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Apr 22, 2020

Caris Life Sciences MI Exome

Caris Life Sciences has launched MI Exome, a whole-exome next-generation sequencing-based assay.

The test covers 22,000 genes and detects point mutations, indels, copy number alterations, and about 250,000 exonic, intronic, and intergenic SNPs. MI Exome also includes analysis of tumor mutational burden, microsatellite instability, loss of heterozygosity, and homologous recombination deficiency, and can be used to interrogate bacteria, viruses and fungi, including cancer-related pathogens, to support microbiome analysis. Average turnaround time is less than 14 days. When paired with the Caris Molecular Intelligence profiling services, the test can help detect and characterize cancer to guide individualized treatment decisions, the company said.

Apr 22, 2020

NuProbe VarMap Panels

Houston-based sample preparation firm NuProbe has launched its VarMap targeted next-generation sequencing product line. NuProbe's first target enrichment assays include multi-gene panels for non-small cell lung cancer and melanoma. They require 500x sequencing depth to detect and quantitate tumor-specific mutations at 0.1 percent variant allele frequency. The assays allow for detection of low-abundance tumor-specific mutations to help with therapy selection and minimal residual disease monitoring, the company said.

Apr 21, 2020

Biocept RUO Target Selector Kits

Biocept has announced the availability of new research-use-only kits allowing molecular laboratories to perform some of its Target Selector molecular assays in house on both formalin-fixed paraffin-embedded tissue and circulating tumor DNA samples. The first available kits, for EGFR mutations, are being made available now and additional assays targeting other oncogene mutations are planned for launch in the future, Biocept said.
 
The firm's Target Selector technology platform utilizes patented "Switch-Blocker" technology to enrich specimens for specific mutations of interest, resulting in high assay sensitivity and specificity. According to the company, this high performance allows detection of minute fractions of mutated DNA in a liquid biopy sample, and could also allow laboratories to eliminate macro-dissection of tumor blocks or provide results with small DNA inputs compared to most tissue-based assays. Target Selector assays can be used in combination with a variety of low-cost analytical platforms including qPCR, Sanger sequencing, microarrays, and mass-spectrometry, in addition to next generation sequencing, the firm said. 
Apr 17, 2020

Randox: Qnostics SARS-CoV-2 Molecular Controls

Randox has launched whole pathogen molecular controls for SARS-CoV-2. The controls were developed by UK scientists and are being made available by Randox under the Qnostics brand name. The controls are for use to ensure accurate coronavirus test and system performance and are manufactured using whole pathogens to mimic the patient sample. The controls contain the entire SARS-COV-2 genome, incuding conserved regions recommended by the US Centers for Disease Control and Prevention and the World Health Organization, and they are compatible for use with commercial and in-house testing methods. 

Apr 16, 2020

Illumina SARS-CoV-2 Data Toolkit

Illumina has released a suite of data analysis tools and workflow functionality for researchers sequencing SARS-CoV-2, the virus that causes COVID-19.

The toolkit helps detect and identify the viral genome sequence in samples and contribute findings to public databases directly from BaseSpace Sequence Hub. It includes new and updated DRAGEN functionality, including a new RNA pathogen detection pipeline, a metagenomics pipeline for outbreak surveillance, an SRA import app, and a GISAID sharing app. 

The research-use only toolkit is compatible with many Illumina workflows, including the respiratory virus target enrichment workflow.

Illumina is making the toolkit available to researchers worldwide for free until October 2020. Illumina is also offering a free one-year license to any researcher using its Clarity laboratory information management system for COVID-19 testing.

Apr 16, 2020

Eurofins Genomics US SARS-CoV-2 Plasmid DNA Controls

Eurofins Genomics US and its subsidiary BlueHeron Biotechnology have launched three SARS-CoV-2 plasmid DNA controls for verifying the presence of the virus. The controls are intended for use in both R&D and diagnostic applications and target key segments in the virus genome. One of them, CVGP, covers a large part of the viral sequence.

Apr 16, 2020

Loop Genomics SARS-CoV-2 Long-Read Sequencing Service

Loop Genomics has launched a service for sequencing SARS-CoV-2, the virus that causes COVID-19, using long amplicons and synthetic long reads linked by universal molecular identifiers.

