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Nov 12, 2020

Illumina NextSeq 1000, P3 Reagent Kit for NextSeq 2000

Illumina's mid-throughput NextSeq 1000 sequencing system is now commercially available. The instrument offers 400 million reads per run and is more affordable than the NextSeq 2000. It has onboard informatics for rapid secondary analysis.

Illumina has also launched the P3 reagent kit for its NextSeq 2000 sequencing system. The high-output flow cell offers 1.1 billion reads per run, more than three times more than previously available on Illumina's mid-throughput systems. The kit will be available in four configurations: the 100-cycle kit delivers 110 Gb per run; the 200-cycle kit, 220 Gb; and the 300-cycle kit, 330 Gb. A 50-cycle kit is also available for infectious disease, small RNA, and spatial transcriptomics applications.

Nov 12, 2020

MRC Holland SALSA digitalMLPA

MRC Holland has released SALSA digitalMLPA, a novel technique that enables the simultaneous detection of up to 1,000 copy number variants. It combines MRC Holland's proprietary Multiplex Ligation-dependent Probe Amplification (MLPA) technology for target amplification with next-generation sequencing, using the company's Coffalyser digital MLPA analysis software. Up to 192, and soon up to 384, digitalMLPA samples can be analyzed in parallel. The first digitalMLPA assay available is D001 Hereditary Cancer Panel 1, which targets 28 genes associated with various hereditary cancers.

Nov 11, 2020

IsoPlexis IsoSpark, IsoSpark Duo Systems

IsoPlexis has launched its IsoSpark and IsoSpark Duo systems for functional proteomics. The IsoSpark has an 18-inch footprint and a 4-chip capacity, while the IsoSpark Duo has a 8-chip capacity to allow users to simultaneously run two chip families. The firm said that both systems are fully compatible with its suite of IsoPlexis applications. The systems are available for pre-order, with shipping planned for January 2021. 

Nov 10, 2020

Newomics Microflow-nanospray Electrospray Ionization (MnESI) Source

Newomics has launched the Microflow-nanospray Electrospray Ionization (MnESI) Source for the analysis of antibodies, proteins, nucleic acids, and lipids derived from cells and human plasma. The MnESI Source, which the company comarkets with Thermo Fisher Scientific, delivers small amounts of sample to Newomics M3 multi-nozzle emitters, which are coupled with Thermo Scientific Orbitrap mass spectrometers. The source is designed to effectively ionize and introduce oligonucleotides, protein complexes, and viral particles under native conditions.

Nov 10, 2020

Streck Zulu RT qPCR Instrument

Streck has launched the Zulu RT, a rapid, modular qPCR instrument capable of simultaneously performing four independent experiments. The instrument uses proprietary thermal technology (ramp speeds of 15° C/second for heating and 12° C/second cooling) and powerful optics that enable it to perform a 40-cycle, six-channel, three-step real-time PCR protocol in less than 20 minutes for volumes from 10 µL to 50 µL. The system's modularity allows multiple users at once, in essence acting as four individual thermal cyclers in one, Streck said.

Nov 10, 2020

New England Biolabs: Monarch HMW DNA Extraction Kits

New England Biolabs has released two high molecular weight (HMW) DNA extraction kits. Both the Monarch HMW DNA Extraction Kit for Cells & Blood and the Monarch HMW DNA Extraction Kit for Tissue utilize a novel glass bead-based technology that allows for more efficient and cost-effective extraction. They can extract DNA up to several megabases in size from cells, blood, tissue, or bacteria, with workflows that range from 30 minutes to 90 minutes in duration. The extracted DNA can be used in downstream applications such as long-read sequencing, optical mapping, and linked-read genome assembly. The new kits complement the company's Monarch Genomics DNA Purification Kit and can be used alongside its NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing kit.

Nov 10, 2020

NIPD Genetics: Amfira PGT

NIPD Genetics has launched Amfira PGT, a preimplantation genetic test to detect genetic abnormalities in embryos. The test consists of two panels, the PGT-A panel for aneuploidies for individuals or couples undergoing in vitro fertilization, and the PGT-SR panel for structural rearrangements for couples diagnosed with a structural rearrangement. Both panels can detect selected male polyploidies, as well as deletions and duplications larger than 10 megabases. The turnaround time is five to seven days from sample receipt.

