Posts Tagged by NuGEN

NuGEN Webinar: Sample Prep for NGS Cancer Detection in 500+ Gene Targets

Available on demand until March 22, 2016

SAN CARLOS, Calif.–(BUSINESS WIRE)–NuGEN Technologies is pleased to present a Webinar featuring the company’s newly launched Ovation Cancer Panel 2.0 Target Enrichment System–a sample preparation technology that allows NGS (next generation sequencing) detection of multiple changes in more than 500 individual genes implicated in cancer– from a single sample preparation.

Released in August, the new reagent kit updates NuGEN’s well-established Ovation Cancer Panel Target Enrichment System. It enables comprehensive and efficient NGS analysis of cancer samples in a single workflow by both (1) enriching for an improved and larger selection of cancer-related genes and (2) enabling the detection of gene-level copy number variations in addition to SNPs, mutations and indels. The new method can be used with either fresh or FFPE tissue sections to deliver sensitive and reproducible targeted genomic analysis. It can also be rapidly customized to provide target enrichment kits for any gene sets defined by the researcher within a target size range that may include thousands of genes or just a few.

Typically, to analyze single nucleotide mutations and copy number changes in a sample, researchers have had to employ completely different analysis of both types of changes. NuGEN’s new method allows simultaneous targeted analysis of both types of changes, from a single sample preparation, on a choice of Illumina NGS systems. It thus allows more comprehensive and efficient analysis of cancer samples.

The Webinar, which originally aired on September 22, 2015, is moderated by John Sterling, managing editor of Genetic Engineering and Biotechnology News. It features presentations by Luke Sherlin, PhD, NuGEN’s Director of Technical Support, and Stephanie Huelga, PhD, NuGEN’s Lead Bioinformatics Scientist. The speakers present data from target-enrichment studies with a 509 cancer gene panel using a simple protocol that generates sequence-ready libraries from good quality DNA as well as DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. The Webinar also includes a question and answer session with participating scientists.

The Ovation Cancer Panel 2.0 Target Enrichment System is the latest release in the company’s drive to offer tools for targeted resequencing that provide basic and clinical researchers with a holistic view of the underlying molecular biology of disease.

The Webinar will be available on the website of Genetic Engineering and Biotechnology News free of charge until March 22, 2016. To log on, please click here.

About NuGEN

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.

The Harris Communications Group is an award-winning life science PR firm in Boston.

NuGEN Launches BaseSpace Cloud App to Help Streamline NGS Analysis

 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.
Media Contact:
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.

 

Life Science PR: NuGEN launches sample prep kit for NGS analysis of multiple gene changes

Optimized for analysis of SNPs, mutations and copy number changes in 500+ cancer gene targets

Rapidly customizable for discovery, validation and highly-targeted clinical diagnostic testing in a single assay

NuGEN Technologies, of San Carlos, CA, today launched a sample preparation product that allows NGS detection of multiple changes in more than 500 individual genes implicated in cancer.

The reagent kit, based on NuGEN’s Single Primer Enrichment Technology (SPET), is called the Ovation Cancer Panel 2.0 Target Enrichment System. The new kit updates NuGEN’s well-established Ovation Cancer Panel Target Enrichment System both by enriching for an improved and larger selection of cancer-related genes, and by enabling the detection of gene level copy-number variations (CNV) in addition to SNPs, mutations and indels, in a single workflow. It can be used with either fresh or FFPE tissue sections to deliver sensitive and reproducible targeted genomic analysis.

The method can also be rapidly customized to provide target enrichment kits for any gene sets defined by the researcher within a target size range that may include thousands of genes or just a few.

The new product is the latest release in the company’s drive to offer tools for targeted resequencing that provide basic and clinical researchers with a holistic view of the underlying molecular biology of disease.

“We’re excited by this latest product introduction,” said NuGEN CEO Elizabeth Hutt. “The Ovation Cancer Panel 2.0 Target Enrichment System enables a more comprehensive picture of the biology of a particular sample. And by making it possible to analyze mutations, SNPs and gene copy number changes in a single assay, the new system will save researchers time and money and allow more efficient use of samples.”

Typically, to analyze single nucleotide mutations and copy number changes in a sample, researchers have had to employ completely different analysis platforms. NuGEN’s new method allows simultaneous targeted analysis of both types of changes, from a single sample preparation, on a choice of Illumina NGS systems.

According to Robert P. Sebra, Ph.D., Director of Technology Development at the Icahn Institute and Department of Genetics and Genomic Sciences at the Icahn School of Medicine at Mount Sinai in New York: “The underlying cause of cancer involves critical alterations in the genome. These alterations may include point mutations, changes in gene copy number, combinations of these, and other genomic changes. Having a common NGS workflow to simultaneously detect multiple types of variations would be invaluable because it would conserve precious patient samples and offers the ability to reproduce or validate results.”

