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Nov 20, 2020

DNAStar Lasergene 17.2 Software

DNAStar has released Lasergene 17.2 software for DNA, RNA, and protein sequencing assembly and analysis. In the latest release, DNAStar has fully integrated the SeqMan NGen application into SeqMan Ultra, greatly improving the workflow for both Sanger and next-generation sequencing analysis.

Users performing sequence assemblies can now go from project setup to finished assembly in one application. For users working with Sanger sequencing data, the new software offers improvements such as the ability to preview and trim trace data prior to assembly; better access to a built-in vector trimming database; and the ability to easily export an image of the assembly for collaboration or publication.

For those doing NGS assembly, the new version includes an updated variant annotation database to enrich the analysis of variants detected in human resequencing data. These updates include dbNSFP version 4.1, new allele and gene frequencies, and a new integration with Mastermind, a database of genomic literature from Genomenon.

Nov 19, 2020

Twist Bioscience RUO SARS-CoV-2 NGS Assay, Biotia COVID-Dx Software

Twist Bioscience has launched its research use-only SARS-CoV-2 next-generation sequencing assay.

The capture-based assay is for detection, characterization, and environmental monitoring of the virus from nasopharyngeal, oropharyngeal, anterior nasal, and mid-turbinate nasal swabs, as well as nasopharyngeal wash/aspirates, nasal aspirates, and bronchoalveolar lavage specimens. It was validated on Illumina's NextSeq platform and includes Twist's synthetic SARS-CoV-2 RNA controls. The limit of detection is 800 viral copies/ml.

The test comes with COVID-Dx comprehensive data analysis software from Biotia, which provides an RUO report on the presence or absence of SARS-CoV-2 virus, the full sequence of the virus, genetic variants, and phylogenetic analysis.

Nov 17, 2020

GeneMatters Automation for Pioneer Telegenetics Platform and RISE Patient Engagement Tools

GeneMatters has added automation features to its Pioneer Telegenetics Platform and has launched RISE Patient Engagement Tools to support patients undergoing genetic testing and counseling.

The Pioneer Telegenetics Platform, available since 2017, is designed to integrate telehealth genetic counseling service delivery and patient management. The platform now includes several automation features designed to reduce administrative burden, provide real-time communication, and allow GeneMatters to quickly deploy custom workflows to meet partner needs.

The RISE (Reach, Inform, Support, and Educate) Patient Engagement Tools specifically support patients and can be used independently or as a complement to Pioneer, and will include modules for genetic care such as scheduling, patient triage, patient education, and results delivery.

Nov 17, 2020

NuProbe Augury

NuProbe has launched an early-access program for its "Augury" platform, an automated design product for customized liquid biopsy NGS panels. Based on proprietary sequence-design algorithms, Augury procedurally generates NGS panels for cell-free DNA analysis, covering the entire coding regions of between one and 30 genes of interest. 

According to the company, these panels typically detect mutations down to 0.2 percent variant allele frequency, and copy number variations down to 4 percent tumor fraction, using 10 to 20 ng of cell-free DNA input. Users can choose to build panels that either cover the full coding regions of the genes of interest, or select hotspot loci. NuProbe expects typical panels to be designed within two days and analytically validated within 12 weeks.

Nov 16, 2020

Twist Bioscience Comprehensive Viral Research Panel

Twist Bioscience has released the Twist Comprehensive Viral Research Panel, a next-generation sequencing-based, research-use only assay that includes 3,153 viral genomes and enables identification of new and divergent viral species. The product uses over a million unique probes targeting sequences compiled from RefSeq, FluDB, and VIPRdb, representing all viral families containing at least one virus known to infect humans.

The panel covers all viral types: single- and double-stranded DNA and RNA genomes. It detects viral co-infections and can be used for metagenomic surveillance applications in stool samples.

The panel will be bundled with analysis software from One Codex.

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.

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Bloomberg reports AstraZeneca may conduct another study of its candidate SARS-CoV-2 vaccine after dosing error.

Moderna is applying for an Emergency Use Authorization for its coronavirus vaccine, according to the New York Times.

The National Health Service is to conduct a trial of Grail's blood-based screening test for cancer.

In PLOS this week: somatic mutation patterns of glioblastomas among Lebanese patients, phenome-wide study using UK Biobank data, and more.