Quantcast

Industry news that matters to you.  Learn more

Utility Of Rubicon Genomics’ ThruPLEX-FD Kit Validated In Study Showing “Liquid Biopsy” Can Track Genomic Evolution Of Cancer In Response To Therapy

Rubicon Genomics, Inc., a leader in the development and commercialization of innovative sample-specific nucleic acid library preparation products used in research and clinical testing, recently reported that its ThruPLEXTM-FD Prep Kits contributed to the success of a breakthrough study recently published in Nature1 that showed that genomic data extracted from the plasma of cancer patients can be used to track drug resistance and potentially guide treatment.

AB SCIEX Proteomics Scientist Wins HUPO 2013 Science and Technology Award

The Human Proteome Organization (HUPO) recently awarded Christie Hunter, Ph.D, director of proteomics applications at AB SCIEX, its 2013 Science and Technology Award at an award ceremony during last week’s HUPO 2013 conference in Japan. Dr. Hunter was recognized for her contributions to the development and commercialization of a breakthrough approach for targeted proteomics. The analytical strategy of targeted proteomics was recently named “Method of the Year” by Nature Methods.

Targeted proteomics is a standardized, biological research workflow that focuses on reproducibly quantifying a specific subset of proteins within a sample. It generates data that is vital for biologists to answer hypothesis-driven, biological questions.

A decade ago, proteomics research was dominated by discovery workflows, which provided valuable information on a single sample but lacked the reproducibility to generate robust quantitation across a larger sample set. New innovation was needed at the time to move the field beyond simply producing large lists of identified proteins and toward providing highly quantitative answers.

This led to the development of a multiple reaction monitoring (MRM)-triggered, tandem mass spectrometry (MS/MS) workflow at AB SCIEX to rapidly create high sensitivity MRM assays to target peptides that are unique to their associated proteins. This workflow was made possible by the combination of triple quadrupole and linear ion trap functionality in a single system called the AB SCIEX QTRAP® System.

Dr. Hunter ‒ in collaboration with researcher Dr. Leigh Anderson, the founder of the Plasma Proteome Institute and head of SISCAPA Assay Technologies ‒ pioneered a workflow that applied MRM to the targeted quantification of proteins and peptides in plasma by mass spectrometry. In their initial publication[1], Dr. Hunter and Dr. Anderson demonstrated that a targeted workflow could be applied to multiplexed quantitation of proteins in human plasma with high reproducibility and high confidence in the results.

The impact of the paper resulted in broad adoption of the MRM technique around the world to accelerate the verification and validation of putative protein biomarkers, generating more than 800 citations, according to Google Scholar. Less than a decade after this important work, most proteomics laboratories today use a triple quadrupole-based mass spectrometer to perform MRM analysis.

“We congratulate Dr. Christie Hunter on receiving such a prestigious award from HUPO in recognition of her significant contributions to the rise of targeted proteomics as a viable technique to advance biomarker research,” said Dave Hicks, Vice President and General Manager of the Pharmaceutical and Academic Business at AB SCIEX.

“Dr. Hunter and her AB SCIEX colleagues continue to participate in exciting collaborations with leading proteomics researchers around the world to drive new innovations in software, chemistries and instrumentation that further expand quantitative proteomics workflows for the growing community of mass spectrometry users at large,” added Hicks.

Currently, Dr. Hunter is playing a pivotal role in the development of higher specificity workflows for targeted protein quantitation to overcome situations where sensitivity is limited by interferences or background. She is involved in the investigation of the utility of differential mobility separations for added selectivity of quantitation of peptides in complex mixtures. She is also working to enhance data-independent acquisition strategies, such as SWATHTM Acquisition, for quantitative proteomics to increase the multiplexing and reproducibility that can be achieved in a single experiment.

Source: AB SCIEX

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! 

MentisCura to Deploy EEG Diagnostics for Dementia at China’s Largest Geriatric Hospital in 2014

MentisCura Diagnostics (www.mentiscura.com) and WanJiaYuan International Geriatric Hospital recently announced the signing of an agreement to implement MentisCura’s proprietary diagnostic tools to improve care for patients with CNS disorders.

Mentiscura’s diagnostics will be part of a state-of-the art technology suite being deployed at the WanJiaYuan International Geriatric Hospital, expected to open in June 2014. The hospital, based in Nanyang in the Henan province, will be a 120,000 square meter, 1200 bed campus, one of the largest facilities of its kind in the world to focus solely on setting new standards of quality of managed care for the elderly, with at least 200 beds dedicated to dementia patients. WanJiaYuan International Geriatric Hospital also aims to establish a leadership position in geriatric research through the development of a center of excellence attracting over 100 international experts.

“We are honoured to be associated with a project that is of an unprecedented scale, even by international standards. The high-throughput and non-invasive nature of our electrophysiological analysis makes it uniquely useful in a real world clinical setting, where physicians need to assess patients and make care decisions before these diseases have reached a late and untreatable stage. From a five-minute standard EEG recording, our powerful analytical systems are able to provide immediate diagnostic output, offering genuine clinical benefit and scalability for even the largest facilities,” said Kristinn Gretarsson, CEO of MentisCura.

