Posts Tagged by life science
|October 6, 2015||Posted by Anharris under Client Releases, Highlight 2, Innovation, Life Science, Press Releases|
Sequence data generated with NuGEN’s target enrichment technology can be processed in BaseSpace using new app to mark duplicates and perform quality trimming
San Carlos, CA -OCT. 6– NuGEN Technologies is pleased to announce that scientists and clinicians using its Ovation Target Enrichment System to prepare biologic samples for genomic analysis can now process resulting sequence data in BaseSpace–a cloud computing platform, hosted by Illumina, Inc.
“NuGEN’s new Ovation Target Enrichment System Data Processing Application will allow the large community of Illumina sequence platform users to further streamline the rapid and convenient workflow of our Ovation Target Enrichment System products,” said Alan Dance, VP of Marketing at NuGEN.
The Ovation Target Enrichment product line employs Single Primer Enrichment Technology (SPET), a novel approach for enrichment of genomic DNA targets or cDNA for RNA target regions. SPET products allow researchers and clinicians to quickly and accurately enrich biologic samples for sensitive detection of a wide range of genomic markers including mutations, SNPs, indels, gene fusions, alternately spliced transcripts and copy number variants.
The new NuGEN-application, published on BaseSpace on September 30, provides an intuitive user interface for uploading sequence data. The application performs quality trimming and probe trimming on the parsed data – removing data derived from bases with low sequencing quality scores and aligning high quality data to the UCSC human reference genome.
Subsequently, PCR duplicate reads created during the library amplification process are identified using a random N6 sequence, unique to the Ovation Target Enrichment System workflow positioned adjacent to the barcode index.
Output files from the Ovation Target Enrichment System Data Processing Application for BaseSpace include processed BAM files with PCR duplicates removed or marked, processed FASTQ files with duplicates removed, and UCSC bigWig tracks with duplicates removed for visualization using the UCSC human genome browser.
For full details, visit http://www.nugen.com/content/ovation-target-enrichment-system-data-processing-application.
NuGEN Technologies Inc. is a rapidly-growing, privately-held company providing innovative products and systems for the preparation of biologic samples for targeted genomic analysis. Founded in 2000 and based in San Carlos, CA, NuGEN has long been at the cutting edge of genomic technology, with accurate, cost-effective reagent kits for even the most challenging sample types. NuGEN products are used in more than 1000 leading life science institutes and in diagnostic and pharmaceutical companies in 40 countries.
Anita Harris, Harris Communications Group
The Harris Communications Group is an award-winning PR and marketing firm specializing in outreach for health care, life sciences and technology, worldwide.
|July 28, 2015||Posted by Anharris under Highlight 2, Innovation, Life Science, PR, Uncategorized|
MULTI-SITE STUDY VALIDATES END-TO-END RNA-SEQ SAMPLE PREP WORKFLOW FOR HUMAN WHOLE BLOOD CLINICAL SAMPLES
System integrates PreAnalytiX GmbH and NuGEN Technologies innovations to ensure reliable, reproducible, cost-effective RNA-Sequencing analysis. Corporate study alliance model critical to standardization, bringing genomics to the clinic.
San Carlos, CA and Piscataway, NJ, July 15, 2015— A multi-site study has clinically validated an end-to-end workflow for the collection, storage, transport and preparation of human whole blood samples for RNA-Sequencing (RNA-Seq). The study, initiated in January 2015, integrated products from PreAnalytiX GmbH and NuGEN Technologies, which worked collaboratively with RUCDR Infinite Biologics at Rutgers University to measure the system’s efficacy for transcriptome profiling with clinical samples.
“We have determined that the PreAnalytiX/NuGEN integrated workflow ensures reproducible, accurate and sensitive results in RNA-Seq of whole blood. Importantly, this integrated workflow enables gene expression from total RNA, allowing researchers to study both protein coding and regulatory transcripts from human whole blood,” said Dr. Andrew Brooks, Chief Operating Officer of RUCDR Infinite Biologics, who led the study. Brooks is also an associate professor of Genetics at Rutgers University and directs the Bionomics Research and Technology Center at the Environmental and Occupational Health Science Institute there. Brooks will outline the study results on Tuesday, July 14 at the International Leaders in Biobanking Conference, in Toronto.
“This study is critical for clinical researchers because it demonstrates that by using the combined PreAnalytiX and NuGEN workflow, scientists in laboratories around the world can confidently share not only their data but also their samples,” Brooks said. “And, by joining forces to validate the combination of their proprietary technologies, PreAnalytiX and NuGEN have taken the lead with RUCDR to deliver the standardization needed for broader adoption of genomics in the clinic.”
