CLN Article

Industry Playbook

Broad Institute Teams With Web and IT Giants on Genome Analysis Software

The Broad Institute of MIT and Harvard is collaborating with Amazon Web Services, Cloudera, Google, IBM, Intel, and Microsoft to enable cloud-based access to its Genome Analysis Toolkit (GATK) software package. Through these collaborations, the GATK Best Practices pipeline will be available to cloud service users through a software-as-a-service mechanism, expanding access beyond traditional desktop solutions.

“By providing a cloud-hosted solution, we can greatly expand access and facilitate usage of these genome analysis tools,” said Eric Banks, senior director of data sciences and data engineering at Broad and a creator of the GATK software package. “There are currently more than 31,000 registered users of the Broad Institute’s GATK. The vast majority set up an extensive local computer and storage infrastructure to process the huge amount of information required to conduct genomic analyses. These collaborations will provide new options that can remove traditional barriers of scale while offering the same high level of data quality.”

Broad will also work with these collaborators to drive the creation of GATK4, the next generation of GATK. GATK4 will use the Apache Spark distributed computing framework to facilitate parallelism and in-memory computations, thus speeding up the methods. GATK4 will also extend the range of use cases supported by GATK to include cancer, structural variation, and copy number variation.

Rheonix, NYUCD Partner on Rapid Zika Diagnostic

Rheonix and the New York University College of Dentistry (NYUCD) have joined forces to develop a rapid diagnostic for Zika virus infection. The National Institute of Dental and Craniofacial Research will fund the project with a $656,414 supplement to an existing Small Business Innovation Research Phase I/II Fast-track grant that the two organizations previously received. The Rheonix/NYUCD team intends for this rapid diagnostic to be a fully automated screening and self-confirming assay that will simultaneously detect and confirm the presence of Zika virus in a single, small sample of saliva or blood. The proposed approach will build upon previous work in which Rheonix and NYUCD developed a dual assay for the simultaneous detection of HIV antibodies and viral RNA in a single specimen. “The Zika virus appears to disappear from blood in six to 10 days, but is still detectable in saliva and urine,” said Daniel Malamud, PhD, professor of basic sciences at NYUCD. “Anti-Zika antibodies can be detected several days after infection. A combined RNA and antibody test will enable detection of both early and late Zika virus infections.”

DiaSorin to Buy Focus Diagnostics, Quest’s Immuno- and Molecular Dx Business

In the second quarter of 2016, DiaSorin plans to acquire Quest Diagnostics’ immunodiagnostic and molecular diagnostic products business, Focus Diagnostics, for $300 million in cash. As a result of this deal, DiaSorin will have access to a new set of molecular products cleared for distribution in the U.S. and Europe, including Focus’ Simplexa molecular product line, HerpeSelect HSV serology line, and DxSelect immunofluorescence antibody and ELISA assays. DiaSorin expects to continue to manufacture Focus products from the company’s base facility in Cypress, California, and hopes the acquisition will increase its presence in the growing market of infectious diseases molecular testing. It also plans to leverage its global commercial infrastructure to help the Focus business expand internationally. However, the acquisition does not include Quest’s diagnostic information service laboratories that currently operate under the Focus Diagnostics brand. These labs primarily serve hospital and biopharmaceutical companies, and will remain part of Quest.