Case Studies
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Identification and tracking of pathogen variation has gained substantial importance in the ongoing COVID-19 pandemic. To support the rapidly expanding user needs to process higher sample numbers for SARS-CoV-2 sequencing, Oxford Nanopore Technologies has developed a partially automated version of the end-to-end ARTIC SARS-CoV-2 PCR Tiling protocol, in collaboration with Hamilton. This increases the throughput of this protocol while reducing hands-on time needed. Automation helps to increase consistency and reproducibility of results between runs.
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Sequence-based surveillance of circulating pathogens gives us important information about the spread and transmission networks of those diseases, as well as insight into emerging variants. Not only does this data help scientists to discover how viruses adapt and evolve, but it can also be used to assess the efficacy of vaccines—or inform new vaccine formulations.
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Advancing scientific discoveries, at scale, requires complete sequencing data, as well as suitable workflows to address high-throughput needs. Long-read sequencing technologies are quickly becoming the new gold standard to explore the full extent of genetic variation.
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High-throughput human sample prep and sequencing on PacBio Revio system
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Automation of the QIAGEN QIAseq FX DNA Library Kit on the Hamilton NGS STARlet Generates High-Quality Libraries for Whole-Genome Sequencing.
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Unlocking the potential of genomic technologies through long DNA molecules is transforming human genetics research and clinical applications. Optical Genome Mapping (OGM), powered by ultra-high molecular weight (UHMW) DNA, is an emerging technology.
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Automating the Roche AVENIO Tumor Tissue CGP Kit on the HAMILTON NGS STAR Generates High-Quality DNA Libraries for Comprehensive Genomic Profiling.
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Automating the Roche KAPA EvoPlus Kit on the HAMILTON NGS STAR V Generates High-Quality DNA Libraries for Whole Genome Sequencing.
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Automated Extraction of Ultra High Molecular Weight (UHMW) DNA for Bionano Optical Genome Mapping on the Hamilton Long String VANTAGE
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Long-read sequencing technology provides great potential in several clinically relevant areas of human genomics. Recent advancements allowing increased sequencing throughput and accuracy at a more affordable cost have already been made. However, the applied workflows still contain bottlenecks, especially in the extraction process steps that increase variability in HMW DNA (50 kbp -250 kbp) yield and quality, while hindering the processing of higher sample numbers. Overcoming these hurdles by robust high-throughput, automated solutions will support the growing number of large-scale population genomics studies and clinical research applications.
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Rapidly emerging long-read sequencing technologies, including PacBio Single Molecule, Real-Time (SMRT®) sequencing, provide substantial advantages for (de novo) genome assembly, detecting structural variants, and higher accuracy in repetitive or high GC content regions. A key requirement for long-read, third-generation sequencing approaches is the extraction of HMW DNA (50 kb – 250 kb). As the field matures and sample numbers increase, robust, high-throughput sample preparation methods are needed to support large-scale studies in pan-genomics and clinical research applications.
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The rationale behind the automation of the assay is mainly in terms of a quality improvement and enhancement of productivity, provided by minimizing the bias that might be otherwise introduced by manual library preparation. Moreover, the automated system is sufficiently flexible to adapt and therefore easily meet evolving needs
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New England Biolabs Inc. (NEB), the European Molecular Biology Laboratory (EMBL GeneCore), and Hamilton have developed automated versions of the poly(A) mRNA enrichment and rRNA depletion workflows with a seamless transition into the NEBNext Ultra II Directional RNA Library Preparation Kits.
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Exome sequencing is becoming a widely used method for analyzing mutations associated with inherited disorders. QIAGEN and Hamilton have developed an automated protocol that allows the use of both their kits – QIAseq Human Exome (QHEx) and Actionable Exomes:NextGen Sequencing Analysis Kit xHYB (xHYBa). The single-day workflow of the kits is combined with automation and rapid analysis using QIAGEN’s CLC LightSpeed module to create a fast, cost-effective workflow.
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The detection and surveillance of veterinary pathogens by molecular analysis is an invaluable tool for risk assessment and the reduction of financial losses. Animal diseases not only cause the loss of productivity but can also pose a threat to food safety. Therefore, constant evaluation of the entire food production chain, from farm to fork, is indispensable for public health.
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Digital PCR (dPCR) is used to measure absolute levels of target nucleic acids reliably and precisely in samples with high background, down to very low concentrations. In addition, it is also possible to estimate the slightest changes in target molecule levels. Compared to conventional qPCR setups, dPCR has greater resolution, is less sensitive to amplification biases and to the presence of inhibitors.
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Library preparation is a key requirement for Next-Generation Sequencing (NGS) applications and is among the most expensive segments of the sequencing workflow.