Brooks explained that total RNA derived from patient blood samples is used for a myriad of clinical genomics applications—such as discovery and analysis of disease-related biomarkers, identification of new therapeutic targets and monitoring disease progression and treatment. But there are factors that present challenges to data integrity when using whole blood. Collection, storage, purification, handling and transport methods may vary. Nucleic acids can degrade during handling and processing, resulting in unreliable results and bias in transcript abundance. Whole blood also contains high levels of uninformative ribosomal RNA and reticulocyte globin RNA, which can reduce sequencing efficiencies and increase costs. Moreover, variation between sites and operators makes it difficult to standardize results among researchers and laboratories. “If researchers across multiple sites obtain different results, we need to be sure the variations are attributable to changes in the biology and not the technology,” he said.
At the Biobanking Congress, Brooks reported tight correlation in results across three sites in New Jersey with multiple operators, using several nanograms of total RNA from each of 10 subjects. That is, using PreAnalytiX technology for extraction, storage and transportation of samples and NuGEN technology for library formation and depletion of ribosomal RNA and globin prior to whole transcriptome analysis, the study team found high reproducibility of results across sites, operators and equipment. “The combined workflow led to reproducible whole blood collection and storage; reproducible and robust RNA extraction; reproducible and consistent library creation; and tight performance correlations across and within sites,” he said.
“This integrated sample prep workflow will be important for scientists seeking new genetic biomarkers for disease. It will be valuable to pharmaceutical clinical trials for determining if a therapeutic leads to genetic changes in a particular cancer. And it is important to the future of clinical research because it allows the development of guidelines and standards for scientists who want to share samples, not just data, globally, across sites and experiments,” Brooks said. “Without such standardization, many results might never advance to the clinic.”
The study used the PreanalytiX PAXgene Blood RNA System for whole blood collection, storage and RNA extraction and NuGEN’s Insert Dependent Adaptor Cleavage (InDA-C) technology from the NuGEN Ovation Human Blood RNA-Seq System to prepare strand-specific RNA-Seq libraries and for ribosomal/globin depletion. RUCDR Infinite Biologics oversaw sample collection, processing and data analysis.
NuGEN Technologies is the leader in providing solutions which make biological samples accessible for genomic analysis, enabling scientists to capture the truest biology achievable, independent of the quantity or quality of the samples. The company has commercialized numerous proprietary DNA and RNA sample preparation products for use in research and diagnostic applications. Founded in 2000, NuGEN Technologies, Inc. is privately held and headquartered in San Carlos, CA. For more information please visit www.nugen.com
About RUCDR Infinite Biologics
RUCDR offers a complete and integrated selection of biological sample processing, analysis and biorepository services to government agencies, academic institutions, foundations and biotechnology and pharmaceutical companies within the global scientific community. RUCDR provides DNA, RNA and cell lines with clinical data to hundreds of research laboratories for studies on mental health and developmental disorders, drug and alcohol abuse, diabetes and digestive, liver and kidney diseases. RUCDR completed an $11.8 million expansion and renovation of its facilities in May 2013. Read more at www.rucdr.org
NuGEN and Ovation are registered trademarks of NuGEN Technologies, Inc.. PreAnalytiX and PAXgene are registered trademarks of PreAnalytiX GmbH.
The Harris Communications Group is an award-winning Life Science PR and thought leadership firm based in Cambridge, MA.
|June 23, 2012||Posted by Anharris under Health, Innovation, Life Science, Technology|
Had a great time at the BIO International Convention in Boston, last week. Met teams from Norway, Australia, France, India, Israel…not to mention New York, North Carolina, Maryland, Oklahoma, etc.
Attendance, at 15,000, was down from its 25,000 high here five years ago but I found participants friendly and accessible. HarrisCom advisor Christa Bleyleban said she counted more than 70 parties or networking gatherings (not a few of which I attended).
While the overall theme was” innovation,” it was a trend toward collaboration that I noticed most.
- Cancer collaboration clusters in Oslo, Toulouse, the UK and Massachusetts were showcased at a program sponsored by the Massachusetts Technology Transfer Center, on Sunday.
- A collaboration between four Massachusetts and four Israeli companies was announced on Tuesday
- Collaborations between Massachusetts and Catalonia, in Spain, and between Massachusetts and Medicon Valley, in Sweden and Denmark, were announced on Wednesday.
- Also on Wednesday came the announcement that seven global companies have joined forces to fund preclinical neuroscience research in Massachusetts universities. While the funding is a paltry $2–the announcement will come as good news for scientists seeking early stage funding–but heightens concerns that industry will waylay– or have too much power in setting agendas for– basic research.
At a meeting sponsored by Polaris Ventures, industry execs and VCs discussed the shift of VC funds from biotech to the tech sector–which is occurring in part because tech investments can lead to quicker returns. One observer commented that pharma companies themselves are the new VCs–investing in early stage research rather than doing the research themselves.
