Epigenetic changes mark up ovarian cancer cells

Posted on January 3, 2012 by Jyoti M.. Filed under Case Studies, Paper Trail, Research

A genome wide methylation screen finds a potential new biomarker for ovarian cancer

In the forty years since the ‘War on Cancer’ was declared, ovarian cancer is the only form of the disease where mortality rates remain unchanged, in part due to a lack of early detection tests and specific treatments. In 2011, an estimated 15,000 women in the U.S will die of ovarian cancer.

A recent study in PLoS One by Campan et al. describes the identification of a new candidate biomarker, IFFO1, in a genome-wide DNA methylation screen of blood samples from ovarian cancer patients. Less invasive than tests that require tissue samples, and chemically and biologically more stable than RNA markers for gene expression, DNA methylation changes that can be tracked in blood samples are promising biomarkers for cancer detection and treatment. Read more…

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NextBio Public Tutorials: Exploring the experimental details behind NextBio results

Posted on November 30, 2011 by NextBio. Filed under Tutorials

In part II of the NextBio Public tutorials, we show you how to find the experimental details underlying your NextBio query results.

Critics of GWAS are quick to point out that the genetic associations identified in such studies rarely reach clinical significance. However, integrating associations identified in genome-wide studies with evidence from more directed experiments can speed up the process of taking genomic variants from the bench to the clinic. Watch our tutorial to find out how to dig down into the experimental results associated with a gene query in NextBio, or read on to learn more about our study* on one particular gene, POU5F1B. Read more…

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Tumor suppressor or oncogene? The argument continues…

Posted on November 14, 2011 by Jyoti M.. Filed under Paper Trail, Research

Integrated approaches identify a new tumor suppressor function for soluble EPHA7 in follicular lymphoma

Scanning the whole genome for tumor-associated mutations has the potential to reveal new drug targets or diagnostic biomarkers that could help personalize therapy for patients. However, the complex patterns of genetic disruptions in cancer frequently prevent such candidate genes from reaching clinical significance. Combining tumor genomics with functional genetic screens and experimental models can increase the pace at which genome-wide findings are translated into clinically relevant applications.

A recent paper in Cell describes the identification of a novel tumor suppressor, EPHA7, in a genome-wide screen of follicular lymphoma samples. Supporting this finding with experimental results from animal models and cancer cell lines, the researchers also demonstrated that the gene product, a soluble protein, had the potential to dramatically improve tumor clearance in mice. Read more…

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Instant fit: tailoring prescriptions in the clinic

Posted on November 10, 2011 by Jyoti M.. Filed under Conferences, News

Scientists present clinical trial results for the first bedside genetic test

How quickly can clinicians accurately determine the way a patient will respond to medication, or their chances of getting a disease? It might even begin the minute they walk in the door. ‘Genotyping by eye’, as Atul Butte from Stanford University phrased it at a recent Xconomy forum, can be as instantaneous as noticing a patient is obese, a factor that increases chances of diabetes more than any known genetic variant today.

More precise genetic tests are fast catching up to this idea of near-instant genotyping as well. Researchers from the University of Ottawa recently demonstrated the success of a ‘bedside’ genetic test to optimize treatments for patients undergoing coronary stent implantations. At the Transcatheter Cardiovascular Therapeutics symposium this week, the lead investigator, Dr. Derek So, presented the results of the RAPID GENE clinical trial, a point-of-care genetic test to identify carriers of a common genetic variant that reduces the efficacy of standard anti-platelet therapies. Read more…

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NextBio Public Video Tutorials: Using NextBio to explore a gene

Posted on October 31, 2011 by NextBio. Filed under Tutorials

In part I of the NextBio tutorials, we explain how and why NextBio helps explore data relevant to a gene query

A single gene can be studied in many ways-   genome-wide analysis for associations with diseases, experimental studies of function in cell lines or animal models, or pharmaceutical research as a potential drug target. At NextBio, we aggregate these diverse kinds of data, normalize and integrate them on a common platform, coalescing diffuse “data clouds” to address focused research questions.

