Sequencing

Company Announcements

In May, Agilent Technologies announced in its quarterly conference call that it expects to spend $15 million in the second half of this fiscal year, and $35 million in both fiscal 2018 and fiscal 2020 on its sequencer development work with Lasergen (see IBO 4/15/18). In June, the Wellcome Sanger Institute and Pacific Biosciences announced the results of a collaboration to sequence more than three thousand of the world’s most dangerous bacteria, which are part of the National Collection of Type Cultures. Zymo Research and CosmosID partnered in June to combine their respective microbiomics portfolio and microbiome database to identify bacterial constituents of microbial communities, as well as microbial kingdoms such as fungi. In June, Lexogen and Bluebee announced a collaboration to implement Lexogen’s QuantSeq Unique Molecular Identifiers (UMI) data analysis pipeline on the Bluebee genomics analysis platform. The Milwaukee Journal Sentinel reported in June that Roche plans to close its facility in Madison, Wisconsin, following the launch of a new target enrichment product late next year, which will supplant the products currently manufactured at the facility. All of the location’s 79 people are expected to be laid off by June 2020. In June, Phase Genomics received a two-year, $1.5 million Phase II Small Business Innovation Research grant from the National Institute of Allergy and Infectious Diseases. The grant will be utilized to develop an affordable, high­-throughput Hi­C kit and computational analysis platform to accelerate microbiome research and discovery.  

Product Introductions

In May, Hamilton Bonaduz launched the ID NGS-V STARlet solutions for post-PCR sample preparation steps of the ForenSeq DNA Signature Prep Kit from VeroGen. Up to 96 samples can be processed without any user intervention. Five panels have been validated: the Precision ID Identity Panel, Precision ID Ancestry Panel, Precision ID mtDNA Whole Genome Panel, Precision ID mtDNA Control Region Panel and Precision ID GlobalFiler NGS STR Panel v2. MediSapiens released in May the cloud-based Genius, a genomics data management and querying platform for working with population-scale genomic resources in real time without the need to invest heavily on IT infrastructure. In June, Databricks introduced the Databricks Unified Analytics Platform for Genomics, a single platform for genomic data processing, tertiary analytics and AI. Pacific Biosciences debuted in June the Microbial Multiplexing Kit. Multiplexing can be achieved by incorporating a unique barcode for each microbe into the SMRTbell adapters after shearing genomic DNA using a streamlined library construction process. In June, 10x Genomics launched its Single Cell Mouse Immune Profiling Solution, providing the ability to simultaneously and deeply characterize single-cell gene expression and paired receptor sequences of T- and B-cells in mouse models of disease. New England Biolabs released in June the NEB Next Single Cell/Low Input RNA Library Prep Kit for Illumina sequencers. The Kit incorporates a template switching protocol and the Ultra II FS enzymatic DNA fragmentation technology for enzymatic cDNA fragmentation, end repair and dA-tailing reactions in a single enzyme mix. The company is also offering a reagents-only module for cDNA synthesis and amplification. In June, Oxford Gene Technology expanded its SureSeq myPanel NGS Custom Cancer Panel content to cover 120 fully optimized cancer-related genes. Illumina launched in June two new consumables for its NovaSeq 6000 Sequencing System: the S4 200 Cycle Kit enables customers to extend their research across more applications including single-cell and exome sequencing; and the S Prime (SP) Flow Cell, designed for smaller run sizes and/or applications that require lower sequencing output. That kit will be available in 100 and 300 cycle configurations, with an output of 250G (300 cycle). In June, Thermo Fisher Scientific debuted the Ion AmpliSeq HD technology for library preparation. The company stated that it provides clinical researchers for the first time with the flexibility to custom design gene panels without sacrificing the ultra-high sensitivity required to find low-frequency variants in cell-free DNA (cfDNA) and highly heterogeneous solid tumor samples. The AmpliSeq HD enables custom design flexibility for SNVs, small insertions/deletions (indels), fusions and CNV detection with a limit of detection as low as ≤ 0.1 percent in blood samples. The heightened sensitivity is enabled with proprietary molecular tags, and dual barcoding of the fragments of interest. Thermo Fisher Scientific introduced in June the dual barcode indexing-based Oncomine TCR Beta-SR Assay for immuno-oncology research, designed to characterize T-cell clonality in the tumor microenvironment. Oncomine TCR Beta-SR Assay is designed to specifically interrogate the CDR3 region of the beta chain of the T-cell receptor, a region that is responsible for antigen recognition and important in uniquely identifying T-cell clones. Twist Bioscience launched in June the expansion of its NGS solutions product line to include the high-throughput Twist Human Core Exome Kit, a library preparation and target enrichment kit, with the ability to run up to 96 samples simultaneously. Twist Bioscience believes it is the only company to offer double-stranded DNA probes within a comprehensive target enrichment kit used for exome and targeted sequencing. In June, QIAGEN introduced customizable QIAact target enrichment panels for analysis of more than 13 hereditary disease groups for its GeneReader NGS System. The solutions integrate QIAGEN’s QCI analysis and interpretation solutions, in particular the HGMD Human Gene Mutation Database.  

Sales and Orders of Note

In June, Fabric Genomics announced the addition of 10 new commercial partners: the Centre for Proteomic and Genomic Research in South Africa; King Fahad Medical City in Saudi Arabia, its first customer in Middle East; Sheffield Diagnostic Genetics Service in England; Children’s Hospital of Eastern Ontario–Research Institute and the University of Calgary’s Department of Medical Genetics, both in Canada; Landspitali, the National University Hospital of Iceland; the Kennedy Center (Clinical Genetics Clinic) in Denmark; and the National Center for Global Health and Medicine and a2 sigma, both in Japan. In June, UPMC and the University of Pittsburgh announced the establishment of the UPMC Genome Center, calling it the largest and only CLIA-certified, high-throughput whole-genome sequencing center in the state of Pennsylvania. The center boasts five Illumina NovaSeq 6000 Systems, along with liquid handling robots for automated sample preparation and processing.