In that regard, I partnered with the Communications Strategy Group on a press conference and outreach in which the Swiss company AC Immune announced a $400M licensing agreement with Genentech for development of an antibody to combat Alzheimer’s disease.
Also of interest was a keynote talk, sponsored by Scientific American, in which CNN’s Fareed Zakariah asked whether the US will continue to maintain its lead in technologic innovation.
For more details, please visit my postings at New Cambridge Observer.
–Anita M. Harris
Anita Harris is President of the Harris Communications Group, an award-winning PR, marketing and communications firm headquartered in Cambridge, MA.
|June 6, 2012||Posted by Anharris under Cool Companies, Health, Innovation, Life Science|
Met the other day with Rob Johnson, who will soon be launching UK-based Alacrita, a global life science consulting firm, to Cambridge, MA.
Johnson co-founded the company two years ago with Anthony Walker, who had previously served as Executive Director of Global External R&D Europe at Eli Lilly. Johnson had led business development at Onyvax, a biotech company that developed biopharmaceuticals to combat cancer.
Drawing on the capabilities of more than 50 consultants worldwide, Alacrita provides strategic, operational, technical advice or hands-on project management to organizations of all sizes in the pharma, biotechnology and life science industries, Johnson said.
The company name is based the Latin, “alacritas,” or “lively.”It is meant to convey “a cheerful readiness.”
Clients may be academic institutes, tech transfer experts, life science investors, startups or established companies in need of expertise in business development and marketing, intellectual property, product development, and regulatory affairs, according to Johnson.
Whitepapers available for free on Alacrita’s Web site include:
- Biotech in Israel: A Land of Promise » May 2012 – by Anthony Walker, PhD
- FDA Approvals Provide Reason For Cheer » March 2012 – by Robert Johnson
- Deal Watch Annual Review 2011 » January 2012
- Viewpoint: Pharma Industry Myths » January 2012 – by Anthony Walker, PhD
- Europe’s stellar decade of prostate cancer innovation » September 2011 – by Rob Johnson
- Are we all biotech now? » June 2011 – by Anthony Walker and Rob Johnson
- China: Opportunities for biotech firms » March 2011 – by Rob Johnson and Li Zeng
- Re-Profiling: a Hidden Threat to Originators? » February 2011 – by Dr Jo Davies
- Deal Watch Annual Review 2010 » January 2011 – by Roger Davies and Jill Ogden
- Mitigating Out-sourcing Risk » December 2010 – by Robert Johnson and Anthony Walker
- Deal Watch: a Review of Notable Deals » October 2010 – by Sharon Finch
Alacrita’s US offices will be located in the Cambridge Innovation Center in Kendall Square, Johnson said.
–Anita M. Harris
Anita Harris is president of the Harris Communications Group, a strategic PR & marketing communications firm located in Cambridge, MA.
|January 6, 2012||Posted by Anharris under Cool Companies, HarrisCom News, Health, Innovation, Life Science|
Life Science Startup to Target Multiple Disease Mechanisms
I’m pleased to report that Harris Communications Group Advisory Board Member Robert Langer of MIT is involved in yet another life science startup.
It’s a biotech company called “Blend Therapeutics” that will develop a new class of medicines possessing “unprecedented ability to precisely control each agent’s therapeutic action in concert… ” The goal is to “predictably, effectively, and safely target the multiple mechanisms underlying complex diseases, ” according to a press release.
Blend was founded by three leaders in the fields of chemistry and nanomedicine: Langer, who is David H. Koch Institute Professor at the Massachusetts Institute of Technology; Stephen J. Lippard, PhD, Arthur Amos Noyes Professor of Chemistry at MIT; and Omid Farokhzad, MD, Director of the Laboratory of Nanomedicine and Biomaterials and Associate Professor of Anesthesia, Brigham and Women’s Hospital and Harvard Medical School.
Blend has received financial backing from Flagship Ventures, New Enterprise Associates and NanoDimension.
Langer said: ” We see unparalleled opportunity to translate innovative science into important drugs for patients in need, and we’re excited by the strength of our founding investors and management who share our vision of building a successful biotechnology company that is foremost about improving the lives of patients.”
In addition to Langer, Lippard and Farokhhzad, Blend’s Scientific Advisory Board includes eight thought leaders in the fields of chemistry, cancer biology, immunology and medicine:
• Dennis Ausiello, MD, Chief of Medicine and Jackson Professor of Clinical Medicine, Massachusetts General Hospital and Harvard Medical School
• Philip Kantoff, MD, Chief Clinical Research Officer and Professor of Medicine, Dana Farber Cancer Institute and Harvard Medical School
• Alexander Klibanov, PhD, Novartis Professor of Chemistry and Bioengineering, Massachusetts Institute of Technology;
• Ulrich von Andrian, MD, PhD, Mallinckrodt Professor of Immunopathology, Harvard Medical School
• Bruce R. Zetter, PhD, Charles Nowiszerski Professor of Cancer Biology, Children’s Hospital Boston and Harvard Medical School.