In the first of our NextBio Public tutorials, we explain how to use simple NextBio functions to find this aggregated data relevant to a gene, beginning with GWAS associations, to descriptions of tissues and cell lines and results from pharmacological experiments, all in a matter of minutes.

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Crowdsourcing solutions for life

Posted on October 21, 2011 by NextBio. Filed under Conferences, Guest Blogger, Open Science

From the lab to scientific publishing to clinical solutions, the Open Access movement is changing the way science advances

(Guest post by Joseph Jackson)

The 2nd Open Science Summit is the weekend of October 22-23, 2011 at the Computer History Museum in Mountain View, just before the 2011 Open Access (OA) week, which runs October 24th-28th.  Open Science evokes different associations for different people, depending on which part of the scientific process they most regularly engage with.  One critical component focuses on access to scientific literature.  The OA movement has made great strides in the last ten years with the creation and maturation of journals and publishers like PLoS and Biomed Central.

But the most critical shifts toward Open Science arguably are happening in the life sciences.  The technological revolution underway in next generation sequencing is enabling, but also requiring bold new collaborative approaches to manage increasing complexity and accelerate the translation of scientific discoveries into desperately needed therapies.
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SIRT2 finds a place in the family

Posted on October 18, 2011 by Jyoti M.. Filed under Paper Trail, Research

Sirtuin 2 may suppress tumor formation in mice and humans

Sirtuins are a family of proteins that have been implicated in processes ranging from aging and tumor formation to obesity and cerebral ischemia. Seven sirtuin proteins are known to exist in mammals, two of which (SIRT1 and SIRT3), are known tumor suppressor genes. The function of sirtuin 2 (SIRT2) remained unclear however, until recent research from scientists at the National Institute of Health, Vanderbilt University and the University of Texas, Dallas discovered that SIRT2 could play an important role in preventing cancer. In a paper published in Cancer Cell this week, the researchers describe the role of SIRT2 in maintaining genomic stability in cells, a function critical in aging and cancer-related processes.
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Intern Life at NextBio

Posted on October 6, 2011 by Samara M.. Filed under Life at NextBio, NextBio

Interns at NextBio learn to set the stage for a unique kind of data exploration

At NextBio, genomic data snakes through the hands of scientific teams and the automated pipelines they design, connecting people intellectually and socially. Each department is responsible for their own piece of the NextBio puzzle as well as helping new team members cultivate their skills.

The data curation team at NextBio mimics the work of a heart, channeling in the public genomic data that’s essential to the NextBio platform. Beatrice Chiu, who graduated from the Molecular and Cell biology program at UC Berkeley, began her journey at NextBio as a Web Product intern, conducting usability tests to optimize the NextBio user interface. She switched over to the curation team earlier this year to help with a large scale GWAS (genome-wide association study) tagging project. As Beatrice explains, “All studies in the NextBio database usually have a minimum of a biodesign tag, like disease vs. normal, response to a drug, etc. and then a more specific phenotype tag, say for a disease. GWAS studies can also get classified using case-control or other association tags.”
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Nicer with Dicer? Not always.

Posted on October 3, 2011 by Jyoti M.. Filed under Paper Trail, Research

Increases in Dicer gene expression improve some cancers and worsen others

Some of the tiniest players on the field, microRNAs (miRNAs) are short strands of RNA that work to control gene expression in several pathways. Though they don’t encode any proteins, miRNAs regulate genes involved in embryonic growth, cell differentiation, angiogenesis and other cellular processes. They have also gained steady prominence in cancer research, with several studies connecting abnormal miRNA regulation to cancer progression and metastasis in cell lines, animal models and samples from patients.

The potential diagnostic and therapeutic value of miRNAs has also turned attention to the molecules involved in making miRNAs in cells, particularly the enzyme Dicer. A recent study by Zhihai Ma and colleagues in PLoS One reports that higher Dicer expression correlates to more advanced stages of cutaneous melanoma, characterized by increased metastatic potential, tumor mitotic index, and other stages (as defined by the American Joint Committee on Cancer) .
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