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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! 

Researchers Develop Rapid, Cost-effective Early Detection Method for Organ Transplant Injury

A recently reported blood test for the early detection of organ transplant injury could enable more timely therapeutic intervention in transplant patients and thus help to avoid longer term damage. As described by scientists at the University Medical Center Göttingen and Chronix Biomedical, a molecular diagnostics company, the new method uses Bio-Rad Laboratories’ Droplet Digital PCR (ddPCR™) technology to overcome the obstacles of earlier tests, which were both time-consuming and costly. The method was presented at the American Association of Clinical Chemistry (AACC) 2013 annual meeting and has been accepted for publication in Clinical Chemistry.

Approximately 28,000 organ transplantations (known as grafts) are performed each year in the U.S., with another 100,000 patients on waiting lists. However, transplant patients are often subject to organ rejection: acute rejection of liver transplants within three years is nearly 22 percent, while heart and lung rejection is close to 50 percent. In addition, nearly half of all of kidney transplants fail within 10 years.

Graft-derived cell-free DNA (GcfDNA) in the circulation of transplant recipients is a potential rejection biomarker. But previous attempts to determine GcfDNA, which require parallel sequencing of donor and recipient DNA, are expensive and require a long turnaround and use of donor DNA. University Medical Center Göttingen and Chronix Biomedical researchers sought to develop a new method in an attempt to address these drawbacks.

Using ddPCR for Fast, Cost-Effective Test

The researchers applied Bio-Rad’s ddPCR technology to quantify graft-derived cfDNA in recent liver transplant patients and in stable patients who had undergone a transplant procedure more than six months earlier. ddPCR technology allowed them to develop a cost-effective and fast laboratory test that detects cfDNA being released into the blood stream by dying cells from the transplanted organ.

“GcfDNA from dying graft cells are the most direct and sensitive indicator of organ rejection and we needed an instrument that could measure it,” said Chronix Biomedical’s Chief Technology Officer and the study’s senior author, Ekkehard Schuetz, MD, PhD. “ddPCR added an additional level of reliability and precision to traditional PCR.”

Sequencing methods typically require batch sampling, but by using ddPCR, researchers are able to run single samples. Additionally, this method is reducing test time from three days or more to one day and costs by 90 percent. The study authors were able to address the need for donor DNA by preselecting SNPs that ensure enough heterogeneity between donor and recipient. The new blood test can also deliver results up to several days before the conventional aspartate aminotransferase (AST) and bilirubin tests for liver transplantation rejection, with the potential for an immediate positive impact on patient care.

“We will now be able to detect subclinical rejection and early intervention may allow us to avoid a full-blown rejection,” said Michael Oellerich, M.D., FACB, FRCPath and Lower Saxony Distinguished Professor of Clinical Chemistry at the University Medical Center Göttingen and study Principal Investigator. “This test may be useful to personalize immunosuppression and to improve long-term outcomes.”

“Detecting non-host cfDNA is the third example for the commercial potential of cfDNA diagnostics. Researchers will now be able to extend the applications from fetal cfDNA in maternal blood and personalized biomarkers for minimal residual disease in cancer to solid organ transplantation,” said Howard Urnovitz, PhD, Chronix Biomedical’s Chief Executive Officer.

“We are looking forward to the improvements in precision medicine we can offer with ddPCR and this example in transplantation highlights the diagnostic value for the technology,” said Paula Stonemetz, Director Diagnostic Business Development, Digital Biology Center, Bio-Rad Laboratories.

The researchers were awarded a National Academy of Clinical Biochemistry (NACB) Distinguished Abstract Award at the 2013 AACC annual conference. The results are part of a larger planned study to determine if cfDNA is the earliest indication of a transplant organ rejection.

Source: EurekAlert!

New Biomarker Could Reveal Alzheimer’s Disease Years Before Onset

A study published recently reported the identification of what may be the earliest known biomarker associated with the risk of developing Alzheimer’s disease (AD). The results suggest that this novel potential biomarker is present in cerebral spinal fluid (CSF) at least a decade before signs of dementia manifest.

“If our initial findings can be replicated by other laboratories, the results will change the way we currently think about the causes of Alzheimer’s disease,” said Dr. Ramon Trullas, research professor at the CSIC Institute of Biomedical Research of Barcelona and lead author of the study that was published in Annals of Neurology. “This discovery may enable us to search for more effective treatments that can be administered during the preclinical stage.”

