Multi-Site Study Validates End-to-End RNA-Seq Sample Prep Workflow For Human Whole Blood Clinical Samples
San Carlos, CA, Piscataway, Jul 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 outlined the study results on July 14, 2015, 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 (AnyDeplete) 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 Technologies, Inc.
Based in San Carlos, CA, NuGEN Technologies, Inc. provides innovative products used to prepare biologic samples for targeted genomic analysis. NuGEN products are used in more than 1000 leading life science institutes and in diagnostic and pharmaceutical companies in 40 countries. It has a long history of launching products with market leading specs, including the recent launch of Ovation SoLo RNA Seq System that enables targeted depletion of unwanted transcripts and library construction from single cells, and Ovation Fusion Panel Target Enrichment System that enable detection of gene fusions across 502 genes that are implicated in cancer. To learn more about NuGEN visit www.nugen.com.
Priya Balachandran, NuGEN Technologies, Inc., firstname.lastname@example.org