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Mar 20, 2020

Oncocyte DetermaIO

Oncocyte said it has completed CLIA Validation for and launched DetermaIO, previously the Insight Genetics IM Score Test. The test is now available for research use within the biopharmaceutical and academic communities. DetermaIO is a gene expression profile test that evaluates the immune microenvironment in biopsies from cancer patients to identify individuals more or less likely to respond to anti-PD-1/PD-L1 immunotherapy.  The test differentiates itself from other immunotherapy diagnostic tests by having the capability to determine if the immune microenvironment is active or quiescent. DetermaIO has the potential to be used to stratify patients in the more than 3,000 PD-1/PD-L1 ongoing clinical trials that are collectively expected to recruit over 500,000 patients, the company said.

Mar 20, 2020

DNAstack COVID-19 Beacon

DNAstack has released Beacon for SARS-CoV-2, the virus that causes COVID-19, to enable the scientific and medical communities to share and discover knowledge about the genetics of the virus in real time. Beacon, which is available here, will allow information about genetic variants to be shared instantly using software that follows an open international standard, the company said.

Researchers can use the new Beacon to discover sequences with specific genetic mutations and map their geographic and evolutionary origins. The platform integrates derivative data from genetic sequencing libraries such as GISAID and links to Nextstrain pathogen evolution visualizations. 

The COVID-19 Beacon is compliant with the Beacon API, an internationally recognized open-source protocol developed by the Global Alliance for Genomic and Health (GA4GH). The system is deployed on Microsoft Azure, a cloud computing platform with global reach and scalability.

Mar 19, 2020

Paragon Genomics CleanPlex SARS-CoV-2 NGS Panel

Paragon Genomics has launched its CleanPlex SARS-CoV-2 Panel for COVID-19 coronavirus detection, tracking, and research through amplicon-based target enrichment for next-generation sequencing applications. According to the firm, the panel covers the entire genome of the SARS-CoV-2 virus responsible for the global COVID-19 pandemic. Paragon said that the panel's four-step workflow converts viral RNA into sequencing-ready libraries within five hours. Powered by Paragon's CleanPlex's technology, versions of the panel are available for both the Illumina and MGI sequencing platforms. 

Paragon is also offering free consultation for researchers interested in designing custom NGS panels for coronavirus research.

Mar 13, 2020

Bio-Rad Exact Diagnostics SARS CoV-2 Standard

Bio-Rad has launched a standard for SARS-CoV-2 testing through its Exact Diagnostics product line. The standard contains synthetic RNA transcripts of the virus as well as human genomic DNA, enabling labs to test the entire process of a molecular assay, including extraction, amplification, and detection of the virus.

Mar 13, 2020

Microbiologics Synthetic RNA for SARS-CoV-2

Microbiologics is now offering synthetic RNA for SARS-CoV-2 to assist in the efforts to monitor the spread of COVID-19. The material mimics the viral nucleic acid and provides the exact targets specified by the US Centers for Disease Control and Prevention for test development, the company said.

Specifically, it is a 1,044-nucleotide RNA specific for the SARS-CoV-2 N (nucleocapsid) gene. It contains all three markers (N1, N2 and N3) detected by the CDC Real-Time RT PCR Panel for detection of 2019 novel coronavirus. The RNA material assists in the development of diagnostic assays and the evaluation of the performance of nucleic acid tests for determination of the presence of SARS-COV-2.

The RNA is available in two different concentrations: 1x106 and 1x109 genome copies per tube. The material can be shipped within the USA without handling restrictions or permitting requirements. The company noted that permits may be required outside the USA and interested parties should check with local authorities.

Mar 12, 2020

Twist Bioscience Synthetic SARS-CoV-2 RNA Controls

Twist Bioscience has made two synthetic SARS-CoV-2 RNA controls available for use in quality control in the development and validation of next-generation sequencing- and reverse-transcription PCR-based tests.

The sequence-verified controls are designed to cover the full viral genome of two specific virus variants: MN908947.3, considered the reference genome, isolated from a patient in Wuhan, China, and MT007544.1, isolated from a patient in Australia.

Twist noted that customers purchasing synthetic controls are subject to the firm's biosecurity screening protocols.

Mar 11, 2020

ZeptoMetrix NATtrol SARS-CoV-2 Recombinant Construct

ZeptoMetrix has released its newly inactivated and non-infectious NATtrol SARS-CoV-2 Recombinant construct for laboratory quality control and test validation.

