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GenMark Diagnostics ePlex Respiratory Pathogen Panel 2

Jun 29, 2020

GenMark Diagnostics said its ePlex Respiratory Pathogen 2 (RP2) Panel is now available for US commercial distribution and clinical use. The panel is designed to provide results in less than two hours for SARS-CoV-2 and other common respiratory pathogens, including influenza, adenovirus, rhinovirus, and respiratory syncytial virus (RSV). 

GenMark said that earlier this month, it had applied to the US Food and Drug Administration for Emergency Use Authorization of its ePlex Respiratory Pathogen 2 Panel. In March, the company received EUA for its ePlex SARS-CoV-2 Test.

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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.

Oct 14, 2020

Paragon Genomics CleanPlex ARS-CoV-2-Related NGS Assays

Paragon Genomics has launched four new coronavirus-related CleanPlex next generation sequencing (NGS) assays. The new panels widen the capabilities of the firm's CleanPlex SARS-CoV-2 Research and Surveillance Panel, which allows researchers to sequence the SARS-CoV-2 genome and obtain accurate nucleic acid-level information on the virus for strain typing, mutation monitoring, and other epidemiological studies.

Paragon's CleanPlex ACE2 & TMPRSS2 Panel identifies genetic mutations in patients that are related to disease susceptibility and severity. The test targets genes affecting the binding affinity and expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine rotease 2 (TMPRSS2). The panel interrogates the entire coding region of ACE2 and TMPRSS2, along with more than 70 curated unique quantitative trait loci that regulate their expression. Paragon noted the panel uses CleanPlex technology's three-hour workflow to produce enriched NGS libraries for all major sequencing platforms.

Paragon's CleanPlex SARS-CoV-2 FLEX Research Panel anticipates increases in SARS-CoV-2 viral mutations and offers extra assurance that mutation detection and genome coverage remain optimal. The FLEX panel specifically focuses on variant analysis and tracking of mutations over time. The test also includes degenerate primers and human RNA primer controls for more confident negative sample calling, especially when viral copies are not present or are at extremely low counts, the firm said.

The company also launched its plated 384 Unique Dual-Indexed PCR Primers for Illumina sequencing of its CleanPlex SARS-CoV-2 NGS panels. The primers will allow additional multiplexing capability so that researchers can simultaneously run up to 3,072 CleanPlex sequencing samples on Illumina NovaSeq instruments.

In anticipation of the upcoming flu season, Paragon is also releasing an early-access edition of the CleanPlex Respiratory Research Panel, which combines assays for SARS-CoV-2, influenza A subtypes H1N1, H1N2, H3N2, and influenza B. The combination panel allows for simultaneous influenza detection with SARS-CoV-2 detection or whole-genome sequencing. The extra sensitivity and additional coverage of the multiplex PCR-based method also works for high-throughput sample pooling and screening strategies, the firm said. Paragon expects to expand the panel to include respiratory syncytial virus and possibly other respiratory viruses in the future.

Oct 13, 2020

Purigen Biosystems Ionic Cells to Pure DNA Low Input Kit

Purigen Biosystems has launched its Ionic Cells to Pure DNA Low Input kit for DNA extraction and purification prior to next-generation sequencing or qPCR.

The automated workflow takes one hour and provides consistent yields for as many as 10,00 cultured or sorted cells and as few as 10. According to Purigen, the kit delivers a higher proportion of DNA longer than 20 kb than column-based products. The kit includes six fluidic chips  for use on its benchtop Ionic Purification system and the necessary reagents to process 48 samples.

Oct 12, 2020

Exact Sciences Oncotype MAP Pan-Cancer Tissue Test

Exact Sciences has introduced the Oncotype MAP Pan-Cancer Tissue rapid, comprehensive tumor profiling panel test for patients with advanced, metastatic, refractory, or recurrent cancer. Oncotype MAP provides clinically actionable information from genomic alterations in hundreds of cancer-related genes, including tumor mutations, copy number variants, fusions, tumor mutation burden, microsatellite instability, and protein expression, allowing physicians to understand a patient's tumor profile and effectively recommend targeted therapies or clinical trials, the company said.

The test, which Exact acquired as part of its merger deal with Paradigm Diagnostics in February, was previously called PCDx. 

Oncotype MAP has a turnaround time of three to five business days to guide timely treatment decisions, a sample requirement of as little as 3 mm of tissue or 2-3 slides, and accurate and comprehensive results based on next generation sequencing and immunohistochemistry. Exact also noted that patients who used a previous generation of the test had a 43 percent rate of progression-free survival compared to 5 percent for patients who did not utilize the test.

The Oncotype MAP test report is based on NCCN Compendium-based recommendations, along with potential evidence-based therapies and clinical trials. The report is currently tailored to support clinical decision-making by showing actionable biomarkers associated with more than 100 evidence-based therapies, more than 45 combination therapies, and more than 650 active clinical trial associations, Exact added.

Oct 12, 2020

Creative Biogene NGS Library Preparation Kits

Creative Biogene has launched new next-generation sequencing library preparation kits for DNA and RNA. The kits cover all steps of library construction, including fragmentation, amplification, adapter ligation, enrichment, and both dual- and single-index barcoding. Creative Biogene's kits are for research use only and can be adapted for automated lab protocols.

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Bio-Rad Laboratories Opus Real-Time PCR Systems and BR.io Software

Bio-Rad Laboratories has launched two new qPCR instruments, the CFX Opus 96 and CFX Opus 384 Real-Time PCR Systems. The systems offer enhanced usability, with features designed for academic, commercial, and biopharma labs. The firm also announced early access to BR.io, a cloud-based software that enables users to design experiments, analyze data, and access their experiments remotely.

Oct 07, 2020

Swift Biosciences Swift 2S Sonic DNA Library Kit

Swift Biosciences has released the Swift S2 Sonic DNA Library kit for next-generation sequencing of sheared DNA. The sample preparation kit is available in two configurations, for PCR indexing and for PCR-free indexing by ligation. It is compatible with Swift's Normalase technology and requires two hours of sample handling time.

The kits can be used for targeted hybridization capture with panels from Swift, Integrated DNA Technologies, and Twist Bioscience. The Swift HiFi Polymerase Master Mix supplied in the kits is suitable for pre-hybridization PCR to produce yields of 500 ng or greater, from as low as 1 ng DNA input.

The 96 reaction Swift 2S Sonic DNA library kit has a list price of $2,150.

Kaiser Health News reports San Francisco and Alameda counties in California are no longer using Verily Life Sciences' COVID-19 testing program.

The New York Times reports that developers in New York City are increasingly interested in life science spaces.

A UK study has found that antibodies against SARS-CoV-2 may decline over time, Reuters reports.

In PNAS this week: genetic and epigenetic variation in individuals with diabetic kidney disease, spontaneous genetic alterations in Saccharomyces cerevisiae, and more.