Posts Tagged ‘droplet digital pcr’

Bio-Rad’s Droplet Digital PCR Highlighted at ASHG Annual Meeting

 :: Posted by American Biotechnologist on 10-22-2013

More accurate and precise assessment of copy number variation (CNV), the number of copies of a particular gene that are present in a genome, may lead to improved diagnosis and therapy for cancer and other diseases including autoimmune disorders. However, current technologies to determine copy number can be inaccurate, labor intensive, or prohibitively costly, diminishing their effectiveness in clinical applications.

Using Bio-Rad Laboratories’ Droplet Digital PCR (ddPCR™) technology, researchers can rapidly, accurately, and economically determine copy number states. Groups from the University of California, Davis, and the University of Colorado School of Medicine, among others, will present promising new research results at this year’s annual meeting of the American Society of Human Genetics (ASHG), held in Boston from October 22-25, 2013.

“Since its introduction in 2011, Bio-Rad Laboratory’s ddPCR technology has demonstrated the potential to be a transformative technology based on its greater precision, reproducibility, and sensitivity than conventional approaches such as real-time PCR,” said George Karlin-Neumann, the scientific affairs director at Bio-Rad’s Digital Biology Center.

Less than two years since Bio-Rad brought digital PCR systems to the market, studies using ddPCR assays have resulted in nearly 50 peer-reviewed publications.

Using ddPCR to Improve Pediatric Care

One example of how CNV determination with ddPCR technology shows promise for clinical applications is newborn CNV screening. 22q11.2 Deletion Syndrome (22q11DS) is the most common microdeletion syndrome in humans and is associated with more than 100 different diagnostic findings including craniofacial defects, developmental delay, and autism spectrum disorders. Researchers in Dr. Flora Tassone’s lab at the University of California, Davis have developed an inexpensive, rapid, sensitive, and specific alternative to fluorescent in-situ hybridization (FISH) – the currently accepted diagnostic tool – using ddPCR technology to identify newborns with 22q11DS. At the ASHG meeting, they will demonstrate for the first time the efficacy of ddPCR in large population screening studies (Program Number 2590F).

Researchers on Dr. James Sikela’s team at the University of Colorado School of Medicine are investigating DUF1220 copy number reduction and its association with microcephaly, a neurodevelopment disorder related to pediatric brain size. They will demonstrate how ddPCR is an effective technique for determining copy numbers of highly duplicated sequences such as DUF1220 and how ddPCR may be used for similar studies in future research where array comparative genomic hybridization (aCGH) analysis or qPCR are not accurate enough (Program Number 3215F).

In addition to the research findings described above, Bio-Rad’s ddPCR technology will be showcased in 11 other presentations. For more information, visit Bio-Rad’s booth at ASHG (booth #839). Bio-Rad will also be hosting an ASHG lunch workshop on Thursday, October 24 at 12:30 PM in room 211 as well as a hospitality suite on Thursday, October 24 at 7:45 PM at the New England Aquarium, 1 Central Wharf in Boston, featuring presentations from UC Davis and Harvard Medical School researchers. Please visit booth #839 for further details.

Complex Diseases Traced to Gene Copy Numbers

 :: Posted by American Biotechnologist on 10-17-2013

Duke researchers have connected very rare and precise duplications and deletions in the human genome to their complex disease consequences by duplicating them in zebrafish.

The findings are based on detailed studies of five people missing a small fragment of their genome and suffering from a mysterious syndrome of craniofacial features, visual anomalies and developmental delays.

When those patient observations were coupled to analyses of the anatomical defects in genetically altered zebrafish embryos, the researchers were able to identify the contribution specific genes made to the pathology, demonstrating a powerful tool that can now be applied to unraveling many other complex and rare human genetic conditions.

The findings are broadly important for human genetic disorders because copy-number variants (CNVs) — fragments of the genome that are either missing or existing in extra copies — are quite common in the genome. But their precise contribution to diseases has been difficult to determine because CNVs can affect the function of many genes simultaneously.

Read more…

Bio-Rad’s New ddPCR Library Quantification Kit Optimizes Performance of Ion Torrent NGS Systems

 :: Posted by American Biotechnologist on 09-24-2013

Bio-Rad Laboratories, Inc., today announced the availability of its new ddPCR™ library quantification kit for Ion Torrent library preparation. Used with Bio-Rad’s QX200™ Droplet Digital™ PCR system, the new kit provides researchers with the ability to precisely and directly measure amplifiable library concentrations.