This non-infectious quality control incorporates a recombinant construct associated with targeted detection regions of the virus that may be used in the development of molecular assays designed to detect SARS-CoV-2. It can also be used in BSL-2 facilities in place of the live virus, as non-infectious, external quality controls for assays developed to detect SARS-CoV-2, the company said.

Mar 10, 2020

Fluidigm AccuLift Laser Capture Microdissection System

Fluidigm has launched the AccuLift Laser Capture Microdissection System, which enables precise and efficient capture of individual cells or larger tissue regions from frozen and FFPE tissue sections for DNA, RNA, and protein biomarker analysis using sequencing, real-time PCR, or mass spectrometry. Fluidigm said that it collaborated with Lance Liotta, codirector of the Center for Applied Proteomics and Molecular Medicine at George Mason University, to develop the AccuLift product portfolio. The new system features a patent-pending design including a high-precision stage and uniquely aligned IR and UV lasers. It also features a new capture method developed in Liotta's laboratory that increases the efficiency of cellular capture and extraction.

Mar 10, 2020

BioDynami NGS RNA Library Prep Kit

BioDynami has released a new sequencing library preparation product called NGS RNA Library Prep Kit. It takes 3 ng to 100 ng of purified RNA as input material, is compatible with different types of indexes for multiplexing, and is designed for Illumina sequencing. The workflow takes 2 hours in total, with 10 minutes of hands-on time.

Mar 09, 2020

IsoPlexis CodePlex Secretome and Single-Cell Innate & Myeloid Solution

IsoPlexis has released two new products for use with its IsoLight cellular proteomics instrument.

CodePlex Secretome is a fully automated approach to obtaining highly multiplexed bulk cytokine data that requires five minutes of hands-on time for sample loading. CodePlex Secretome multiplexes more than 30 cytokines, and is modular so users can simultaneously examine as few as eight samples or as many as 64.

The new Single-Cell Innate & Myeloid solution detects the functional single-cell differences from innate and myeloid cells by identifying what each cell secretes in a highly multiplexed (32-plus cytokines) manner to reveal the sources of cellular difference through functional phenotyping. It joins other IsoLight single-cell chip applications which allow researchers to visualize single-cell-level data and pinpoint biological drivers.

Mar 06, 2020

Biogazelle HTPathwaySeq and HTTargetSeq

Belgian CRO Biogazelle has launhced HTPathwaySeq and HTTargetSeq RNA sequencing and data-analysis services. HTPathwaySeq generates in-depth information on drug mode of action, highlights molecular similarities between compounds, and reveals potential compound-induced toxicities, all of which help provide critical data for candidate prioritization in drug development.
 
HTTargetSeq supports the development of RNA-targeting oligonucleotides such as short interfering RNAs (siRNA) and antisense oligonucleotides (ASO). The service accurately identifies off-target genes, which the company noted is important for the anticipation of safety issues and potential repurposing of off-target genes as novel therapeutic targets.
 
Both services are performed directly on cell lysates from 96-well culture plates, and data interpretation results are shared through Savana, Biogazelle’s proprietary visualization app.
Mar 05, 2020

Berkeley Lights TCRseq Kit

Berkeley Lights has launched a T Cell Receptor Sequencing Kit (TCRseq Kit), which enables users of the company's Beacon and Lightning instruments to recover functionally validated T cell receptors from a cell sample with as few as 10,000 input cells. The kit enables Berkeley Lights platform users to first characterize T cell function using the company's Cell Therapy Development Suite and then sequence only the T cells that matter, therefore functionally replacing existing methodologies that require re-expressing hundreds of TCRs to identify rare sequences, the company said.

After performing a T cell functional assay on the Beacon or Lightning instrument, the user selects single human T cells of interest and exports them from the company's OptoSelect chip to a well plate. Using TCRseq Kit reagents, RNA from single T cells is recovered and V(D)J regions of the TCR alpha and beta chains are amplified. The resulting cDNA is ready for the user to index and sequence using sequencing platforms. The TCRseq Kit includes reagents and protocols for processing up to 192 single human T cells, Berkeley Lights said.

Mar 05, 2020

Thermo Scientific SureTect PCR Assays

Thermo Fisher Scientific has released five new Thermo Scientific SureTect PCR assays and related software for food testing. The tests, which are designed to run on the Applied Biosystems QuantStudio 5 Food Safety PCR system, are for the detection and identification of Campylobacter jejuni, C. coli, and C. lari; E. coli O157:H7 and STEC screening; STEC identification; Staphylococcus aureus detection; and Vibrio cholerae, V. parahaemolyticus, and V. vulnificus detection and identification. They typically provide negative and presumptive-positive results within less than 24 hours, with some protocols taking as little as nine hours.

