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2014: A Year of Clinical Next Generation Sequencing

SelectScience
22 Dec 2014
Sonia Nicholas
Managing Editor and Clinical Lead

Editorial article

Although some scientists remain skeptical about the use of next generation sequencing (NGS) technology in the clinical diagnostics arena, the past year shows a steady advance in the use of this technology in clinical laboratories.

In January, the Massachusetts General Hospital (MGH) Center for Integrated Diagnostics in Boston announced that it was routinely profiling patient tumors with advanced molecular assays. The MGH had recently launched a novel targeted RNA-seq next-generation sequencing assay for clinical detection of gene fusions for ALK, RET, and ROS1; targets that are particularly important for patients with lung adenocarcinoma, for which there is the FDA-approved crizotinib inhibitor that has been demonstrated to be effective.

In April, PathGroup, a provider of pathology services in the US, announced the launch of the SmartGenomics™ Heme Profile. The profile includes NGS of 77 clinically actionable genes mutated in hematolymphoid cancers; providing genomic profiling and information for patients that have failed or been unsuccessful on repeated therapy for the group of cancers that include leukemias, lymphomas and myeloproliferative/myelodysplastic diseases.

In September, LabCorp® announced the launch of Enlighten Health Genomics; a business designed specifically to build on the diagnostic potential of NGS technology. The new service offers state–of-the-art diagnostic capabilities, NGS analysis and interpretation, and informed genetic counseling. The initiative is aimed at reducing medical costs and improving patient outcomes.

In the same month, Sophia Genetics became the first European company to obtain a CE-IVD mark for the clinical use of a Next Generation Sequencing (NGS) bioinformatic pipeline for routine genetic testing; and researchers developed a new metagenomic DNA sequencing method to diagnose tuberculosis on the Illumina MiSeq.

In October, the Life Technologies branch of Thermo Fisher Scientific announced that its Ion PGM Dx NGS System had been CE-Marked for IVD use in European countries. The system uses Ion Torrent NGS technology and is validated using a number of challenging germline variants, with library kits based on the trusted Ion AmpliSeq technology.

Finally, in November, Vela Diagnostics announced the launch of the first CE-IVD NGS Oncology Panel for melanoma testing. The Sentosa® SQ Melanoma Panel simultaneously detects 127 hot spot mutations and sequence variants, the panel is run on the automated Sentosa® NGS system.

There are still many challenges to be faced in bringing NGS to the routine diagnostic laboratory, but this last year has shown that great strides are being made in making advanced sequencing technology a viable reality.

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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.PCR and Thermal CyclingPolymerase chain reaction (PCR) kits and thermal cyclers are used for the in vitro amplification of DNA permitting subsequent analysis and experimental procedures. Explore a range of high-quality polymerase, primers and nucleotides or simplify your workflow with a PCR mastermix. Find reverse transcription PCR (RT-PCR) and cDNA synthesis kits for RNA products and libraries. Quantitatively measure the amplification of DNA with real-time PCR (qPCR) and droplet digital PCR (ddPCR) kits and systems, and discover automated PCR setup solutions to increase throughput. Alternative DNA amplification methods also include recombinase polymerase amplification (RPA) kits. Find the best PCR kits and thermal cyclers and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.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.ImmunologyImmunological techniques measure and characterize immune responses. Immunology kits and analysis systems often use techniques such as ELISA, radioimmunoassay (RIA) and immunodiffusion assays, Immunohistochemistry, and flow cytometry. Immunologists use equipment such as flow Cytometers, plate readers, plate washers and fluorescent microscopes.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. For NGS, library preparation is paramount to successful sequencing. In this section, explore a range of library preparation kits, from targeted, amplicon-based or hybridization-based kits including epigenomic, transcriptomic and genomic workflows to fragmentation kits. Find the best next-generation sequencing products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Clinical NGSNext Generation Sequencing (NGS) refers to the use of massive parallel sequencing of multiple small fragments of DNA. This high-throughput genomic analysis yields enormous amounts of sequence data, which if appropriately analyzed could have huge potential for clinical laboratories. For this to happen there are technique and bioinformatic hurdles to be overcome.

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