Magic-BLAST 1.2.0

Mar 01, 2017

Version 1.2.0 of the BLAST RNA-seq mapping tool, Magic-BLAST is now available. The new release allows researchers to handle multiple SRA accessions, offers improved splice site detection, and multi-threading performance. The update also fixes issues with macOS installation. The release are available here, and the executables are available here.

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Jan 16, 2019

HTG Molecular EdgeSeq Reveal

HTG Molecular today launched its HTG EdgeSeq Reveal software. According to the firm, the software streamlines biomarker data analysis from samples analyzed with the HTG EdgeSeq Precision Immuno-Oncology Panel on its EdgeSeq system. When used with the panel, the software allows applications including immunophenotyping of tumor infiltration lymphocytes, monitoring of immunotherapy response biomarkers, and elucidating immune-escape mechanisms know to drive disease progression. The firm noted that users will be able to conduct molecular profiling using a wide variety of sample types, potentially allowing them to support translational applications and determine potential biomarkers for companion diagnostic development. 

Jan 16, 2019

Oxford Nanopore Field Sequencing Kit

Oxford Nanopore Technologies has launched a Field Sequencing Kit for sequencing library preparation from genomic DNA that requires no refrigeration. The kit, which requires 400 nanograms of high molecular weight DNA as input, generates libraries in 10 minutes using a two-step protocol. A transposase simultaneously cleaves template molecules and attaches tags to their ends. After that, rapid sequencing adapters are added to the tagged ends. The unopened kit, which is shipped cold, is stable for up to one month at 30 °C and up to three months at 2 °C to 8 °C.

Jan 14, 2019

NRG, Macrogen ArrayMagic

NRGene and Macrogen have launched a joint sequencing-based genotyping service called ArrayMagic, which the firms said provides ultra-high-density SNP genotying at a low cost per datapoint. As part of the service, the team will launch a dedicated website to advise customers on how to send samples to Macrogen. The partners then employ a sequencing library prep method, developed by iGenomX, to create an ultra-low coverage sequencing dataset for each sample. NRG then applies its database and analytical tools to impute a high-resolution SNP set from the data. 

Jan 11, 2019

TATAA Biocenter Alu Assays

TATAA Biocenter is now offering ultra-sensitive qPCR assays targeting human-specific Alu repeats, which comprise about 10 percent of the human genome. The assays are available for different target lengths, which makes it possible to characterize the integrity of gDNA. The ration measured with TATAA ALU-60, which amplifies 60-bp targets, to TATAA ALU-187, which amplifies 187-bp targets, assesses the level and fraction of cell-free DNA in liquid biopsy samples. The assays can detect even miniscule amounts of human genomic DNA contamination, and contaminated reagents can be cleaned with the Heat/Run gDNA removal kit. The ALU quality control panel was in part developed for the CANCER-ID consortium, TATAA said.

Jan 09, 2019

Asuragen AmplideX PCR/CE HTT Kit

Asuragen said today that it has launched its AmplideX PCR/CE HTT kit. The tool detects CAG trinucleotide repeats within the HTT gene, which are linked to the development of Huntington disease. According to the firm, the kit offers a streamlined, single-well PCR workflow that allows researchers to detect and size expansions with greater than 200 CAG repeats in about six hours. The kit provides all necessary reagents to size the expansion using 10 ng of DNA isolated from whole blood samples. The assay also addresses sample zygosity and preserves the CAG repeat profile in the presence of adjacent SNPs. The assay runs on Thermo Fisher Scientific Applied Biosystems Genetic Analyzers, including the 3130, 3500, and 3700 platforms.

Jan 08, 2019

Yourgene Sage 32 Plex

Yourgene Health has launched the Sage 32 plex test, a high-throughput noninvasive prenatal testing and analysis solution for clinical laboratories. It runs on Thermo Fisher Scientific's Ion Torrent sequencing platform and allows 32 samples to be processed in parallel. The test, which will be available internationally, has improved performance due to workflow enhancements and upgraded analysis methods. Yourgene plans to launch a CE-IVD-marked version of the library preparation kit for the Sage 32 plex workflow in the coming months. The Sage test differs from Yourgene's other NIPT, the Iona test, in that it screens for a wider range of conditions, including trisomies 21, 18, and 13; sex chromosome aneuploidies; and clinically relevant microdeletions. The analysis uses a cloud-based bioinformatics solution called Sage Link.

Jan 07, 2019

Twist Bioscience Synthetic DNA, TAPI

Twist Bioscience is now offering to synthesize genes up to five kilobases in length for $0.15 per base pair and with a turnaround time of 15 to 25 days. In addition, the company is making its Twist Application Programming Interface (TAPI) available to all customers ordering synthetic DNA.

