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New Products: New Product Launches from AGBT and More

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Agilent Technologies has launched SureSelect XT Human Methyl-Seq and HaloPlex target enrichment systems.

The XT Human Methyl-Seq kit combines the company's SureSelect target enrichment system with bisulfite sequencing to enable analysis of both under- and over-methylated cytosine sites in the human genome. According to the company, it targets promoters, CpG islands, so-called "shores" and "shelves" found 4 kilobases up- and downstream of the CpG island, and known differentially methylated regions. The kit includes more than 3.7 million individual CpG dinucleotide sequences.

The HaloPlex target enrichment system is a library prep-free single-tube protocol that reduces sample-prep time to less than a day. According to the company, the system is ideal for desktop sequencers and combines the speed and specificity of PCR with the scalability and capture-size flexibility of in-solution hybridization formats.


Boreal Genomics has launched an early access program for its OnTarget Allele Enrichment System, which depletes wild-type alleles to improve detection of known and unknown rare cancer mutations.

The system enables researchers to enrich rare cancer mutations down to 0.01 percent frequency from plasma, frozen, or formalin-fixed paraffin-embedded samples in less than two hours, according to the company.


BioTeam has launched a MiniLIMS for the Ion Torrent PGM. The MiniLIMS is a web-based LIMS system and the first independent software solution that connects directly to the Ion Torrent service. BioTeam also provides service and support for the serve.


Eureka Genomics is now offering 16S metagenomics sequencing and analysis. The company developed proprietary algorithms for the analysis by partnering with Robert Edgar, who has developed algorithms for the human microbiome project, including UCHIME. Sequencing is done on the Illumina platform.


Pacific Biosciences said that several products are now fully compatible for sequencing experiments with its PacBio RS system through the company's Partner Program. Available products include Covaris's g-Tube for shearing genomic DNA and Fluidigm's Access Array for target enrichment, as well as informatics software Additionally, a number of companies now have made their informatics compatible with the RS, including Era7 Bioinformatics, which has BG7 Bacterial Genome Annotation for gene and RNA prediction from de novo assembly; Sapio Sciences's Exemplar LIMS system, which has pre-loaded PacBio protocols; GenoLogics's LIMS system; CLC Bio's Genomics Workbench and Server; Partek's Flow for variant detection; DNAStar's SeqMan NGen for sequence assembly; and Golden Helix's SNP and Variation Suite 7.


Complete Genomics has launched a Genomic Discovery Software Partners Program, which will include as partners Ingenuity Systems, Golden Helix, and DNAnexus. Partners in the program offer sequence analysis solutions that are compatible with Complete Genomics' data including Ingenuity's Variant Analysis, Golden Helix's SNP and Variation Suite, and DNAnexus's cloud-based solutions for data visualization and interpretation.


New England Biolabs has launched its NEBNext Oligo Modules for singleplex and multiplex library construction for sequencing. The kit can be used for ChIP-seq, DNA sequencing, or mRNA sequencing on Illumina platforms.


Researchers from the University of Maryland and the Massachusetts Institute of Technology have released TopHat 1.4.1 and CummeRbund 1.1.3, respectively.

The updated TopHat, available here, fixes a bug that was causing errors in the new transcriptome mapping option for paired reads.

The new CummeRbund release, available here, fixes bugs and adds new features. New features include a csSpecificity method that provides a "condition-specificity" score and a csDendro method that is useful for identifying relationships between conditions for subsets of features.

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.