The service provides reads averaging 6 kb to 7 kb using only Illumina's short-read next-generation sequencing platform. The SARS-CoV-2 has a genome of approximately 30 kb. Along with consensus error correction, the technology allows researchers to characterize highly similar strains that have mutations thousands of bases apart.

Apr 15, 2020

Bio-Techne ExoDx Prostate Test At-Home Collection Kit

Bio-Techne has launched the Exosome Diagnostics ExoDx Prostate Test At-Home Collection Kit for patients who are concerned about their prostate health.

The ExoDx Prostate or EPI test is a urine-based genomic test that helps inform the prostate biopsy decision.

Due to shelter in place orders issued to reduce the spread of COVID-19, appointments have been cancelled for millions of men for important procedures such as biopsies to detect the presence of prostate cancer, the firm noted. The at-home collection kit enables physicians and their patients to employ a telehealth solution when patients share frustration, anxiety, and fear over whether they might harbor high-grade prostate cancer, Bio-Techne said.

Apr 14, 2020

Biolytic Lab Performance Dr. Oligo 768XLc Nucleic Acid Synthesizer

Biolytic Lab Performance has launched its Dr. Oligo 786XLc platform for high-throughput DNA and RNA synthesis.

The platform uses 384-well synthesis media with 2 to 100 nmol per well, with optional trityl collection, oligo desalting, and elution capabilities. It is designed to be efficient, with optimized reagent usage and a layout that lowers maintenance and operational costs.

Applications including gene synthesis, genetic diagnostic test kits, PCR, CRISPR-Cas9, RNAi, and next-generation sequencing.

Apr 10, 2020

Denovix RNA Assay

DeNovix has launched its RNA fluorescence quantification assay, which the firm said is suitable for multiple platforms including stand-alone fluorometers, plate readers, or any DeNovix fluorescence-based instrument. According to DeNovix, the assay's proprietary chemistry allows quantification of RNA in the presence of dsDNA or other biomolecules that could interefere with absorbance-based-techniques. The assay provides accurate and specific quantification between 250pg/µL and 1500ng/µL. 

Apr 10, 2020

Active Motif Recombinant COVID-19 Antibodies

Active Motif said that in February it successfully isolated antibodies from patients in China recovering from COVID-19, and that the full suite of antibodies is now available for research applications and diagnostic test development. In collaboration with Fudan University and its Public Health Clinical Center, the company used its proprietary single-cell AbEpic screening technology to isolate the antibodies from patients, whose samples were screened to obtain whole human IgG antibody clones that have been sequenced, expressed, and characterized for binding directly to the SARS-CoV-2 S1 protein.

Apr 10, 2020

Codex Synthetic DNA Products for COVID-19 Research; Dx/Vaccine Development

Codex has launched a number of newly developed products and services for COVID-19 research and diagnostic/vaccine development. The new products include:

  • SARS-CoV-2 diagnostic RNA controls: safe positive controls that replace the need for live virus in RT-PCR and NGS testing protocols
  • SARS-CoV-2 antigen panels and antibody libraries: allow for rapid design and iteration of antigens or antibody libraries for the development of vaccines and therapeutics using the company's BioXp 3200 gene automated synthesis platform.
  • SARS-CoV-2 spike protein DNA vaccine construct, mRNA vaccine scaffold, and live attenuated vaccine scaffold for vaccine development
  • SARS-CoV-2 synthetic DNA parts: span the whole genome and useful for developing DNA, RNA, and viral vector vaccines and pan-genome diagnostics
  • SARS-CoV-2 full-length synthetic genome: the Wuhan-Hu-1 strain of SARS-CoV-2 cloned in a bacterial artificial chromosome for the development of vaccines, therapeutics, and diagnostics.
Apr 08, 2020

GC Genome/Celemics: SARS-CoV-2 BTSeq Sequencing Service

Korean firms GC Genome and Celemics have launched a SARS-CoV-2 sequencing service. As part of the service, GC Genome will use Celemics' Barcode-Tagged Sequencing (BTSeq) technology, which can analyze sequence sizes of less than 1 kb to a maximum of 30 kb with an error rate of less than .001 percent per base pair, the companies said. This enables analysis of both PCR products and full SARS-CoV-2 genomes. Turnaround time is usually less than 10 days but can be minimized to one day, the companies said. The partners said that the service can reveal information on the epidemiology and pathogenesis of the virus and enable mutant surveillance.

