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Life Technologies Launches Compendia Oncomine NGS Power Tools for Cancer Researchers, Discovers Novel Gene Fusions

Life Technologies Corporation (NASDAQ: LIFE) recently announced the introduction of Oncomine® Next Gen Sequencing Power Tools, an analytics offering that will allow cancer researchers to explore results from in-depth analysis of next generation sequencing (NGS) data, including data from The Cancer Genome Atlas. In total, more than 4,500 paired tumor and samples have been analyzed to date.

Team Finds Markers Related to Ovarian Cancer Survival and Recurrence

Researchers at the University of Illinois have identified biomarkers that can be used to determine ovarian cancer survival and recurrence, and have shown how these biomarkers interact with each other to affect these outcomes. Their findings appear in the journal PLOS ONE.

Researchers try to find molecules called biomarkers that help determine a person’s likelihood of getting a disease or, if they have already been diagnosed, how far the disease has advanced. Genes, transcription factors and microRNAs are often used as biomarkers because these molecules can be heralds of disease or portents of susceptibility.

Genes are segments of DNA that code for proteins or other molecules that perform the functions of the cell. Transcription factors regulate these genes by binding to specific DNA sequences, preventing or inducing the genes to be “expressed” at higher or lower levels. MicroRNAs, as their name suggests, are small RNA molecules that regulate an intermediate stage of gene expression. Transcription factors and microRNAs also can regulate each other.

The relationships among transcription factors, microRNAs and target genes can be visualized as interconnected networks. These intricate webs are often used to determine how diseases such as cancer proceed. Analyzing how these networks function in cancer can offer insight into how tumor cells proliferate and differentiate, undergo (or resist) programmed cell death, and how likely they are to become invasive.

According to the American Cancer Society, an estimated 22,240 women will be diagnosed with ovarian cancer in 2013, and 14,230 will die of the disease; this makes ovarian cancer the fifth most common cause of cancer death in women.

The high prevalence of ovarian cancer and ovarian cancer deaths in the U.S. prompted U. of I. animal sciences professor Sandra Rodriguez-Zas and doctoral researcher Kristin Delfino to search for biomarkers associated with ovarian cancer survival and recurrence.

“We knew that there are specific biomarkers that have been associated with ovarian cancer, but we were looking at whether we could more accurately predict survival or age at cancer recurrence considering hundreds of interacting biomarkers simultaneously,” Rodriguez-Zas said.

The team used data from the Cancer Genome Atlas, which contains information about ovarian cancer patients’ age, survival, cancer recurrence, treatment, tumor stage, tumor grade and genomic expression. The researchers then performed statistical tests to tie these factors to patients’ survival time, measured in months from diagnosis to death, and their recurrence time, measured in months from diagnosis to recurrence.

“The networks change for people who have different rates of survival, so we looked at what’s being expressed in high-survival patients compared to what’s being expressed in low-survival patients,” Delfino said.

The team was able to confirm the association of 21 microRNAs with ovarian cancer. They also found 838 target genes and 12 transcription factors associated with ovarian cancer survival and 734 target genes and eight transcription factors associated with ovarian cancer recurrence.

“We were able to find many biomarkers that held the same relationship with survival no matter the cancer treatment, as well as some that were unique in their relationship with survival depending on the treatment the patient had received,” Rodriguez-Zas said.

Delfino said that a network-based approach is more predictive of ovarian cancer survival and recurrence than a single-molecule-based perspective.

“We took a step back and looked at everything from a network point of view instead of just individually to see how the components interacted with each other and how the biomarkers were associated with ovarian cancer survival and recurrence,” Delfino said.

“This demonstrated that the consideration of networks of microRNAs, transcription factors, and target genes allows us to identify reliable indicators of cancer survival and recurrence and serves as the basis for effective prognostic tools,” Rodriguez-Zas said.

Delfino believes this study opens the door to the creation of less invasive diagnostic tests and more specialized treatment options for women with ovarian cancer.

