Qiagen Buys Ingenuity to Provide Software Complement to Molecular Testing Solutions

Qiagen said this week that it acquired Ingenuity Systems for $105 million in cash in order to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions — from sample preparation to data interpretation.

Under its new parent, Ingenuity will continue to operate out of its offices in Redwood City, Calif., and retain all 120 current employees, while CEO Jake Leschly takes on new responsibilities within Qiagen's life science business unit.

Ingenuity will also continue to develop and offer products under its existing licensing scheme. Its portfolio includes a knowledgebase of curated genomic variants; Ingenuity Pathway Analysis, its web-based application for modeling and analyzing biological pathways; Ingenuity Variant Analysis, which selects clinically relevant genomic variants from NGS data (BI 1/13/2012); and Ingenuity iReport, its software for reporting the results of gene expression experiments from RNA-seq, microarray, and qPCR platforms.

Qiagen plans to incorporate content from Ingenuity's knowledgebase into a curated database that it sells with wet lab assays offered through its GeneGlobe portal — which provides access to hundreds of PCR- and NGS-based assay panels for exploring pathways and diseases such as cancer, cardiovascular disease, and central nervous system disorders. In total, GeneGlobe offers more than 60,000 annotated molecular assays.

Also, Qiagen later this year plans to begin offering an integrated workflow that will provide its customers with kits for sample and library prep, target enrichment, and sequencing, as well as informatics support. Its software component will include solutions that are currently being developed with German software-development firm SAP for sequence read alignment and variant calling (BI 7/6/2012) and Ingenuity's variant analysis and interpretation tools.

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Thermo Fisher to buy Life Technologies for $13.6B

Thermo Fisher Scientific Inc. has offered to pay about $13.6 billion to buy genetic testing equipment maker Life Technologies in a cash deal that will create a giant company serving research and specialty diagnostics.

The Waltham, Mass., company said Monday it has agreed to pay $76 in cash for each share of Life Technologies, which is based in Carlsbad, Calif.

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FDA Approves Dako Assays as CDx for Genentech Breast Cancer Drug

Dako today said that the US Food and Drug Administration has approved two assays for use as companion diagnostics for a Genentech drug targeting HER2-positive metastatic breast cancer.

FDA simultaneously approved Dako's HercepTest and HER2 IQFISH pharmDx assays and Genentech's drug Kadcyla (ado-trastuzumab emtansine).

Kadcyla is for patients with HER2-positive metastatic breast cancer who have been previously treated with Genentech's Herceptin (trastuzumab) and a taxane chemotherapy.

Dako, an Agilent company, and Genentech, a Roche company, have been collaborating on the development of companion diagnostics for Genentech's drugs for a few years. In May 2012 the two firms inked a pact to collaborate on the FDA submission of Dako's assays for Kadcyla.

A month later the HercepTest and HER2 FISH pharmDx were approved by FDA as companion diagnostics for Genentech's breast cancer drug Perjeta (pertuzumab). In late 2011, FDA gave the thumbs up to Dako's HER2 CISH pharmDx kit as a companion diagnostic for Herceptin in the treatment of breast cancer patients.

And in 2010, the agency approved the use of HercepTest and HER2 FISH pharmDx to help guide treatment of patients with metastatic gastric or gastroesophageal junction adenocarcinoma with Herceptin. cancer

Interesting story about Nicholas Tatonetti & his New Computational Tools to Study Drug Effects

Courtesy Genomeweb & Julia Karow
 
Studying for a dual degree in mathematics and molecular biology, Nick Tatonetti became interested in using computational models to study biology and make sense of its massive datasets. As a bioinformatics PhD student at Stanford, he developed new statistical models and computational approaches for analyzing drug effects and drug-drug interactions.

At Columbia, Tatonetti is now focusing on molecular mechanisms of drugs. "We can actually think of each time a patient is being given a drug as an experiment," he says. "When the drug goes into the human system, it interacts molecularly, and then phenotypes come out of this system," which can be connected to molecular mechanisms in new ways.

In particular, he is developing techniques that use clinical data to develop networks that highlight interactions between different systems in the human body, such as two organs. "And once we know that certain gene products or pathways are working together at a systems level, we can start integrating all of the molecular data we know to fill out a complete picture" and to predict phenotypes from, for example, RNA expression data or genotypes, he adds.

Paper of note

A study revealing a new drug-drug interaction by using a machine learning algorithm Tatonetti designed that scanned through millions of adverse event reports from the Food and Drug Administration appeared in Science Translational Medicine this year. That is his favorite paper, he says, "because it represents the most comprehensive innovations on both the algorithmic side and the evaluation side."

Looking ahead

Tatonetti says that over the next five years, there will be major advances in using genetic data in medicine. "It may not be that we need to store lots of genetic data in the clinical record, but that we need to understand the genetic data better so that we can provide results and suggestions to physicians," he says. Personalized medicine will not only involve genotypes, though, but also environmental exposures. Putting genetics into the context of these, he says, will increase its clinical impact.

And the Noble goes to…

If he were to win the Nobel, it would be for developing a new scientific approach, based on informatics methods and computational methodologies, that discovers a fundamental biological or medical truth. "Where that truth may be, in what system, in what disease, I could not say, but I love the idea that we're in the midst of changing the way that we do science," Tatonetti says. "That's what informatics is about, advancing the tools of the scientific method itself."

NextBio Teams Up with Emory, Aflac, to Locate Biomarkers for Pediatric Brian Tumors

NextBio said this week that it is partnering with Emory University’s Winship Cancer Institute and the Aflac Cancer Center to work on identifying biomarkers that can predict brain cancer metastasis in children, which will help clinicians determine which patients should receive radiation therapy.

The partners will use NextBio Clinical software to analyze and interpret molecular and genomic data collected from children with medulloblastoma, a childhood brain tumor that affects around 500 children in the US every year and accounts for 20 percent of all brain cancers in children below the age of 19.

Specifically, “this study will look at clinical and genomic data from real patients, as well as data from mouse models and frozen human tissue samples, and then will correlate these data sets with other data from the public domain,” Alpana Verma-Alag, NextBio’s head of clinical development, explained in a statement.

Tobey MacDonald, director of Aflac’s brain tumor program and associate professor of pediatrics at Emory, noted that there is currently no way to tell which patients have a higher risk of metastasis and as such all children suffering from medulloblastoma receive radiotherapy even though “it causes long term side-effects and toxicity in young growing brains.”

“[The] ability to perform genomic studies on patients and then to use NextBio Clinical’s correlation engine to compare the genomic profile of primary tumors with that of metastatic tumors, both across our data and across the large amount of data that NextBio has curated from the public domain, makes achieving our goal of improving outcomes for people with medulloblastoma seem nearer in sight,” he said in a statement.

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