Apr 03, 2020

AmpTec Universal COVID-19 Positive Control IVT RNA EURM-019

AmpTec has released a Universal COVID-19 Positive Control IVT RNA, called EURM-019, to facilitate quality control of the detection of SARS-CoV-2 at core facilities and hospital laboratories. The EURM-019 material consists of single-stranded RNA fragments of the SARS-CoV-2 genome and can also serve as a benchmark to validate SARS-CoV-2 RT-PCR tests kits in development. AmpTec is supplying the control on behalf of the European Commission.

Apr 03, 2020

Thermo Fisher Scientific AcroMetrix Coronavirus 2019 (COVID-19) RNA Control

Thermo Fisher Scientific has launched the Thermo Scientific AcroMetrix Coronavirus 2019 (COVID-19) RNA Control to help validate and monitor COVID-19 molecular diagnostic tests. The non-infectious positive control consists of synthetic RNA transcripts containing the N, S, E, and Orf1ab regions of the SARS-CoV-2 genome. The RNA is ready for reverse transcription, PCR amplification, and detection. The kit contains two vials of RNA at concentrations that will result in low-positive and ultra-low-positive results in most commonly used PCR-based testing methods. The control is available globally as a research-use-only product and is not intended for clinical use.

Apr 03, 2020

Horizon Discovery Arrayed CRISPR Knockout Screening for Primary Human B Cells

Horizon Discovery has added an arrayed CRISPR knockout screening service for primary human B cells to its cell-based screening services. The new B cell screening service will enable researchers to identify genes that affect the function of B cells and examine how this impacts other immune cell types, particularly in infectious diseases, cancer, and auto-immune disorders, such as COVID-19, Burkitt's lymphoma, and multiple sclerosis, the company said.

Apr 03, 2020

Agilent K6460S Clinical Edition TQ LC/MS System

Agilent this week launched the K6460S Clinical Edition TQ LC/MS system, a triple quadrupole liquid chromatography/mass spectrometry system designed to improve in vitro diagnostic workflows in clinical labs. The system is listed as a Class I medical device with the US Food and Drug Administration and includes the clinical edition of Agilent MassHunter software to enable an easy and intuitive submission-to-reporting workflow. TQ LC/MS increases the specificity, selectivity, and accuracy of many clinical diagnostic assays compared to traditional binding assays, Agilent noted in a statement. The platform also received approval from China's National Medical Products Administration in January.

Apr 03, 2020

SensID Control Materials for Qiagen Therascreen PIK3CA RGQ PCR Kits

SensID, a Germany-based provider of controls and reference materials for clinical genomics, has introduced a set of controls for Qiagen's US Food and Drug Administration-approved and CE-IVD marked Therascreen PIK3CA RGQ PCR kits. Qiagen's kit was launched in Europe in February 2020 to aid in the identification of activating PIK3CA mutations in FFPE or blood plasma samples from patients with advanced breast cancer. The kit received FDA approval in 2019 and has been commercialized in the US as a companion diagnostic test for alpelisib (Novartis' Piqray).

SensID and Qiagen collaborated to develop the new control materials, which include 11 clinically actionable PIK3CA mutations estimated to be present in approximately 40 percent of HR+/HER2- advanced breast cancer cases and to confer a greater likelihood of responding positively to PI3K inhibitors. The control set contains seven vials (DNA in buffer) in a format matched to the reaction mixes of the Therascreen kit, and each set provides sufficient materials for about 40 runs, the company said. SensID also offers certified DNA-free human plasma that can be used in conjunction with the sample set, if suitable plasma is not available locally.