The Ion AmpliSeq library kit is used to prepare libraries for Ion Torrent next-generation sequencing (NGS) systems. Using the ddPCR library quantification kit to quantify Ion AmpliSeq gDNA and RNA libraries maximizes the number of useable reads, enables consistent loading, and optimizes the utilization of every sequencing run. The resulting data provide additional measures of library quality not provided by other methods, including the percentage of nonamplifiable species such as adapter dimers and the size range of library inserts.

Additional key benefits of the ddPCR library quantification kit for Ion Torrent systems include:

  • Superior performance — produces highly precise measurements of amplifiable library concentrations without the use of standards
  • Visualization of library quality — ddPCR fluorescence amplitude plots highlight well formed and poorly formed libraries
  • Efficient utilization of sequencing runs — enables consistent loading and maximum efficiency of the Ion Torrent sequencing platforms

Kits for other NGS platforms are also in development. For more information on the ddPCR library quantification kit, please visit: www.bio-rad.com/ion-torrent.

Ion Torrent and Ion AmpliSeq are trademarks of Life Technologies Corporation.

Breaking Leukemia’s Limits of Detection with Droplet Digital™ PCR

 :: Posted by American Biotechnologist on 09-17-2013

Extremely Rare Mitochondrial DNA Deletions Associated with Aging Can Be Accurately Detected with Droplet Digital™ PCR

 :: Posted by American Biotechnologist on 09-12-2013

jason bielasA study published recently in Aging Cell identifies a new tool to accurately analyze extremely rare mitochondrial DNA (mtDNA) deletions associated with a range of diseases and disorders as well as aging. This approach, which relies on Droplet Digital PCR (ddPCR™) technology, will help researchers explore mtDNA deletions as potential disease biomarkers.

The accumulation of mtDNA mutations is associated with aging, neuromuscular disorders, and cancer. However, methods to probe the underlying mechanisms behind this mutagenesis have been limited by their inability to accurately quantify and characterize new deletion events, which may occur at a frequency as low as one deletion event per 100 million mitochondrial genomes in normal tissue. To address these limitations, researchers at the Seattle, Washington–based Fred Hutchinson Cancer Research Center developed a ddPCR-based assay known as “Digital Deletion Detection” (3D) that allows for the high-resolution analysis of these rare deletions.

“It is incredibly difficult to study mtDNA mutations, let alone deletions, within the genome,” said Dr. Jason Bielas, assistant member of the Public Health Sciences Division at Fred Hutchinson Cancer Research Center and lead author of the study. “Our 3D assay shows significant improvement in specificity, sensitivity, and accuracy over conventional methods such as those that rely on real-time PCR.”

Bielas added, “The increase in throughput afforded by Droplet Digital PCR shortened the analysis of deletion events to days compared to months using previous digital PCR methods. Without the technology, we could not have made this discovery.”

At the center of the study was Bio-Rad Laboratories’ QX100™ ddPCR system. Using the QX100 system, Bielas and his team analyzed eight billion human brain mtDNA genomes and identified more than 100,000 genomes with a deletion. They discovered that, contrary to popular belief, the majority of the increase in mtDNA deletions was not caused by new deletions but rather by the expansion of previous deletions. They hypothesized that the expansion of existing mutations should be considered the primary factor contributing to age-related accumulation of mtDNA deletions.

How the 3D Assay Works
3D is a novel three-step process that includes enrichment for deletion-bearing molecules, single-molecule partitioning of genomes into droplets for direct quantification via ddPCR, and breakpoint characterization using next-generation sequencing.

Once the enrichment process is completed using methods previously developed by Bielas and colleagues, the concentration of molecules within the droplets is adjusted with the QX100 system so that the majority of droplets contain no mutant genomes, while a small fraction contain only one. This process allows each deletion to be amplified without bias and without introducing the artifacts that are common in qPCR.

Following amplification, deletions can be analyzed using ddPCR to determine the absolute concentration of mutated molecules. Using the relationship between droplet fluorescence and amplicon size, Bielas and his team were able to characterize the size and complexity (whether they were a result of a few clonal expansions or a large collection of random deletions) of rare mitochondrial deletions in human brain samples.

The 3D assay provides an important new tool that will allow researchers to better study the mechanisms of deletion formation and expansion, and their role in aging. Droplet Digital PCR’s high throughput and increased sensitivity will also allow Bielas’ lab to target other low-level disease-causing mtDNA deletions in skeletal muscle, brain tissue, and blood.