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Thermo Fisher Scientific Announces Next-Generation Sequencing Assay for Liquid Biopsy Research

Thermo Fisher Scientific

Oncomine Cell-Free DNA Assay is designed to target and detect mutations down to 0.1 percent allele frequencies from whole blood derived from lung cancer tumors

11 Jul 2016
Alex Waite
Editorial Assistant

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Clinical oncology researchers who need to draw more meaningful genetic data, now have access to the new Oncomine Lung Cell-Free DNA (cfDNA) Assay designed to target mutations in non-small cell lung cancer (NSCLC) samples derived from circulating cfDNA in blood.

When combined with Thermo Fisher Scientific’s Ion S5 System, the research assay meets a critical need for a multi-targeted, next-generation sequencing (NGS)-based solution that enables highly sensitive detection across a broad set of gene variants.

Research using liquid biopsy samples, is quickly becoming a strong complementary candidate to drive the future of precision medicine in oncology. By sequencing genetic material taken from standard blood samples, clinical researchers are able to improve their understanding of the tumor

composition and changing tumor heterogeneity. In particular, the approach is gaining interest because it is minimally invasive less expensive, and easily repeatable when compared to a typical tissue biopsy.

“When biopsies are not possible due to a tumor’s location, which is often the case with lung cancer, analyzing DNA that is freely circulating in the blood can provide a holistic view of tumor heterogeneity,” said José Luis Costa, Ph.D., principal researcher of the Institute of Molecular Pathology and Immunology of the University of Porto in Portugal. “Such a broad profile may not always be captured in a solid tumor biopsy because a sample may not reflect the tissue’s full molecular makeup.

“Using NGS, our lab was able to amplify more difficult samples and detect mutations down to 0.14 percent allelic fraction in blood plasma,” continued Costa. “This is an important benefit as data from liquid biopsy samples may help clinical researchers better understand how time and treatment can affect the mutational profile of tumor tissue, and how it may respond to therapeutic intervention in the future. The Oncomine Lung cfDNA Assay offers a targeted approach to access this information.”

The new assay contains gene targets, such as EGFR and KRAS, confirmed as relevant by industry-leading clinical research partners at the OncoNetwork Consortia. Enabling analysis with as little as 1 ng of DNA obtained from a single tube of blood, this assay helps clinical researchers obtain results from the initial sample or samples collected over time from the same subject. Verification data using the Oncomine Lung cfDNA Assay shows 90 percent sensitivity and >98 percent specificity at 0.1 percent limit of detection.

The Oncomine cfDNA Assay is part of a comprehensive solution that enables sample to answer variant data analyses in a single workflow. By using tag sequencing, a technology in which DNA fragments are each tagged with a unique molecular tag, Ion Torrent informatics software simply and easily detects and determines mutations to help limit the number of false positive data points for single nucleotide variants (SNVs) and insertions-deletions (indels) detected at such low allele frequencies.

Precision medicine is an exciting field in which Thermo Fisher is firmly committed to advancing,” said Jim Godsey, vice president of research and development for clinical next generation sequencing at Thermo Fisher. “As liquid biopsies become more prevalent, our end-to-end solution, from automated sample prep, to targeted NGS and analysis, will help take the field a step closer to one day making peripheral blood monitoring a routine approach for oncology treatment.”

Oncomine Lung cfDNA Assay is for research use only; not for use in diagnostic procedures.

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Genome AnalysisGenomics, the study of genomes, includes functional genomics, evolutionary genomics and comparative genomics. There are many genomic technologies such as DNA sequencing of whole genomes, computational biology and bioinformatics. DNA and nucleic acids must be isolated and concentrated from cells for analysis with kits, automated analyzers and software. Other useful technologies for studying genomics include PCR, microarrays and electrophoresis.Data AnalysisData analysis hardware and software is available to make data processing straight-forward yet powerful. Data software can be used for math and stats, technical graphing and image analysis. In addition, software is available for specific data analysis of electrophoresis, densitometry, ELISA and DNA sequencing.Chem / BioinformaticsCheminformatics and bioinformatics are computational techniques used in chemistry and biology, respectively, for data acquisition, processing and storage. Cheminformatics focuses on compound information, whereas bioinformatics is mainly applied to analysis and modeling of genomics, genetic and sequencing information. Hardware and software is available for data acquisition, analysis, management and storage.HematologyIn Haematology / Hematology, complete blood cell counts (or full blood counts) are obtained using automated blood count analyzers to enumerate blood cell types.  Hematology also encompasses haemostasis and coagulation, thrombophilia and hemophilia, plasma viscosity and ESR analysis, hemoglobinopathies, cell morphology and haematinic measurement.DNA / RNA Extraction and PurificationPurified DNA and RNA are required for numerous downstream molecular biology applications. Consequently, the importance of high-quality DNA/RNA extraction and purification equipment cannot be underestimated. 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Find the best DNA sequencing products, including DNA sequencing kits, genomic libraries and genetic identity kits in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Gene Expression and Molecular CloningMolecular cloning is a set of techniques that utilizes vectors to transfer recombinant DNA into host cells and is an essential tool for investigating the expression of genes and proteins in bacterial or mammalian cells. A variety of vectors optimized for gene cloning and expression in a range of host organisms are available, alongside competent cells for genetic replication. Here, you can explore a range of molecular tools, high-quality genomic and cDNA libraries, premade clones, transformation and transfection reagents and mutagenesis or gene expression detection assays and expression arrays. Find the best gene expression and molecular cloning products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.BiomarkersBiomarkers are biological markers which can be measured and evaluated to indicate a biological state. The use of biomarkers in research and diagnosis can indicate a normal or disease state or drug response of cells / tissues. Biomarkers include genetic markers, cell surface markers such as antigens, antibodies or receptors and secreted molecules such as cytokines. An assay system is required for identification of biomarkers. :Software PlatformsSoftware platforms are useful for various stages of laboratory experiments from data collection to data storage and processing. For instance lab software is available for system control, data management, data analysis and qualification / validation.Clinical GeneticsMolecular Genetics covers the analysis of hereditary genetic disease and chromosomal abnormalities. Genetics can be analysed using DNA, RNA, and protein microarrays, PCR, RT PCR and DNA sequencing. Genetic equipment includes genetic workstations, thermal cyclers, cooling blocks and electrophoresis products. Diagnostic kits are used for DNA / RNA extraction and purification.Next Generation SequencingNext-generation sequencing (NGS), also known as whole-genome sequencing, high-throughput sequencing and massive parallel sequencing, produces and analyses thousands to millions of nucleotide sequences at once. Sequencing systems operate via varying technologies depending on the manufacturer, including sequencing by synthesis, ligation, pyrosequencing, ion semiconductor and single-molecule real-time sequencing. 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Analyzing mutations is crucial in diagnostics, drug development, and personalized medicine. Explore mutation detection tools in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.Blood AnalysisThe analysis of blood is vital for many areas of life sciences and forensic investigations. Blood samples can be tested for a number of different reasons such as diagnosis, glucose levels, cholesterol and drug testing.TumorsTumor research focuses on understanding abnormal cell growth that leads to cancer. Identifying biomarkers, studying tumor microenvironments, and developing targeted therapies are critical for advancing cancer treatment. Early detection and personalized treatment options are key to improving outcomes for patients. Browse our peer-reviewed product directory to explore tools for tumor research, diagnostics, and cancer therapies; compare products, read customer reviews, and get pricing directly from manufacturers.

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Thermo Fisher Scientific Announces Next-Generation Sequencing Assay for Liquid Biopsy Research