Apr 01, 2020

Enpicom ImmunoGenomiX Software V2.0

Dutch bioinformatics firm Enpicom has released version 2.0 of its ImmunoGenomiX (IGX) Platform for the management, analysis, and visualization of T- and B-cell receptor sequencing data. The new version supports single-cell sequencing data in addition to bulk sequencing data. The ability to analyze data from both single-cell and bulk sequencing workflows in tandem provides new opportunities for immunomics research and drug development, the company said. Other new enhancements include the IGX-Compare app, which allows users to compare any two data sets to visualize and prioritize matching clones; and more extensive data support, supporting the upload of readily annotated clone tables from, for instance, 10x Genomics or Adaptive Biotechnologies. The new version also features more clonotype grouping definitions and V/J gene usage plotting.

Mar 31, 2020

Berkeley Lights OptoSeq 3' mRNA Library Kit

Berkeley Lights has launched its OptoSeq 3' mRNA Library kit, which allows users to directly link phenotype to genotype. The kit inculdes reagents, primers, probes, and enzymes to prepare and label individual cells for cDNA sequencing. 

According to the firm, customers can use the library prep kit to capture and link genomic information to single-cell phenotypic data in order to learn more about cellular behavior and ramp up discovery, development, and production of cell-based products. 

Mar 30, 2020

Phase Scientific Phasify Viral RNA Extraction Kit

Phase Scientific, which is headquartered in Hong Kong with R&D and manufacturing facilities in Southern California and mainland China, has globally launched the Phasify Viral RNA Extraction Kit, which purifies and concentrates viral RNA in patient viral transport media samples. Phasify is a proprietary technology developed by Phase Scientific that can concentrate target molecules 10-fold to 100-fold, making them easier to detect. The kit can be used with sample volumes of up to 1 ml, and can produce enhanced viral RNA concentration with flexible elution volume up to 10 µl. According to the company, the kit enables a three- to six-cycle threshold reduction compared to solid phase extraction.

Mar 20, 2020

Asuragen Armored RNA Quant SARS-CoV-2 Control

Asuragen is offering an Armored RNA Quant SARS-CoV-2 Control for use in developing assays in response to the COVID-19 pandemic. The new control material targets the SARS-CoV-2 viral nucleocapsid region and, along with the company's new RNAse P construct, aligns with the US Centers for Disease Control and Prevention- and World Health Organization-recommended diagnostic panel. Asuragen said that armored technology encapsulates the in vitro transcribed RNA in a protective protein coat to resist nuclease degradation, enabling its use as RNA extraction, process quality, and positive diagnostic reference controls.

Mar 20, 2020

LGC SeraCare AccuPlex SARS-CoV-2 Reference Material Kit

LGC SeraCare recently launched the AccuPlex SARS-CoV-2 Reference Material Kit, which contains positive reference material targeting the published US Centers for Disease Control and Prevention and World Health Organization consensus sequences, as well as complementary negative reference material targeting the human RNAse P gene. LGC SeraCare said that its kit is superior to "naked" transcribed RNA which does not evaluate the assay extraction step, and safer than heat-treated infectious samples, and are a valuable tool for clinical laboratories seeking to perform assay installation, verification, and performance monitoring.

Mar 20, 2020

Arima Genomics HiChIP Assay and MAPS Pipeline

Arima Genomics has launched its HiChIP chromatin conformation assay. The assay is built on its Arima-HiC platform and introduces chromatin immunoprecipitation sequencing to provide data on long-range chromatin interactions specifically enriched at genomic locations occupied by proteins of interest.

The firm has also created an optimized version of the Model-based Analysis of Proximity Ligation-Assisted ChIP-seq and HiChIP (MAPS) bioinformatics pipeline to help streamline data analysis.

Mar 20, 2020

Twist Bioscience SARS-CoV-2/COVID-19 NGS Target Enrichment Panel

Twist Bioscience is offering a research-use-only target enrichment panel for viral detection and characterization of SARS-CoV-2, the virus that causes COVID-19, using next-generation sequencing. The panels, comprising synthetic double-stranded DNA probes covering the entire viral genome, can also be used for environmental monitoring and surveillance. Kits are available in three sizes: 2 reactions, 12 reactions, and 96 reactions.

Pages

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.

New analyses indicate female researchers are publishing less during the coronavirus pandemic than male researchers, according to Nature News.

A study suggests people with the ApoE e4 genotype may be more likely to have severe COVID-19 than those with other genotypes, the Guardian says.