Nov 09, 2020

NanoString Technologies GeoMx DSP Protein Assays for NGS

NanoString Technologies has launched its GeoMx DSP Protein assays for next-generation sequencing readout.

The assays expand the multiplex detection capabilities of GeoMx digital spatial profiling from tens to hundreds of proteins and include more than 50 targets for immuno-oncology applications. The assays also provide complementary protein content for the GeoMx Cancer Transcriptome Atlas panel.

The firm said it has tested performance on both formalin-fixed, paraffin-embedded and fresh frozen tissue samples.

The products are available immediately through NanoString's technology access program.

Nov 06, 2020

Bio-Rad: StarBright Dyes

Bio-Rad has launched three new dyes for flow cytometry in its StarBright line. StarBright Blue 700, StarBright Violet 440, and StarBright Violet 610 consist of fluorescent nanoparticles conjugated to flow antibodies. The dyes offer narrow excitation and emission profiles for improved resolution in flow cytometry experiments. They are also resistant to photobleaching and highly stable, with minimal lot-to-lot variation, according to Bio-Rad, which enables researchers to achieve consistent and reproducible staining. The dyes work with all common staining buffers for easy integration into multicolor panels and the chemistry is designed to ensure no loss of signal in fixation.

Nov 04, 2020

MyNeo ImmunoEngine

Precision oncology company MyNeo has released a new version of its ImmunoEngine bioinformatics platform. The update incorporates two new machine-learning algorithms, NeoMS, a transformer-based predictor based on major histocompatibility complex (MHC) ligandomic data, and NeoIM, a random-forest classifier trained to classify short peptides as either immunogenic or nonimmunogenic. The Belgian firm specializes in identifying and validating precision cancer therapies.

Nov 04, 2020

One Codex Microbiome Sequencing and Analysis Service

One Codex has launched an end-to-end microbiome sequencing and analysis service. The offering includes sample preparation, shotgun metagenomic sequencing, and analysis on One Codex's informatics platform. According to the company's website, customers provide stool samples to One Codex using the company's sample collection kits. The company extracts DNA and performs quality control checks to produce genomic DNA sequencing libraries, which are then sequenced to a depth of 2 million 2-by-150-bp read pairs. Sequencing data is then analyzed against the company's One Codex Database, consisting of 115,000 microbial reference genomes.

Nov 02, 2020

Castle Biosciences DecisionDx DiffDx-Melanoma

Castle Biosciences has launched DecisionDx DiffDx-Melanoma, a gene expression profile test for use in patients with suspicious pigmented lesions. The test is designed to aid dermatopathologists in characterizing difficult-to-diagnose melanocytic lesions, and classifies these lesions as either benign (gene expression profile suggestive of benign neoplasm), intermediate-risk (gene expression profile cannot exclude malignancy), or malignant (gene expression profile suggestive of melanoma).

The intent-to-treat analysis of the DiffDx-Melanoma validation study showed that the test accurately diagnosed malignant and benign cases at a rate of 96.6 percent, with 99.1 percent sensitivity, 94.3 percent specificity, 93.6 percent positive predictive value, and 99.2 percent negative predictive value, the company said. An intermediate-risk result was identified in 3.6 percent of the cases.

Oct 30, 2020

Oxford Nanopore Technologies: Bonito CRF, SV Pipeline 2.0, DeepVariant

Oxford Nanopore Technologies has released a number of new and updated analysis tools and products. Bonito CRF, a new basecalling algorithm currently available for early users, improves modal raw-read accuracy to 98.3 percent on internal validation sets. The new SV Pipeline 2.0 increases structural variation calling precision to 97.5 percent and recall to 95.5 percent. The new DeepVariant tool, when paired with the existing Medaka tool, identifies SNPs with 99.92 percent recall and precision. The company also said it is commercially releasing the R10.3 flow cells for use with the high-throughput PromethIon sequencer and the low-throughput Flongle sequencing adapter.

Oct 29, 2020

GenomOncology IgniteIQ

GenomOncology has introduced IgniteIQ, software that extracts and adds computable structure to "clinically relevant" data from PDF next-generation sequencing and pathology reports. The company backs the automated extraction with human review to validate the discrete data elements so the extracted information is useful for clinicians, bioinformaticians, and researchers. IgniteIQ can process PDF documents from both electronic medical records and research data warehouses.    