Mar 04, 2020

Biodesix, Oncimmune EarlyCDT Lung

Biodesix has commercially launched Oncimmune's EarlyCDT Lung test in the US, under a commercialization agreement the two firms announced last year. Marketed under Biodesix's Nodify Lung brand, the new Nodify CDT test is designed to assist physicians to identify patients with lung nodules at high risk of lung cancer.

The assay joins Biodesix's existing Notify XL2 test for low-risk lung nodule detection, and, according to Oncimmune, both tests will now be offered together as the Nodify Lung Nodule Risk Assessment strategy, with physicians able to order the two assays from a single blood draw.

Mar 03, 2020

Agilent GenetiSure Cyto Microarrays

Agilent Technologies has introduced GenetiSure Cyto microarrays, a set of three new array for cytogenetic laboratories conducting both prenatal and postnatal research. According to the company, the chips include updated, clinically relevant content from respected databases, with probes that provide high-resolution detection of copy number variations and copy-neutral loss of heterozygosity associated with developmental delay, neuropsychiatric disorders, intellectual disability, congenital anomalies, or unexplained dysmorphic features in constitutional DNA samples.

Feb 28, 2020

TwinStrand Biosciences Duplex Sequencing Technology

TwinStrand Biosciences this week launched TwinStrand Duplex Sequencing Technology kits at the Advances in Genome Biology and Technology meeting. Duplex Sequencing is a biochemistry- and software-based enhancement to existing next-generation sequencing platforms that improves accuracy by more than 10,000-fold, the company said. Optimized chemistry enables users to complete library preparation in one to two days, while cloud-based informatics provide the ability to fully process, analyze, interpret, and graphically present multi-terabyte raw sequencing data. The company will offer its technology initially for two research applications: detection of minimal residual disease in acute myeloid leukemia patients, and a multi-species genetic toxicology assay for rapid identification of carcinogenic chemicals in preclinical testing, as well as detection of patients who have been environmentally exposed.

Feb 27, 2020

RareCyte PD-L1 Assay

RareCyte has launched its PD-L1 liquid biopsy assay, which the firm said will allow users to evaluate PD-L1 expression on circulating tumor cells in a patient's bloodstream. Customers can use the PD-L1 assay and the AccuCyte-CyteFinder system to process blood to cells for CTC enumeration and PD-L1 biomarker expression analysis, or process blood to plasma for optional cell-free DNA analysis. 

Feb 26, 2020

Meridian Bioscience Air-Dryable qPCR Mix

Meridian Bioscience announced its Air-Dryable qPCR mix, a specialized master mix with a magnesium-containing formulation allowing air or oven drying protocols for ambient temperature-stable real-time PCR assays. The mix allows dry down and test stability at ambient temperature, eliminating the need for cold chain storage, the company said. It shows high performance in multiplex reactions following rehydration, which Meridian said makes it suited for automated high-throughput platforms. 

Feb 25, 2020

Blueprint Genetics Mitochondrial Genome Analysis

Blueprint Genetics, a Quest Diagnostics company, has introduced full mitochondrial genome DNA (mtDNA) analysis to its diagnostic panels to increase diagnostic potential across medical specialties such as cardiology, metabolic disease, neurology, ophthalmology, and hearing loss. The analysis uses hybridization-based capture of mtDNA and next-generation sequencing to detect low heteroplasmy levels of mtDNA SNVs, indels, and deletions. It includes sequencing and copy number variant analysis of the entire mitochondrial genome (37 genes) which can be ordered alone or added to any panel. It has also been added to 30 existing panels where mitochondrial DNA testing is expected to have an impact on the diagnostic potential.

Feb 25, 2020

Seven Bridges Aria

Seven Bridges has introduced Aria, a bioinformatics platform for analyzing genotypic and phenotypic data to inform drug discovery. The cloud-based platform features: extract, transform, and load (ETL) processes for managing and building cohorts from phenotypic data; a variant data warehouse for querying whole-genome sequences; and an interpretation framework. Aria also supports in silico exploration of the impact of inactivating genes.