Difficult Diagnosis

Alzheimer’s disease affects more than five million Americans and is the sixth leading cause of death in the United States. At present, the only way to accurately diagnose the disease is by post-mortem neuropathological analysis. The relationship of currently known biomarkers with the cause of the disease is unclear, making it nearly impossible to diagnose preclinical stages of the disease with any real certainty.

The CSIC researchers demonstrated that a decrease in the content of mitochondrial DNA (mtDNA) in CSF may be a preclinical indicator for Alzheimer’s disease; furthermore, there may be a directly causative relationship. The hypothesis is that decreased mtDNA levels in CSF reflect the diminished ability of mitochondria to power the brain’s neurons, triggering their death. The decrease in the concentration of mtDNA precedes the appearance of well-known biochemical Alzheimer’s biomarkers (the Aβ1-42, t-tau, and p-tau proteins), suggesting that the pathophysiological process of Alzheimer’s disease starts earlier than previously thought and that mtDNA depletion may be one of the earliest predictors for the disease.

In addition to enabling an investigation of the potential causal relationship of mtDNA and Alzheimer’s progression, the use of mtDNA as an index of preclinical Alzheimer’s disease provides an important advantage over previous biochemical markers: the detection of this novel nucleic acid biomarker is unhampered by the technical difficulties associated with protein detection. mtDNA can be readily quantified by real-time quantitative PCR (qPCR) or droplet digital PCR (ddPCR).

Quantitation of mtDNA

Prior to this study, researchers had not reported that circulating cell-free mtDNA could be detected in human CSF. But with this study, Dr. Trullas’ team was able to both detect and reproducibly quantitate mtDNA using qPCR, carefully optimized by adhering to the MIQE guidelines.

To validate their qPCR findings, Dr. Trullas’ team used Bio-Rad Laboratories’ QX100™ Droplet Digital™ PCR system. Unlike qPCR assays, the QX100 system provides an absolute quantification of target DNA molecules without the need for a standard curve. In addition, an important factor for their CSF analysis was that the Droplet Digital PCR system did not require sample purification to remove PCR inhibitors, as is necessary for qPCR assays.

“Droplet Digital PCR allowed us to validate our initial qPCR measurements because it provides absolute quantitation at the single-molecule level without relying on a standard curve,” said Dr. Trullas. “As the technology becomes more widely adopted, we anticipate that Droplet Digital PCR will be the future of detecting mtDNA in cerebral spinal fluid.”

Dr. Trullas hopes that other laboratories and hospitals will successfully replicate his group’s research results, confirming that reduced mtDNA levels should be investigated as a possible cause of Alzheimer’s disease. By finding a way to block this degeneration, clinicians may be able to diagnose and treat Alzheimer’s disease before symptoms appear.

Study: Low CSF concentration of mitochondrial DNA in preclinical Alzheimer’s disease [Annals of Neurology]

Source: Bio-Rad

CTC Distributes Data Analysis and Biomarker Platform in Japan

CTC Laboratory Systems (CTCLS) negotiated distribution rights in Japan to Ariana Pharma’s KEM® (knowledge extraction and management) data mining analytics software and services. Originally developed at the Pasteur Institute, KEM is a rules-based (i.e., nonstatistical) data analysis technology for identifying patient-responder sub-populations and biomarker signatures.

Bio-Rad and Myriad RBM Partner to Commercialize Multiplex Biomarker Kits for Life Science Research

Bio Rad Laboratories, Inc. (NYSE: BIO and BIOb), a multinational manufacturer and distributor of life science research and clinical diagnostic products, and Myriad RBM, Inc., a wholly owned subsidiary of Myriad Genetics Inc. (NASDAQ: MYGN), and a leading multiplex biomarker testing company, today announced that they have partnered to develop and distribute high-quality immunoassay kits. Under the terms of the agreement, Myriad RBM grants Bio-Rad exclusive distribution rights, for research purposes, to the largest catalog of quantitative multiplexed immunoassays currently available to run on the Bio-Plex® 200, Bio-Plex® 3D, and Bio-Plex® MAGPIX™ instruments.