Oct 29, 2020

Qiagen QiaSeq Human Exome TR Insights

Qiagen has introduced QiaSeq Human Exome TR Insights, a whole-exome sequencing workflow that combines chemistry and informatics to enable researchers to sequence and analyze genomic variations across the entire human exome. The workflow comprises three components: the QiaSeq Human Exome Panel; Qiagen CLC Genomics Workbench NGS data-analysis and -visualization software; and QCI Interpret Translational, new software the enables evidence-based variant annotation, filtering, and interpretation. The QCI Interpret Translational component is powered by the Qiagen Knowledge Base of roughly 2 million unique variants expertly selected from more than 300,000 scientific articles. The exome panel component features a hybrid-capture chemistry and workflow that minimizes GC-induced bias and improves capture efficiency and specificity. Balanced coverage across difficult target regions ensures minimal dropouts and false negatives, Qiagen said.

Oct 29, 2020

Allelica Coronary Artery Disease Risk Calculator

Allelica has launched a cloud-based tool to enable clinical labs and healthcare providers to calculate an individual's lifetime risk of developing coronary artery disease based on the integration of genetic and traditional risk factors. Built on a secure GDPR- and HIPAA-compliant platform, the technology integrates a newly developed genome-wide polygenic risk score (PRS) for CAD into the pooled cohort equation model. It allows physicians to provide patients with highly customizable visual representations of their risk levels compared to the general population. Users can modify risk factors, like decreases in LDL cholesterol, to show patients how manageable lifestyle changes can actively lower their lifetime risk of heart disease. The calculator was developed and validated using UK Biobank data resources and is the latest addition to Allelica's cloud-based PRS pipeline.

Oct 23, 2020

Fabric Genomics Fabric GEM Algorithm for Genetic Disease Diagnosis

Fabric Genomics has launched Fabric GEM, an algorithm designed to identify the likely genetic cause of rare diseases from next-generation sequencing data. Fabric GEM, the latest product in the Fabric Enterprise software suite, uses artificial intelligence to analyze sequencing data (including complex structural variants) and patient clinical information in order to perform probabilistic disease matching and speed genetic diagnoses. The algorithm was developed in collaboration with Mark Yandell of the University of Utah and Stephen Kingsmore of Rady Children's Institute for Genomic Medicine, Fabric said.

Oct 22, 2020

Bionano Genomics Access v1.6, Solve v3.6

Bionano Genomics has updated its suite of data analysis and visualization software tools for its Saphyr genome mapping platform. The new version of Bionano Access is designed to simplify and accelerate every step in the data-analysis workflow, enabling clinical labs to develop tests on the Saphyr more easily. It builds on the Bionano EnFocus FSHD Analysis tools for the automated analysis of variants in a form of muscular dystrophy to allow for similar automated variant analysis for EnFocus panels for other genetic conditions. These include autism spectrum disorder, developmental delay, and repeat expansion disorders, as well as hematologic malignancies and solid tumors. The new version also enables Bionano EnFocus FSHD data to be analyzed on a PC rather than in the cloud or on a compute cluster. In addition, it reduces the time and increases capacity for analyses run on Bionano's cloud-based platform.

Oct 22, 2020

Lexogen Luthor 3' mRNA-seq Library Prep Kit

Lexogen has launched the Luthor 3' mRNA-seq library prep kit for ultra-low input and single-cell sequencing. At sequencing depth of 1 million reads, the kit allows detection of up to 15,000 genes from one cell and up to 13,000 genes from 10 picograms of purified RNA input. Using T7 high-resolution original RNA (THOR) amplification, the kit amplifies RNA directly, without a cDNA intermediate.

Oct 21, 2020

Qiagen QiaPrep&Amp Viral RNA UM Kit

Qiagen has launched the QiaPrep&Amp Viral RNA UM Kit to simplify and accelerate PCR analysis in epidemiological studies of RNA viruses, including SARS-CoV-2. The new kit combines a two-minute, liquid-based sample preparation step with real-time PCR detection in a workflow that can be automated with standard lab equipment for any throughput, assay, and reaction need for both single-plex and multiplex testing. Qiagen said the workflow comprises taking an aliquot from a nasopharyngeal, oropharyngeal, or nasal swab in transport media; adding the aliquot to a buffer optimized for viral RNA template preparation without degradation; and combining this mixture with RT-qPCR reaction mix for subsequent real-time PCR on any thermal cycler using any assay. The entire workflow takes less than an hour compared to about three hours for standard extraction-based qPCR processes, and can be used to process up to 2,600 samples per eight-hour shift per thermal cycler, the company said.

