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Qiagen, Sentieon Extend Data-Analysis Partnership to Clinical Genomics


CHICAGO (GenomeWeb) – Qiagen and genomic analysis startup Sentieon are extending a fledgling partnership from the pharmaceutical and biotechnology realm into laboratory and clinical genomics.

The two companies today announced plans to integrate Sentieon's DNAseq and TNseq technologies for germline and somatic variant calling into Qiagen's CLC Genomics Workbench for biomedical research and the Qiagen Clinical Insight platform for lab testing.

This follows the recent embedding of Sentieon variant calling technology into several OmicSoft programs for pharma R&D. That deal actually predates Qiagen's January 2017 acquisition of OmicSoft, though the technology integration was not complete until August.

"We started out with Sentieon integrating it into our OmicSoft software, which is for research and discovery — a lot of pharma customers use this," said Frank Schacherer, vice president of products and solutions for the Qiagen Bioinformatics business unit. "Now we are taking the next step and integrating it also into the software stack that is more oriented toward biomedical and clinical applications."

The Qiagen-Sentieon relationship is a result of the OmicSoft acquisition.

"What made us realize the usefulness of the Sentieon solution is that OmicSoft is not just software. OmicSoft also provides access to standardized and unified data sets," including reprocessed data sets from the Cancer Genome Atlas, Schacherer said. "For that, we used the Sentieon software … and realized how much faster and cheaper it was to do it that way than if they had used some other tool set."

Qiagen expects to release CLC Genomics Workbench and Clinical Insight with integrated Sentieon technology by springtime. This combination should happen quickly because of the way the two companies build their technology.

"Sentieon is a tool creator," Brendan Gallagher, business development director of Mountain View, California-based Sentieon, explained. "We're enabling Qiagen to take our software and … put it wherever it makes sense to better serve their customers."

Both partners say their products far outstrip the capabilities of the month-old version 4 of the Broad Institute's Genome Analysis Toolkit and other free variant callers. "We have a drop-in improvement or replacement for those tools that offer better consistency and stability and support and compute efficiency," according to Gallagher.

In 2016, Sentieon won multiple awards in each of the two challenges run by the developers of the PrecisionFDA initiative. DNAseq was named the top overall performer for consistency and also had the highest reproducibility of all the software used for the challenge, beating entries from the Broad Institute, DNAnexus, and others. In the PrecisionFDA Truth Challenge, Sentieon's software had the best SNP recall and the highest indel precision of all competitors.

Sentieon also finished first in the ICGC-TCGA DREAM challenge for tumor-normal somatic variant calling in 2016.

Similarly, TNseq can process data at least 10 times faster than MuTect2 on multi-threaded servers and 20 times faster than a MuTect2 installation on a single-thread server, according to Sentieon data from that year.

"We're really a math and algorithm company focused on processing Illumina data, and we want to process it in the most accurate and efficient means possible," Gallagher said. "We do that through improved algorithm engineering and software development."

Gallagher said Sentieon tools are more stable than free, open-source alternatives. "If you're running GATK, it can crash," he said. Plus, Sentieon's technology addresses a shortcoming in GATK MuTect2 somatic SNP and indel tools, which down-sample sequences.

"If you run the same data through those tools twice, you can get different variants. It doesn't happen all the time, but it happens sometimes," according to Gallagher. "Our tool is pretty much always preferable because we don't do that. Sentieon never down-samples and always can process all the reads from a given sample."

Qiagen's Schacherer said that the integration "completes" his company's offerings in clinical and laboratory genomics. "It covers one of the gaps we had in the GATK-compliant data processing," he said.

"We want to be a good partner to our customers that can solve their bioinformatics problems. We want to be a partner that, if they have some problem with [next-generation sequencing] bioinformatics, they can come to us, whether it's RNA or DNA or low-throughput or high-throughput, we will find a good solution for them," Schacherer explained.

"Many testing laboratories prefer or would like to have a GATK-compliant workflow, essentially, and so that is what Sentieon easily enables for these customers. From the bioinformatics and Qiagen side, they get all the nice user interfaces and ease of usability that they already get from our platform in general."

He said that Qiagen and Sentieon are looking at making this technology "accessible" to additional applications.