Jan 04, 2019

PreventionGenetics Patient Plus

PreventionGenetics announced that it has added the Patient Plus feature to its PGxome whole-exome sequencing tests. Patient Plus invovles sequencing and copy number variant analysis, as well as targeted testing for the key sequence variants in a patient's parental specimens. According to PreventionGenetics, the approach allows researchers to detect de novo variants and phasing of variants in recessive genes.

Dec 21, 2018

Contextual Genomics 'Find It' and 'Follow It' Assays

Contextual Genomics, a Vancouver, Canada-based cancer genomics company, said that it has completed development of two new products: an improved version of its Find It hotspot panel for detection of genomic mutations in solid tumour cancers; and its Follow It hotspot panel for detection of the same genomic mutations in blood plasma.

The Find It panel now screens for 146 somatic genome alterations found in solid tumor cancers to identify optimal therapeutic treatments and recognize acquired drug resistance mutations. The assay is supported by Contextual's cloud-based genome analysis engine (CGIRP).

The Follow It panel screens for cell-free circulating tumour DNA in plasma, and is designed to  be used in patients with widespread metastatic disease at diagnosis and as a time series monitoring tool to read out tumor burden and treatment resistance. Follow It will screen for all of the same somatic genome alterations as Find It and can be used to follow disease progression for patients, including those whose tumors were initially tested with Find It.

Dec 21, 2018

DiaSorin Molecular Primer Pairs

DiaSorin Molecular has introduced three new primer pairs for Legionella species, Chlamydophila pneumoniae, and Mycoplasma pneumoniae, which can be used in laboratory-developed tests. The firm noted that it now offers more than 55 analyte-specific reagents.

Dec 20, 2018

Viracor Eurofins 16S NGS Bacterial Meningitis Test

Viracor Eurofins recently launched its 16S Next-Generation Sequencing Bacterial Meningitis test. The assay amplifies the 16S gene utilizing PCR, followed by NGS to identify and report the bacterial pathogen in a patient's CSF sample. The assay was validated to include the most common bacterial pathogens associated with meningitis: Streptococcus pneumoniae, Neisseria meningitidisHaemophilus influenzaeListeria monocytogenesStreptococcus agalactiae (Group B Strep), and Escherichia coli, as well as other less common pathogens that may be clinically important in immunocompromised patient populations (HIV-positive, solid organ transplant, or hematopoietic cell transplant patients). Physicians will receive test results for difficult-to-diagnose immunocompromised patients within three business days from specimen receipt, the company said.

Dec 19, 2018

Lexogen TeloPrime Full-Length cDNA Amplification Kit V2

Lexogen has launched a new version of its TeloPrime Full-Length cDNA Amplification Kit. TeloPrime allows detection and correct quantification of splice variants and their "true transcription start- and end-sites, in both short and long mRNA molecules," the firm said. According to Lexogen, the upgraded kit provides higher yields and enhanced representation of longer cDNAs from as little as 1 nanogram of RNA. 

Dec 14, 2018

Enpicom Expanded ImmunoGenomics Platform

Enpicom has finalized and launched an expanded version of its ImmunoGenomix platform, which it said will support discovery and development of novel immunotherapies, patient stratification for, and treatment monitoring of immunotherapies. The platform now also accepts B cell receptor as well as T cell receptor sequencing data. 

Dec 14, 2018

Microbiologics Group A Streptococcus and Respiratory Control Panels

Microbiologics has launched its Group A Streptococcus and Respiratory Panels, as well as test meothods to help clinical laboratories deliver accurate results during cold and flu season. The panels include features such as multiplexed pellets, swabs that mimic patient sample processing, and room temperature storage. 

Dec 12, 2018

Expedeon MagniPhi & QualiPhi DNA Polymerases

Expedeon has launched two high-fidelity polymerases, MagniPhi DNA Polymerase and QualiPhi DNA Polymerase. Expedeon offers the products in both 25- and 100-reaction kits, which contain DNA polymerases and their associated reaction buffers. The firm said MagniPhi — a wild-type form of the Phi29 DNA polymerase — is ideal for isothermal DNA amplification. According to Expedeon, MagniPhi's fidelity of synthesis produces up to 100 times fewer errors than Taq polymerase, while the amplification reaction yields more whole-genome amplification compared to normal PCR-based WGA techniques.

Expedeon's QualiPhi — a chimeric form of the Phi29 DNA Polymerase — has been engineered for enhanced sensitivity and efficiency while preserving the high processivity of the wild type Phi29. According to the firm, the polymerase's higher sensitivity allows improved amplification of DNA from low to high input concentrations and higher yields than the wild-type polymerase.

An analysis of UK Biobank data finds hemochromatosis to be more prevalent than thought, according to the BBC.

An analysis finds that female biomedical researchers receive fewer prizes than male ones, and when they do win prizes, they are less prestigious.

In Nature this week: improved genomic analysis using a graph genome reference, tumor mutational burden could predict clinical response to immune checkpoint inhibitors, and more.

Federal researchers tell the Los Angeles Times that the shutdown is causing missed research opportunities as they try to keep their experiments going.

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