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Archives for September 2013

Data Sharing Pivotal to Personalized Medicine

Challenges associated with sharing and synthesizing massive amounts healthcare data to improve patient outcomes emerged as a key theme in a   discussion last week on the future of personalized medicine.

The event at the Bipartisan Policy Center in Washington, D.C. urged doctors, policy experts and healthcare-technology leaders to explore ways to advance the field —informing those in attendance and online, as well as shaping a policy brief the center will issue this fall. Notable sound bites and other insights were shared in real-time on Twitter using #personalizedmedicine through a Dell initiative to expand the reach of the discussion to a worldwide virtual audience.

Better, cheaper healthcare

Significant advancements in personalized medicine, which includes genomics, is making it easier for practitioners to tailor medical treatments and preventive strategies to the characteristics of each patient — advancements that supporters say will improve care and reduce costs. Yet progress is being slowed by a number of factors, including the limited sharing of patient information.

Greater sharing would allow medical institutions that are creating patient databases — some with genomic information — to expand the size of the patient pool, thus making it more likely to identify and treat rare conditions, panelists said. It would also allow patients to personally store and share their data with different practitioners, increasing portability. The day that everyone will have every detail about their personal health on their smartphones didn’t sound that far off.

Mollie H. Ullman-Cullere, who structures genomic data in IT systems according to emerging standards, said the federal government is taking steps toward sharing more information with patients, but more effort is needed. She cited a rule change that will allow patients to obtain test results directly from labs.

“How government is addressing healthcare reform is through patient engagement and informing them as active consumers of healthcare,” she said. “Genetics has to be included in that.”

Big data for doctors

The other component of the data-accessibility issue is how medical researchers should go about building massive databases of patient records. The ultimate application is a big-data program that could analyze a patient’s data against similar patients and generate a course of action for the physician.

But with greater access comes privacy concerns, and a need to persuade policymakers and the public at large that the medical community can be trusted with storing and using patient data for the greater good, some panelists said. Data can help practitioners diagnose patients more accurately and quickly, and identify risk factors much earlier. Both capabilities would lower healthcare costs.

Edward Abrahams, president of the Personalized Medicine Coalition, said he’s noticed a vexing dichotomy that policymakers will need to address in order to boost the amount of information that patients share with medical databases.

“The tricky part is that the public wants control over information, but as patients they may think differently,” he said.

Source: Tech Page One

New Workflow to Provide Scientists with Tools That Enable Single Cell Analysis for Oncology, Immunology and Stem Cell Research

NanoString Technologies, Inc. (NASDAQ: NSTG), a provider of life science tools for translational research and molecular diagnostic products, and BD Biosciences, a segment of BD (Becton, Dickinson and Company) (NYSE: BDX), a leading global medical technology company, recently announced a collaboration agreement for the development of a single cell isolation and analysis workflow.

Under the agreement, the companies will jointly develop a workflow using the NanoString nCounter®Analysis System (including the nCounter Single Cell Assay) and the BD Flow Cytometry cell sorter product line (emphasizing the new BD FACSJazz™ Cell Sorting System). The combined workflow will enable single cell gene expression analysis for research applications such as oncology, immunology and stem cell research. Collaboration activities will also include the development of materials documenting the workflow protocol, as well as co-hosting meetings and webinars to educate scientists about the single cell workflow.

“Maximizing both the quantity and quality of data that can be extracted from a single cell is critical to the emerging field of single cell biology. The nCounter Analysis System can analyze entire gene pathways and provides a highly precise and reproducible digital output, making it ideally suited to the task,” said Brad Gray, President and Chief Executive Officer, NanoString Technologies. “The nCounter Analysis System and the BD FACSJazz Cell Sorting System can together provide a powerful and efficient workflow for single cell gene expression analysis.”

“Our collaboration with NanoString Technologies furthers BD’s commitment to providing researchers advanced solutions for cell analysis and isolation,” said Alberto Mas, President, BD Biosciences. “We believe this new sorting workflow will complement the recent and very rapid advances in genomic studies that value the requirement for greater sample integrity for critical single cell analysis.”

NanoString Technologies’ nCounter Analysis System is a multi-application digital detection and counting system with a highly automated and simple workflow. The company’s Single Cell Gene Expression application provides researchers with a highly flexible and sensitive approach to discovering differences in cell-to-cell gene expression profiles.The application enables up to 800 genes to be detected in a single tube.