Oct 20, 2020

Genome Diagnostics NGSgo-MX11-3 Multiplexing for HLA Typing

Genome Diagnostics has launched NGSgo-MX11-3, its latest addition to a series of singleplex and multiplex amplification strategies for HLA typing by NGS. NGSgo-MX11-3 consists of amplification primers for eleven HLA genes — HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1, DRB3/4/5, DQA1, and DPA-1 — in three mixes per sample. The three-tube design results in low noise levels and well-balanced alleles, making the data quality of the 11-loci multiplex similar to a singleplex strategy, Genome Diagnostics said. NGSgo-MX11-3 is available on a research-use-only basis. The firm anticipates that it will become available as a CE-marked IVD.

Oct 19, 2020

Reaction Biology/4HF Biotec Cell-Based Bioinformatics Service

Drug-discovery CRO Reaction Biology and informatics company 4HF Biotec have introduced a cell-based bioinformatics service that combines Reaction's ProLiFiler cell assay service with 4HF Biotec's Biomarker Analysis and MA Finder informatics tools to help inform drug discovery. Biomarker Analysis searches for mutations, gene copy numbers, and gene expression data, while MoA Finder scans test results to pinpoint modes of action in experimental drug compounds. The service, aimed at the oncology market, will be run at Reaction Biology's lab in Freiburg, Germany.

Oct 16, 2020

IDbyDNA/Illumina RUO Respiratory Pathogen ID/AMR Target Enrichment Panel

IDbyDNA and Illumina this week launched their codeveloped Respiratory Pathogen ID/AMR Target Enrichment Panel for research use only. Developed under a previously announced strategic partnership between the companies, the panel uses IDbyDNA's Explify software platform and Illumina's next-generation sequencing technology to detect more than 280 respiratory pathogens (bacterial, viral, and fungal) as well as genes associated with more than 1,200 antimicrobial resistance markers. Using Illumina's MiniSeq Rapid Reagent Kit, the panel can deliver results in less than 24 hours. IDbyDNA's Explify database includes millions of curated DNA and RNA reference sequences and can identify more than 50,000 microorganisms and more than 6,000 known common and rare pathogens, including antimicrobial resistance.

Oct 14, 2020

Caris Life Sciences CODEai

Caris Life Sciences has launched CODEai (Comprehensive Oncology Data Explorer), a real-world clinico-genomic data platform that uses artificial intelligence technology to integrate the company's catalog of molecular data with cancer treatment information and clinical outcomes data for more than 215,000 patients covering more than 1 million data points per patient.

Integrating genomically profiled patient cases with associated treatments and outcomes, CODEai allows for customized cohort analysis based on a variety of search queries including molecular profiling results, demographic data, diagnostic data, and treatment and survival data. The system also provides data visualization and advanced predictive analytics. The platform is available to members of the Caris Precision Oncology Alliance, a growing collaborative network of cancer centers, as well as to biopharma companies through collaborative relationships. 

Oct 14, 2020

GenomOncology Pathology Workbench

GenomOncology has released a new version of GenomOncology (GO) Pathology Workbench, which the software company said has been updated to process Illumina's TruSight Oncology (TSO) 500 assay and other larger panels. GO Pathology Workbench now can process samples in parallel, cutting sample annotation time by 80 percent. The new release also adds management of higher sample throughput as well as intepretation of copy numbers and structural variants in next-generation sequencing. It draws from datasets not included in previous releases of Pathology Workbench, including gnomAD, MutationTaster, PolyPhen, SIFT, cancerhotspots.org, and the Cancer Gene Census.

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Politico notes that the Biden Administration has not yet nominated a permanent Food and Drug Administration commissioner. 

Anthony Fauci also informed the World Health Organization executive board that the US would be joining the COVAX initiative, according to CNBC.

A new preprint suggests some SARS-CoV-2 variants could affect the effectiveness of current vaccines, the Associated Press reports.

In Nature this week: Australian lungfish provides details on the movement of vertebrate life from water to land, and more.