Feb 25, 2020

Dovetail Genomics Micro-C, HiChIP Kits

Dovetail Genomics has launched the Dovetail Micro-C and HiChIP Kits. The Micro-C Kit is the latest offering in the company's suite of Hi-C products, offering researchers resolution of chromatin contacts down to the mono-nucleosome level. The Dovetail HiChIP combines Micro-C and ChIP-seq into one simple workflow that enables researchers to assay protein-directed alterations to chromatin architecture and its resulting impact on gene expression, the company said. Both products are made for short-read next-generation sequencing platforms.

Feb 25, 2020

Twist Bioscience Comprehensive Exome Panel, Targeted Methylation Sequencing Solution

Twist Bioscience has launched its Twist Comprehensive Exome Panel, an optimal next-generation sequencing target enrichment solution that includes more than 99 percent of protein coding genes. The panel expands on the content of the Twist Human Core Exome to include coverage of protein-coding genes from all three key public genetic databases: CCDS, RefSeq and GENCODE, providing best-in-class coverage of the most up-to-date content, the company said. In addition, the panel can be customized quickly and affordably. Because of the updated and comprehensive coverage, the new panel allows for increased confidence in variant detection experiments, as well as maximum sequencing efficiency and best coverage uniformity.

Twist has also introduced the Twist Targeted Methylation Sequencing Solution to enable the study of methylation pattern changes in research fields including cancer, epigenetics, and non-invasive prenatal testing. The Targeted Methylation Solution offers a high-throughput, highly uniform target enrichment solution to explore methylation. This product is now available for early access customers, the company said. 

Feb 25, 2020

S2 Genomics Singulator 100 System

S2 Genomics this week launched the Singulator 100 System at the Advances in Genome Biology and Technology meeting. The Singulator 100 automates the processing of solid tissue samples into suspensions of single cells or nuclei with high yields and from small samples for a wide range of single-cell biology and genomic analyses. The company said that this enables researchers to reproducibly prepare suspensions of high-quality, highly viable cells or nuclei with minimal variability. The system will begin shipping in spring of this year with kits available for single-cell and nuclei isolation.

Feb 25, 2020

Lexogen RiboCop rRNA Depletion Kits for Bacteria

Lexogen has developed a set of new RiboCop rRNA Depletion Kits for bacteria, which it said efficiently removes 23S, 16S, and 5S rRNA from mixed bacterial samples and monocultures. According to the firm, RiboCop is offered as a standalone kit with the option to choose from three optimized probe mixes for depletion of either rRNA from mixed bacterial samples, or Gram-negative or Gram-positive bacteria grown in monoculture.

The technology uses a set of affinity probes designed for specific depletion of rRNA sequences, and, according to Lexogen, the probe design minimizes off-target effects that can distort NGS data quality. The kits work with total RNA input amounts as low as 1 ng and up to 1 μg, depending on sample composition and the chosen depletion probe mix. RiboCop does not include any enzymatic reactions or mechanical shearing steps and can process intact as well as degraded material, including FFPE, resulting in intact, full-length transcripts. Resulting rRNA-free samples are then suitable for a variety of downstream RNA analysis methods including RNA-seq library preparation approaches.

The protocol is also automation-friendly, the firm added.

Feb 25, 2020

Promega Wizard HMW DNA Extraction Kit

Promega has launched its Wizard HMW DNA Extraction Kit, a tool for researchers working with large fragments of genomic DNA. According to the company, the new HMW DNA product, which joins the firm's existing portfolio of both manual and automated kits to extract a variety of nucleic acids from a broad range of sample types, allows researchers, in a 90-minute manual protocol, to obtain DNA that can provide strong performance in long-read sequencing applications. Data on this performance was demonstrated in a poster presented at this week's 2020 Advances in Genome Biology and Technology (AGBT) meeting, Promega said. When run through a long-read sequencing protocol, the DNA from the Promega kit produced very long maximum reads and high N50 values, indicating a higher proportion of large fragments in the sample. 

Compared to available alternatives, Promega claimed that the Wizard kit purifies a "significantly higher" proportion of fragments over 125kb. The kit supports purification from a variety sample types including whole blood, bacterial cultures, cultured mammalian cells, and plant leaf tissue.

Pages

A tissue sample from the 1960s harbors a near-complete sample of HIV, IFLScience reports.

A new bill would reshape the US National Science Foundation to include a focus on technological development, according to Science.

The Food and Drug Administration's decision to halt a SARS-CoV-2 study has drawn criticism, according to Stat News.

In Genome Biology this week: features affecting gut microbiome and parasite patterns, cellular interactions in lung tumor microenvironment, and more.