The BD FACSJazz Cell Sorting System is capable of identifying, characterizing and isolating single or multiple cells – from complex or extremely rare cell populations – and depositing them in 96 and 384 well plates to provide rapid cell isolation, tracking and identification throughout the process.

For more information about NanoString Technologies, the nCounter Analysis System and the nCounter Single Cell Assay, please visit www.nanostring.com.

For more information on the BD FACSJazz Cell Sorting System, please visit www.bdbiosciences.com/facsjazz.

Source: BD Biosciences

Sanguine BioSciences Signs Agreements with More than 200 Partners to Enable Efficient Personalized Medicine Research

Sanguine BioSciences, a biotechnology company enabling personalized medicine research, today announced that it has signed commercial agreements with, and received orders from, more than 200 biomedical researchers at academic, biotechnology and pharmaceutical companies, to enable more efficient personalized medicine research. Ongoing agreements are in place with a wide range of organizations, ranging from startups, such as Inhibrx, to contract research organizations, such as Applied Immunology, and major drug developers, such as Vertex Pharmaceuticals.

Sanguine directly engages patients diagnosed with severe and chronic diseases to collect and de-identify biospecimen, medical history and other data that can be used in biomarker research. Traditional methods are to obtain biospecimen through hospitals, but this process can result in months of delays as the focus for physicians and staff is on diagnosis and treatment, not facilitating research efforts. By engaging patients directly, Sanguine can meet the needs of researchers and offer timely turnaround of biospecimen and medical data with diverse ranges for age, race, disease state, gender and treatments underway. The patient engagement tactics used by the company have led to a 95 percent retention rate, which also allow for follow-up draws for longitudinal studies.

“In a very short amount of time, and with only recently hiring our first few sales executives, our company has established agreements with ten of the largest drug developers in the world and continues to see high demand for our offering,” said Brian Neman, founder and chief executive officer of Sanguine. “Researchers have specific needs to complete studies in early discovery work, sometimes run with blood samples drawn the same day and other times requiring follow-up draws on exact time schedules, but traditional strategies to obtain these add months to the timeline. Our commitment to patient engagement, transparency and advocacy removes much of this wait time – accelerating the research and increasing the efficiency of the process overall.”

Sanguine is able to meet, review disclosures and collect blood samples in a patient’s home with its own phlebotomists in multiple major U.S. cities. Patients are also able to track how their de-identified biospecimen and data are used through the donor web portal. The company is able to collect and process blood from patients with any disease and has already built large libraries in multiple chronic and severe conditions, including Huntington’s disease, rheumatoid arthritis, systemic lupus erythematosus, Crohn’s disease, ulcerative colitis and others.

In order to maintain appropriate confidentiality, all samples are de-identified immediately upon collection. Sanguine maintains and reviews internal ethical guidelines for the procedures under high scrutiny from an independent review board.

Source: PR Newswire

Researchers Develop Specific Tests to Identify Cancer Biomarkers in Dermatomyositis

Researchers from major universities in the U.S. have developed specific tests to identify cancer biomarkers in patients with dermatomyositis—a systemic inflammatory disease associated with increased risk of malignancy. According to study findings published in the American College of Rheumatology (ACR) journal, Arthritis & Rheumatism, the assays detect antibodies against anti-transcriptional intermediary factor-1 (TIF-1γ) and nuclear matrix protein NXP-2.

Patients with dermatomyositis experience muscle weakness, skin inflammation, and sometimes inflammation of the lung. Most patients with dermatomyositis have auto-antibodies circulating in their bodies that cause distinct clinical disease features. Medical evidence suggests that these auto-antibodies in dermatomyositis patients stem from specific immune responses that shape various characteristics (phenotypes). In addition, up to 20% of those with dermatomyositis are at increased risk of malignancies.

“For the physician treating patients with dermatomyositis, identifying those at higher risk for cancer is a top priority,” explains Dr. David Fiorentino from Stanford University in Redwood City, Cal. “Our team focused on creating specific tests to detect antibodies against two specific proteins and then testing if those antibodies can identify dermatomyositis patients at higher risk of cancer.”

The team used both immunoblotting and immunoprecipitation techniques to detect antibodies against TIF-1γ and NXP-2 proteins. Blood analysis was performed on 111 patients from Stanford University Dermatology Clinic and 102 patients from the Johns Hopkins University (JHU) Myositis Center. Both groups were similar in gender and age at diagnosis.