MaestroTM is a trademark of Blend Therapeutics, Inc. More information is available at http://www.blendtx.com.
—Anita M. Harris
Anita Harris is the president of Harris Communications Group, a Cambridge, MA public relations firm specializing in strategic marketing communications, thought leadership and social media for companies involved in health, science, technology and energy, worldwide. She also blogs at newcambridgeobsersver.com.
|December 6, 2011||Posted by Anharris under Cool Companies, Health, Life Science, Technology|
[Disclosure: please see below]
Two Forsyth Institute scientists and a Lexington, MA entrepreneur have launched PhotOral (TM)to develop and market the first consumer device using blue light to combat gum sisease.
Scientists Nikos Soukos, director of Forsyth’s Applied Molecular Photomedicine Laboratory and J. Max Goodson, senior member of the staff, found when testing the effectiveness of blue light in tooth whitening equipment, their patients’ gum health improved. They determined through research published in 2005 (see below) that such light can selectively kill pathogenic oral bacteria–without harming so-called “good bacteria” that exist in normal mouths–and began work on a device.
This year, Forsyth received a patent for the proposed blue-light treatment method; Soukos, Goodson and entrepreneur Stamatis Astra founded PhotOral; and, in September, PhotOral received an exclusive license from Forsyth to commercialize the technology.
The device will look “either like a mouth guard or a lollipop,” Soukos said.
It will work by shining certain light wavelengths onto the teeth, which act as mirrors to deliver the light to dental pockets between the teeth. Inserted into the mouth twice a day for 30-60 seconds, it should selectively target pathogenic bacteria and, as a cumulative effect, suppress them to prevent periodontal disease. It will not replace brushing or flossing–but, rather, will allow consumers an additional method for improving their oral health.
Most current consumer treatments–such as flossing, tooth brushing and antiseptics–seek to eliminate all sorts of the 700 bacteria found in the mouth, Soukos explained. But some of those bacteria are beneficial. “Our device aims to selectively target ‘bad bacteria’ in order to restore a healthy balance in the mouth.”
By doing so, the team hopes to help prevent or treat gingivitis, which occurs in 90% of adults, and periodontitis, which affects some 34% of adults in the US over 30. Severe periodontitis, which may be treated with medication, by scaling and planning or surgically, affects 13% of all adults. It can lead to loss of bone and teeth and is suggested as a risk factor for coronary based heart disease, atherosclerosis, pre-term births and chronic kidney disease.
Stamatis, the PhotOral CEO, said he is currently raising funds to support prototype production, clinical trials and marketing operations. “The potential market for the device is greater than $7B”
Soukos and Goodson’s research, published in the April, 2005 Journal of Antimicrobial Agents and Chemotherapy, suggested that light in the blue region of the visible spectrum might be useful in preventing, controlling or treating periodontitis-an oral infection that can lead to loss of bone and teeth.
Among the most destructive oral bacteria are the so-called “black-pigmented” bacteria (BPB), which are implicated as pathogens associated with periodontitis. Such bacteria accumulate black pigment consisting mainly of organic compounds called porphyrins . Some porphyrins are photosensitive and, when activated by light, induce a photodynamic reaction that kills the microorganism within seconds.
Before starting their research, Soukos and Goodson knew that other researchers had used lasers to deliver red or green light, which partially inactivated certain oral bacterial. The team also knew, from published reports, that porphyrins absorb blue light more readily than light that is red or green.
The Forsyth scientists employed a halogen lamp source commonly used for tooth whitening to shine broadband light composed mainly of blue and a small percentage of green light on pure cultures of BPB and on dental plaque samples obtained from individuals with chronic periodontitis. They found that the light rapidly killed BPB in pure cultures and that it selectively eliminated BPB in plaque samples containing 50o0-6000 different bacteria. They also found that certain species were more readily inactivated by the light than others and that varying the intensity and exposure time had different impacts on different bacterial species. The researchers concluded that intraoral light exposure can selectively reduce pathogens in dental plaque.
–Anita M. Harris
Anita Harris is president of the Harris Communications Group, a Cambridge, MA public relations firm specializing in strategic communications, thought leadership and content strategy for companies and organizations in health, science and technology, worldwide. The Forsyth Institute and Goodson are former clients; Soukos serves on her advisory board, and she is an unpaid advisor to PhotOral. Harris won a 2006 International Communicator Award for her work in publicizing the Forsyth “Blue Light ” paper. She also blogs at New Cambridge Observer.