Posts Tagged by NGS

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: 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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