Results show that 17% and 38% of subjects in the two cohorts combined had antibodies against NXP-2 and TIF-1γ, respectively. Using the specific assays, researchers found 83% of dermatomyositis patients with cancer had a reaction to NXP-2 or TIF-1γ. Further analysis indicates that cancer, older age, and male gender were linked to NXP-2 or TIF-1γ antibodies, with anti-NXP-2 specifically associated with cancer in men.

“Our findings confirm the link between cancer and age in dermatomyositis, with a sharp increase in frequency at roughly 60 years of age.” concludes Dr. Fiorentino. “By determining the presence or absence of NXP-2 and TIF-1γ antibodies, we believe that this will aid clinicians in identifying those with the highest cancer risk.”

Study: Most patients with cancer-associated dermatomyositis have antibodies to nuclear matrix protein NXP-2 or transcription intermediary factor 1-gamma [Arthritis & Rheumatism]

Source: EurekAlert!

Droplet Digital PCR Enables Reproducible Quantification of microRNA Biomarkers

A study published online in Nature Methods recently demonstrated that Droplet Digital PCR (ddPCR™) technology can be used to precisely and reproducibly quantify microRNA (miRNA) in plasma and serum across different days, paving the way for further development of miRNA and other nucleic acids as circulating biomarkers.

“In the field of circulating microRNA diagnostics, droplet digital PCR enables us to finally perform biomarker studies in which the measurements are directly comparable across days within a laboratory and even among different laboratories,” said Dr. Muneesh Tewari, Associate Member in the Human Biology Division at the Fred Hutchinson Cancer Research Center and lead author of the study.

Challenges in miRNA quantification

miRNAs are small regulatory RNA molecules with diverse cellular functions. The human genome may encode over 1,000 miRNAs, which could target about 60 percent of mammalian genes. Because they are abundant in many cell types, exist in highly stable extracellular forms, and may provide direct information about disease processes, they are being actively studied as blood-based biomarkers for cancer and other diseases.

Quantitative real-time PCR (qPCR) has been used for the analytical measurement of miRNAs in blood samples; however, researchers have found that qPCR measurements of miRNAs in serum or plasma display unacceptably high interday variability, undermining the use of miRNAs as reliable blood-based biomarkers. An approach that yields more dependable results has therefore been sought by researchers in this field.

Advantages of ddPCR for miRNA detection

Digital PCR has many advantages over qPCR including the ability to provide absolute quantification without a standard curve and robustness to variations in PCR efficiency across different samples and assays. These and other advantages are embodied in Bio-Rad Laboratories’ QX100™ Droplet Digital PCR (ddPCR™) system, which was introduced in 2011.

“We chose to use Bio-Rad’s QX100 Droplet Digital PCR system because it was the first system on the market that could make digital PCR practical from a cost and throughput standpoint for routine use in the lab,” said Dr. Tewari.

To assess the imprecision introduced by each workflow step — serial dilution preparation, reverse transcription (RT), and PCR technical replicates — Dr. Tewari and his team conducted nested analyses of ddPCR vs. qPCR on cDNA from a dilution series of six different synthetic miRNAs in both water and plasma on three separate days. In comparison to qPCR, the researchers found that ddPCR demonstrated greater precision (48–72% lower coefficients of variation) with respect to PCR-specific variation

Next, the team performed a side-by-side comparison of qPCR to ddPCR for detecting miRNAs in serum. They collected sera samples from 20 patients with advanced prostate cancer and 20 age-matched male controls and measured the abundance of miR-141, which has been shown to be a biomarker for advanced prostate cancer. Samples were analyzed by qPCR and ddPCR with individual dilution series replicates prepared on three different days. They found that ddPCR improved day-to-day reproducibility seven-fold relative to qPCR. It was also able to demonstrate differences between case vs. control specimens with much higher confidence than qPCR (p=0.0036 vs. p=0.1199).

“Droplet digital PCR will allow us to accurately follow serum microRNA biomarker concentrations over time during a patient’s treatment course, something that has been nearly impossible to achieve with real-time PCR,” he said.

Study: Absolute quantification by droplet digital PCR versus analog real-time PCR [Nature Methods]

Source: EurekAlert!