“In the future we’d like to be able to just take a little sample of your DNA and be able to tell you what’s going to happen, what we can do to prevent it, and how to cut cancer off before it ever reaches that point,” Delfino said. “Everyone is different, and hopefully, we will be able to specify the treatment that will best treat the individual patient.”

Study: Transcription Factor-MicroRNA-Target Gene Networks Associated with Ovarian Cancer Survival and Recurrence

Source: University of Illinois at Urbana-Champaign

H3 Biomedicine and BGI Announce Collaboration to Develop and Share Crucial Cancer Genomic Sequencing Data

H3 Biomedicine Inc., a biopharmaceutical company specializing in the discovery and development of oncology treatments, and BGI, the largest genomics organization in the world, jointly recently announced that they have entered into a partnership to sequence and publish genomic data from pre-clinical cancer models. This research, which aims to identify and validate recurrent gene mutations that are potential targets for drug therapies, is crucial for the entire oncology drug discovery industry. Consistent with their respective ongoing commitments to open-access research, as well as BGI’s distinguished history of published, collaborative research, H3 and BGI will release the cancer genomic data to the global research community upon completion of data analysis.

“We truly believe that genomic information generated from patient samples or material derived thereof should be shared with the scientific community. As a matter of fact, the community has benefited enormously from collaborative efforts like The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC),” stated Markus Warmuth, M.D., president and chief executive officer, H3 Biomedicine. “Open access to this information has enabled countless scientific advances, and our intention is to further accelerate oncology drug discovery by releasing the data we generate with BGI. We see this as a significant step in building shared translational oncology platforms that will bring the research community together to deliver new personalized medicines, especially for those people living with cancers for which there are, today, limited treatment options.”

Recent advances in human cancer genomics have revealed novel cancer target opportunities that will enable personalized cancer medicine approaches. Many of the identified recurrent gene mutations exist at low frequencies and the information necessary to select relevant pre-clinical models to study these mutations does not exist. Under the partnership announced today, BGI will sequence 250 cancer cell lines via next-generation, whole exome sequencing in this first study. H3 Biomedicine and BGI will jointly analyze the data to deliver a highly curated set of genetically profiled, pre-clinical model information that will help to accelerate drug discovery and development efforts.

Yingrui Li, chief executive officer of BGI Americas, said, “We are pleased to collaborate with H3 Biomedicine, and to have this opportunity to apply our state-of-the-art, next-gen sequencing capabilities and bioinformatics expertise to help advance the discovery of novel cancer drug targets and full-scale pharmacogenomics findings. I believe this partnership will yield significant, valuable genomic information that will lay a solid foundation for developing pre-clinical cancer models and new anticancer drugs to benefit human health. BGI, in keeping with our global legacy of collaborative, published research, including our participation in ICGC, looks forward to partnering with H3 Biomedicine in developing and sharing this genomic data with the international research community.”

Source: H3 Biomedicine

Creating a Future of Personalized Medicine: U-M Forms Nonprofit Joint Venture for Advanced DNA Diagnostics

As a key step toward providing patients with treatments based on their own DNA profiles, the University of Michigan and the International Genomics Consortium (IGC) have launched a new joint venture that will help usher in an age of personalized medicine.

TCGA Study Brings Ovarian Cancer Patients Closer to Personalized Medicine

In the June 30 issue of Nature, researchers from The Cancer Genome Atlas (TCGA) Research Network provide a large-scale integrative report on genetic mutations and pathways that distinguish the most common and aggressive type of ovarian cancer from other types of ovarian cancer as well as from other solid tumors. The disease is not defined by one or few cancer-driving genes but rather numerous mutations that individually occur in only a small number of cases. Given the degree of genomic disarray, the study results suggest that genomic structural variation is the driver of ovarian cancer. The findings may be helpful in guiding physicians to choose experimental treatments that are most likely to target molecular alterations effectively in patients with high-grade serous ovarian adenocarcinoma.