genomics

Viewing posts tagged genomics

30 Jun 2017

Surfing with DAVE

By Jay Goth

The growth in cancer genomics has been one of the most exciting scientific and technological developments in cancer research, spurring significant advances in patient care and laying the groundwork for many future advances.

In the year since it was launched, the National Cancer Institute’s Genomic Data Commons (GDC) has collected and harmonized a vast quantity of cancer genomics data—more than 4.5 petabytes—which has been fundamental in the recent progress against cancer and holds the promise for continued improvement in our ability to diagnose, treat, and care for patients.

Now, as a data-analysis system, the GDC is taking major steps toward engaging the broader research community and encouraging further collaboration and data sharing. They recently introduced a new program – Data Analysis, Visualization, and Exploration Tools, an online, open-access cancer research resource called DAVE.

DAVE is a new web interface for exploring and analyzing cancer genomic data, in real time, online, without the need to download or process the data.

DAVE provides an unprecedented level of flexibility in exploring the data. Researchers can create custom cohorts for analysis by selecting patients with particular altered genes or other relevant biological and clinical features. And researchers are no longer bound to analyzing patients only in the context of their original project cohorts—a powerful innovation given the recent evidence that a tumor’s molecular features are far more accurate and informative for cancer subtyping than tissue of origin or histology.

Another step forward for precision medicine! For the details, visit the National Cancer Institute.

29 Jun 2017

Finding the Source of Cancers

By Jay Goth

Investigators at the University of California San Diego School of Medicine and at Xijing Hospital and Sun Yat-sen Cancer Center in China say that DNA methylation can provide effective markers for at least four major cancers.

The biomarkers are able to differentiate malignant tissues from normal tissues and also provide information on prognosis and survival, according to the researchers.

“This new simple method will be of great value to pinpoint the primary source of the tumor.”

–Michael Karin, Ph.D., Professor of Pharmacology, UC San Diego School of Medicine.

“Choosing the proper cancer treatment with the best chance of recovery and survival depends greatly upon accurately diagnosing the specific type or subtype of cancer,” said Kang Zhang, M.D., Ph.D., founding director of the Institute for Genomic Medicine and co-director of biomaterials and tissue engineering at the Institute of Engineering in Medicine, both at UC San Diego School of Medicine.

Read the entire article at Genetic Engineering and Biotechnology News here.

21 Jun 2017

Breakthrough FDA Ruling

By Jay Goth

The Food and Drug Administration (FDA) granted accelerated approval to the immunotherapy pembrolizumab for patients with solid tumors that have one of two specific genetic features known as mismatch repair deficiency and high microsatellite instability. The approval covers adult and pediatric patients whose cancer has progressed despite prior treatment and who have no alternative treatment options.

This is the first time that FDA has approved a cancer treatment based solely on the presence of a genetic feature in a tumor, rather than the patient’s cancer type.

“I think this is a step forward for precision medicine.”

–James Gulley, M.D., Ph.D., head of the immunotherapy section of NCI’s Center for Cancer Research

Having a biomarker to identify patients who are most likely to respond is “an area we have widely anticipated as being the next step in understanding how to better use immunotherapies,” said Dr. Gulley. “It’s a welcome first step, and there’s much more yet to be done.”

For the full article, visit the National Cancer Institute page here.

14 Jun 2017

Institute for Protein Innovation Launched

By Jay Goth

The Institute for Protein Innovation will work to pursue new therapies for currently intractable diseases by bringing together leaders with backgrounds in academic research, the biopharma industry, and biomedical investing.

The Institute plans to curate information related to DNA sequence, protein expression, and functional validation of these reagents, including source code, in a publicly-accessible web portal, with the goal of accelerating the development of new drugs and supporting existing large-scale research efforts, citing the Human Cell Atlas.

The Institute said it will recruit researchers focused on directed evolution, cell-line development, and biophysical protein characterization, in addition to glycoprotein expression and antibody discovery expertise.

“Despite their pivotal importance in research and medicine, proteins lag behind DNA and RNA in institutional research support and funding.”

–Timothy A. Springer, Ph.D., Founder and Latham Family Professor at Harvard Medical School and Boston Children’s Hospital

Read the full article at Genetic Engineering and Biotechnology News here.

New Article in GEN

18 Jan 2017

Big Data: Precision Medicine Research in the Million-Genome Era

By Jay Goth

A major challenge for large-scale precision medicine research is in harmonizing data from different sources. As a simple example, researchers can use a whole genome sequence from a patient with a rare disease to find a list of potentially causal variants for further investigation. Moreover, these variants can be filtered effectively when combined with genomic data from 100,000 people without the disease. Bringing in the additional 100,000 samples can be nontrivial, both because of the size of the data involved and because of different methods of data collection among studies. Read the entire article at GEN

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