Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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 H...

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 produc...

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 prog...

BGI-Shenzhen today said that it has extended its offer to acquire Complete Genomics for around $118 million until midnight New York City time on Dec. 14. BGI's tender offer to acquire all of the shares of Complete Genomics was previously scheduled to expire today. As of the close of business last night approximately 15.4 million shares of Complete Genomics' common stock, or 44 percent of its outstanding shares, were tendered and not withdrawn. The extension of the offer last night coincided with a letter Illumina sent to Complete Genomics' board of directors urging them to reconsider Illumina's offer to acquire the firm for around $123 million. Earlier this week Illumina confirmed that it had made an unsolicited offer of $3.30 per share to acquire Complete Genomics. That offer is 5 percent higher than the price agreed between BGI and Complete Genomics. Complete Genomics turned down Illumina's offer saying that it would likely be turned down by regulator...

Wow this an interesting article enjoy it! With the increasing ubiquity of smartphones, the growing popularity of tablets, and the burgeoning market for third-party applications, the public appetite for touchscreen technology is virtually impossible to ignore. It shouldn't, then, surprise anyone that bioinformatics software developers would look for ways to tap into the multi-touch market. But it's not just about making sure that download tallies are going up. In fact, some life science application developers say they dipped into the app space out of sheer curiosity more than anything else.   "For us, it was an experiment," says Andrew Su, an associate professor at the Scripps Research Institute. His laboratory developed an application called BioGPS, a mobile version of his group's web-based gene annotation portal, which runs on Apple's iPhone. "We imagined that somebody in a meeting or a seminar or at a conference who needed quick access to ...

Courtesy Xconomy After merging with Symyx Technologies in 2010, acquiring Contur Sofware in 2011, and buying VelQuest earlier this year, San Diego scientific software developer Accelrys says today it is buying Aegis Analytical. Accelrys is paying $30 million in cash for Aegis, a company based in Lafayette, CO, (near Boulder) that makes software used to monitor biotech product development and manufacturing processes. In a  statement  today, Accelrys says the deal helps to further expand its suite of software used to manage the life cycle of innovation among pharmaceutical companies and in other industries. Aegis has about 40 full-time and contract employees, and “the idea is to keep the business in Boulder and fairly intact,” Accelrys CFO Michael Piraino told me during a phone interview earlier this afternoon. Aegis CEO Robert Di Scipio will stay with the merged company through the transition to new ownership. About two-thirds of Acce...

wwwtilda Data manager in computational material science Introduction Tilde (wwwtilda, ~) is a data manager in cheminformatics and computational material science. The nowadays situation in these disciplines with a plenty of incompatible data formats is rather confusing. Furthermore a new approach to the scientific data verification and exchange is desired because the traditional peer-reviewed journals and their supplementary materials sections do not solve this task properly. Therefore Tilde aims to simplify data processing and exchanging for the scientists, dealing with popular computer simulation packages in material science (e.g.  VASP ,  CRYSTAL ,  WIEN2K  etc). Now the text outputs of these programs can be collected, and the calculated results therein can be visualized. The example focus is on phonon properties of the crystalline materials: vibrational spectra, band structures, densities of states, vibrational patterns visualization etc. Moreover Ti...