Hutt added: “For cancer research, combined mutation and CNV analysis is a valuable complement to NuGEN’s recently released Ovation Fusion Panel Target Enrichment System, which also uses SPET to detect both known and unknown gene fusions in all exons of a 500 gene panel.”

About NuGEN

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.

About HarrisCom:
The Harris Communications Group is an award-winning PR and digital marketing firm based in Cambridge, MA. 

Life Science PR: 3 Companies Validate NGS Sample Prep Workflow

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.

About NuGEN

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. 

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Life Science PR: NuGEN on fusion detection

Pleased that  HarrisCom  life science PR client, NuGEN Technologies, has published an article in the journal PLOS ONE on a technology that allows scientists to use targeted next generation sequencing to screen for fusion events–gene abnormalities related to certain cancers.  They believe their new method  could help accelerate cancer research and development of treatments and diagnostic tests.   Here’s the press release: 

San Carlos, June   Scientists at NuGEN Technologies, Inc. have simultaneously surveyed RNA of more than 400 targeted genes in a single assay,  using next generation sequencing (NGS) to  detect fusions known to be key drivers of tumor growth in several cancer types. The scientists, who employed an innovative method of targeted sequence library preparation, also discovered low-frequency fusions that had not previously been reported.

The new method, which allows the simultaneous interrogation of multiple, specific genes for RNA sequencing, significantly simplifies fusion detection when compared with standard RNA sequencing approaches.

Based on NuGEN’s Single Primer Enrichment Technology (SPET), the method  “can greatly enhance scientists’ ability to understand the underlying oncogenic impact of a variety of genomic disruptions,” according to Elizabeth Hutt, the NuGEN CEO. “Applications based on this exciting new technology promise to speed up cancer research and lead to more effective diagnoses and treatments.”

As described in the June 1, 2015 issue of the peer-reviewed journal PLOS One, the scientists used the new method to prepare cancerous and normal tissue samples for targeted RNA sequencing.  The goal was to detect the presence of genes that had joined together or “fused”—resulting in disruption of regulatory mechanisms.  Through NGS, the scientists were able to identify multiple known and previously unreported fusions from fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue.
By targeting specific RNAs for sequencing, the scientists report, they were able to reduce the number of sequencing reads and increase the sensitivity of gene fusion detection, when compared with standard RNA-Seq methods.

“Traditional methods require a much larger number of sequencing reads in order to detect fusion events in a background of some 20,000 transcripts,” said Douglas Amorese, NuGEN Vice President of Research and Development. “Other focused methods cannot survey the entire repertoire of previously recognized fusions; they are limited to detection of small numbers of potential events.”

Additionally, the scientists write in PLOS, “The SPET-based assay is easy to use, has low RNA input requirements and can be used with RNA from formalin fixed, paraffin embedded (FFPE) tissue, which is important for clinically relevant samples. “ The assay is fully customizable to target any gene or set of genes in any genome.”

The new technology is one in a suite of sample preparation products NuGEN continues to develop in light of new scientific understanding about the shared molecular mechanisms underlying cancers originating in different tissues, according to Amorese.  While a tumor might appear to originate in a specific organ, the molecular mechanism or change involved may also play a role in cancers originating elsewhere.  (For example, certain breast and ovarian cancers exhibit similar genetic disruptions). This means that therapeutics effective in treating one type of tumor may also be useful in treating other tumors exhibiting similar molecular changes.

“Our technology allows researchers to better understand the cellular pathways that are disrupted,” Amorese said.

NuGEN’s new technology, offered in easy-to-use reagent kits, will initially be employed by researchers and clinical oncologists seeking to group tumors by genomic signature. “Such classifications will make it possible to develop and target therapies more effectively,” Amorese said.

The new, SPET-based technology will also be used by laboratories developing diagnostic tests and by pharmaceutical companies to develop, test and predict the efficacy of specific therapeutics for individual cancer patients. All of the above will   contribute to the realization of precision medicine, Hutt said.

Amorese likened the new SPET method to “a microscope with greater power to detect fusions than has ever before been available.” Now, he said, “you can look for potential fusion events among hundreds of genes known to be associated with tumors just as easily as you can look at a single gene.  Tests that narrowly focus on small subsets of potential fusions can be misleading and fail to take advantage of the power of next gen sequencing.  Those tests are just scratching the surface as it relates to understanding what is happening in the cell.  ” Amorese said.

The complete article, “An Efficient Method for identifying gene fusions by targeted RNA sequencing from fresh frozen and FFPE samples,”  is by  Jonathan A. Scolnick, Michelle Dimon, I-Ching Wang, Stephanie C. Huelga, and Douglas A. Amorese, all of NuGEN Technologies. The article will be available free of charge at 2 pm July 1, 2015 at http://dx.plos.org/10.1371/journal.pone.0128916 http://dx.plos.org/10.1371/journal.pone.0128916 . For an advance copy, please contact Anita Harris, anita.m.harris at harriscom.com.

 

NuGEN Technologies Inc. is a rapidly-growing, privately-held company that provides  innovative products and systems used to prepare 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.