“Our hospital is committed to addressing the growing burden of care associated with diseases of ageing. We are delighted to be collaborating with MentisCura to use its innovative clinical technologies to guide earlier, lower cost diagnosis. We believe that biomarkers of disease will increasingly play an important role in our diagnostic protocol for dementia, as well as monitoring of disease progression and treatment efficacy,” commented Dr. Jin-Jing Pei, MD, Chief Physician at WanJiaYuan International Geriatric Hospital.

MentisCura offers a complete, integrated service to hospitals and general practitioners through sampling, processing and analysis of patient EEG data. The MentisCura Analysis System is a CE marked diagnostic aid, based on advanced, proprietary EEG-biomarker technology platform that accurately correlates changes in electrophysiology to specific disease pathologies, based on the company’s comprehensive proprietary EEG database for dementia and cognitive disorders. The platform supports diagnoses for most common types of dementia, including Alzheimer’s disease and Lewy body dementia.

Source: MentisCura Diagnostics

Researchers Identify Biomarkers for Possible Blood Test to Predict Suicide Risk

Indiana University School of Medicine researchers have found a series of RNA biomarkers in blood that may help identify who is at risk for committing suicide.

In a study reported Aug. 20 in the advance online edition of the Nature Publishing Group journal Molecular Psychiatry, the researchers said the biomarkers were found at significantly higher levels in the blood of both bipolar disorder patients with thoughts of suicide as well in a group of people who had committed suicide.

Principal investigator Alexander B. Niculescu III, M.D., Ph.D., associate professor of psychiatry and medical neuroscience at the IU School of Medicine and attending psychiatrist and research and development investigator at the Richard L. Roudebush Veterans Affairs Medical Center in Indianapolis, said he believes the results provide a first “proof of principle” for a test that could provide an early warning of somebody being at higher risk for an impulsive suicide act.

“Suicide is a big problem in psychiatry. It’s a big problem in the civilian realm, it’s a big problem in the military realm and there are no objective markers,” said Dr. Niculescu, director of the Laboratory of Neurophenomics at the Institute of Psychiatric Research at the IU School of Medicine.

“There are people who will not reveal they are having suicidal thoughts when you ask them, who then commit it and there’s nothing you can do about it. We need better ways to identify, intervene and prevent these tragic cases,” he said.

Over a three-year period, Niculescu and his colleagues followed a large group of patients diagnosed with bipolar disorder, completing interviews and taking blood samples every three to six months. The researchers conducted a variety of analyses of the blood of a subset of participants who reported a dramatic shift from no suicidal thoughts to strong suicidal ideation. They identified differences in gene expression between the “low” and “high” states of suicidal thoughts and subjected those findings to a system of genetic and genomic analysis called Convergent Functional Genomics that identified and prioritized the best markers by cross-validation with other lines of evidence.

The researchers found that the marker SAT1 and a series of other markers provided the strongest biological “signal” associated with suicidal thoughts.

Next, to validate their findings, working with the local coroner’s office, they analyzed blood samples from suicide victims and found that some of same top markers were significantly elevated.

Finally, the researchers analyzed blood test results from two additional groups of patients and found that high blood levels of the biomarkers were correlated with future suicide-related hospitalizations, as well as hospitalizations that had occurred before the blood tests.

“This suggests that these markers reflect more than just a current state of high risk, but could be trait markers that correlate with long term risk,” said Dr. Niculescu.

Although confident in the biomarkers validity, Dr. Niculescu noted that a limitation is that the research subjects were all male.
“There could be gender differences,” he said. “We would also like to conduct more extensive, normative studies, in the population at large.”

In addition to extending the research to females to see if the same or other markers come into play, Dr. Niculescu and colleagues plan to conduct research among other groups, such as persons who have less impulsive, more deliberate and planned subtypes of suicide.

Nonetheless, Dr. Niculescu said, “These seem to be good markers for suicidal behavior in males who have bipolar mood disorders or males in the general population who commit impulsive violent suicide. In the future we want to study and assemble clinical and socio-demographic risk factors, along with our blood tests, to increase our ability to predict risk.

“Suicide is complex: in addition to psychiatric and addiction issues that make people more vulnerable, there are existential issues related to lack of satisfaction with one’s life, lack of hope for the future, not feeling needed, and cultural factors that make suicide seem like an option.”

He said he hopes such biomarkers, along with other tools, including neuropsychological tests and socio-demographic checklists currently in development by his group, ultimately can help identify people who are at risk, leading to pre-emptive intervention, counseling, and saved lives.

“Over a million people each year world-wide die from suicide and this is a preventable tragedy”.

Study: Discovery and validation of blood biomarkers for suicidality [Molecular Psychiatry]

Source: Indiana University School of Medicine