Posts Tagged ‘Bio-Rad Laboratories’

Emerging Applications of Bio-Rad’s Droplet Digital™ PCR Technology

 :: Posted by American Biotechnologist on 11-06-2013

Since its introduction in 2011, Bio-Rad Laboratory’s Droplet Digital PCR (ddPCR™) technology has demonstrated the potential to be a transformative technology, particularly in clinical applications.

In the past, tools developed for such applications have been limited by their inadequate precision and/or their lack of sensitivity for detecting rare species. But thanks to ddPCR technology, researchers can now focus on more of these “needle-in-a-haystack” problems. Less than two years since Bio-Rad brought ddPCR systems to the market, their application has resulted in nearly 50 peer-reviewed publications citing the technology.

The advantages of ddPCR technology have already had an important impact on medical research.

“The HIV community, for instance, has benefited from ddPCR’s ability to make more sensitive measurements, which can also depend on its attribute of increased precision,” said George Karlin-Neumann, the scientific affairs director at Bio-Rad’s Digital Biology Center. “To have greater sensitivity down to very, very low levels depends on being able to distinguish something from nothing. You need a system that inherently has very low noise.”

Droplet Digital PCR Is a Sensitive Tool for Detecting Residual HIV DNA

A great example of the clinical potential of ddPCR systems is the work of Matt Strain and Douglas Richman of the Center for AIDS Research at the University of California, San Diego School of Medicine, who validated the technology’s performance in HIV provirus detection. Subsequently, in collaboration with Deborah Persaud of Johns Hopkins Children’s Medical Center in Baltimore, the researchers used the technology to demonstrate that an infant born with HIV was functionally cured.

In a recent BioTechniques podcast, Dr. Strain said that ddPCR assays demonstrate an increase in precision and accuracy over their entire dynamic range relative to real-time PCR assays, particularly at low numbers. Additionally, the total cost per sample of Droplet Digital PCR assays is at least 10 to 100 times less than that of older chip-based digital PCR systems.

“When you’re talking about factors of a hundred or more in cost, there really isn’t any comparison,” said Dr. Strain.

Dr. Richman will present information on using ddPCR to detect latent HIV, including assaying rare events in a large number of cells and retrieving clinically relevant data.

A Glimpse at Droplet Digital PCR’s Future in Diagnostics

The research group headed by Hanlee Ji, an assistant professor at Stanford University School of Medicine, focuses on translational and clinical questions of cancer genetics that, once answered, have the potential to improve cancer patient care. The investigators have developed numerous methods for the accurate interrogation of cancer genomes that overcome challenges associated with clinical samples and the genetic variability resulting from tumor evolution. In this endeavor, Droplet Digital PCR is one of their chief tools.

“Droplet Digital PCR has accelerated our discoveries,” said Dr. Ji. “Given its ease of use, superior performance in terms of accuracy, and rapid development time for novel assays, Droplet Digital PCR has repeatedly demonstrated its vast utility and potential for future diagnostic application.”

Dr. Ji recently gave a talk on using ddPCR technology to track the presence, expansion, and disappearance of pathogenic genetic variants in cancer, infectious diseases, and other human diseases over time, and also discussed the technology’s potential for highly informative diagnostics. He now uses Bio-Rad’s recently launched second-generation ddPCR instrument, the QX200™ Droplet Digital PCR system, the only digital PCR system that works with both DNA-binding dye and TaqMan probe chemistries.

The QX100™ system boasts a lineup of prestigious users including:

  • Jim Huggett,the author of the digital MIQE (dMIQE) guidelines and a scientist at LGC (the UK’s designated National Measurement Institute for chemical and bioanalytical measurement)
  • David Dodd of the University of Texas, Southwestern
  • Leonardo Pinheiro of Australia’s National Measurement Institute
  • Ross Haynes of the U.S. National Institute of Standards and Technology
  • Vicki Hwang of the University of California, Davis
  • Alec Morley of Flinders University and co-author of the first paper to use digital PCR
  • Keith Jerome of the University of Washington
  • Gary Lee of Sangamo BioSciences
  • Sabita Sankar of MolecularMD
  • Donna Sullivan of the University of Mississippi Medical Center

There are also a number of emerging applications using ddPCR technology including microRNAs, single-cell gene expression, gene linkage, multiplexing, EvaGreen applications, and validating next-generation sequencing data.

For more information on the QX200 Droplet Digital PCR system, visit www.bio-rad.com/QX200.

To view Bio-Rad’s six-part webinar series on Droplet Digital PCR and the complete list of Droplet Digital PCR system publications, visit http://www.bio-rad.com/ddPCR-Webinars.

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.

Free Webinar: ‘Viewing Cancer Genomes at High Resolution’

 :: Posted by American Biotechnologist on 10-08-2013

Large-scale cancer genomics studies have established an extensive and unprecedented catalog of somatic mutations in multiple cancer types. This landscape was determined using mostly highly cellular, untreated primary tumors and is mostly static with limited implications to understand cancer progression and drug response in the clinic.

Tumors are composed of multiple cell types: stromal, immune or malignant cells. Malignant cells can also show sub-clonal heterogeneity, where different clones carry various somatic mutations and show variable oncogenic potential or drug sensitivity. Finally this sub-clonal population can change during the progression of cancer or as a consequence of the treatment. Additional genomic heterogeneity arises through the characteristic signatures of the various mutational processes that drive genome disruption during tumorigenesis, which highly powered technologies are beginning to resolve.

In a webinar presented by Bio-Rad and Genome Biology, Elaine Mardis (Washington University in St Louis), a world leader in the field of cancer genomics, and Olivier Harismendy (University of California San Diego), who is developing clinical assays in which next-generation sequencing is combined with digital PCR, discuss the latest developments and outstanding questions that relate to viewing cancer genomes at high resolution. The webinar will be open for audience discussion.

► Register for the webinar
New York (U.S.A. – New York) Wednesday, October 23, 2013 at 10:00:00 AM EDT
San Francisco (U.S.A. – California) Wednesday, October 23, 2013 at 7:00:00 AM PTD

Better Chromatography through Modular Design

 :: Posted by American Biotechnologist on 10-07-2013

“It looked like a Medusa,” said Farah Mavandadi. “I was scared of it.”

Mavandadi, a senior product manager at Bio-Rad, was not describing a monster in a nightmare or a creature seen from a diving bell, but rather a research-scale chromatography system. Sprawling over a lab bench, instead of snakes the system had bunches of electronic cables and fluidic tubing that writhed and tangled around its various components.

Despite resembling an unholy mashup between Rube Goldberg and Jason and the Argonauts, this system was highly valued by the researcher who had wrangled it together, lovingly making each complex connection and hand-coding each component into the analytical software. The reason? Flexibility. Despite its messiness, the researcher could rearrange her system to get the most efficient fluidic path, to have right kind of detector in place, or make any other tweak in order to perform the best possible separation. Between having an “easy” instrument and having one she could change as her chromatography needs required, this researcher chose to face “Medusa.”

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.