sequencing to Replace Genotyping Arrays

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SAN FRANCISCO (GenomeWeb) – Startup Gencove, which spun out of the New York Genome Center last year, aims to make next-generation sequencing more accessible by offering low-cost and low-coverage whole-genome sequencing services.

Joe Pickrell, co-founder and CEO, said that Gencove's expertise is in developing the imputation algorithms and informatics necessary to extract useful information from low-coverage sequence data. The result, he said, is a product that is cost-competitive with genotyping microarrays but with more data.

Previously, Pickrell had developed an app called Seeq for individuals who wanted to participate in genetic studies and get genetic ancestry data. Gencove is essentially Seeq with a different name, Pickrell said. In addition, the company is shifting away from the consumer ancestry business to focus on selling its services to academic, biotech, and pharmaceutical researchers instead.

Last year, the company raised $1 million in funding from early-stage technology investors and currently has five full-time employees.

Gencove now offers three products — its core 0.4-fold whole-genome sequencing product, 1x whole-genome sequencing coverage, and a custom designed product that combines one of the low-coverage sequencing products with increased coverage on specific targets. Pricing is $50 for the 0.4x genome, $90 for the 1x genome, and pricing varies for the custom product depending on the specific project.

Although next-generation sequencing is now ubiquitous, Pickrell said that many academic groups with plenty of sequencing capacity choose to use Gencove's service because of the customized library prep and algorithms. Library prep for low-coverage sequencing is different in that it relies on miniaturization, which enables less input material to be used, Pickrell said. But, the main advantage that Gencove says it offers is in the imputation algorithms. "There were not existing tools to do that," Pickrell said, "so we developed our own."

The imputation algorithms use statistics to infer a specific genotype using known haplotypes from other datasets, like the 1,000 Genomes or HapMap datasets. The method has a cost advantage over deeper sequencing and also has an advantage over genotyping microarrays because it generates more data and it does not rely on an a priori set of known variants, Pickrell said. 

"A lot of genotyping arrays have biases in that they look only at variants previously discovered in European populations," Pickrell said. But, whole-genome sequencing can be used regardless of ancestry, and despite sequencing to low coverage, novel variants can still be discovered if the sample size is large enough.  

Pickrell said that the group has done some pilot projects and determined that when sequencing to 1x coverage, a variant needs to be present about 10 times in order to confidently call it. He added that the firm does plan to publish results of its work, but did not yet have a timeline for that.

Although Gencove's first product was an ancestry test geared toward individual consumers, Pickrell said that the company has decided to change its focus to the research market, and as a result will suspend its individual ancestry service in June. 

After launching the consumer product, Pickrell said the company began hearing from researchers interested in using the service for studies where genotyping arrays would traditionally be used. "We had to make a decision on where to allocate resources," Pickrell said.

The company has disclosed three projects it is currently involved in: collaborations with the Broad Institute, the University of Michigan, and the Baker Institute's Systems Genomics Laboratory in Australia.

With the University of Michigan, Gencove is using its platform to do genome-wide association studies to calculate risk of certain diseases in conjunction with an ongoing study at the university on income dynamics. With the Baker Institute, it is studying risk for celiac disease, and with the Broad Institute, Gencove is working to develop imputation algorithms that can be used for dog genetics.

Currently, Gencove is a service-based company, but Pickrell said that the firm is considering developing the software into a kit that could be sold as a standalone product. In addition, he said that while currently the services are research use only, he anticipates that low-coverage whole-genome sequencing could eventually be used for clinical purposes, adding that moving into the clinical space is "definitely on the roadmap" and would likely take the form of a partnership with a hospital system. Whether the company would develop diagnostic-based tests or focus more on disease risk prediction is still being considered.

In terms of competition, Pickrell said that although other companies are not currently offering low-coverage sequencing services, the main competition is in the genotyping array market. The array market has seen somewhat of a resurgence in recent years due to growing consumer demand for ancestry and health-based tests from companies like 23andMe and Ancestry.com.

Pickrell thinks that Gencove will be able to compete in the research market on price and because sequencing inherently provides more information than arrays. In addition, it would likely compete with research groups already doing genotyping-by-sequencing. Although not as widespread as microarrays, several groups have developed genotyping-by-sequencing pipelines, and researchers particularly in the crop and livestock genomics space have turned to genotyping-by-sequencing.

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