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Product Watch: WaferGen's SmartChip TE; NEB's Microbiome DNA Enrichment Kit


WaferGen Biosystems this week launched the SmartChip TE, a PCR-based target-enrichment product for sample preparation prior to targeted re-sequencing on next-generation platforms.

SmartChip TE addresses CLIA-certified and clinical research laboratories' needs in sequencing-based testing, WaferGen said. The product runs on the company's SmartChip Real-Time PCR system, and relies on massively parallel individual PCR reactions to provide cleaner and better-controlled amplification, thereby providing more accurate results in the downstream sequencing step, according to the company. Each target is amplified in an individual reaction, yielding close to equimolar products without the possible side reactions that occur in competing systems employing highly multiplexed PCR and/or target capture.

Following successful proof-of-concept studies at Ghent University and a major US-based teaching hospital, SmartChip TE has been performing well at several major commercial clinical sequencing service providers including BGI and Ambry Genetics, WaferGen said.

An important part of SmartChip TE is a database of validated assays covering the whole human exome, which WaferGen developed in collaboration with the laboratory of Jo Vandesompele at Ghent University. Having PCR assays ready on demand provides WaferGen's customers with fast turnaround times for their custom panels, and enables them to build the required flexibility in their study design by allowing them to easily change genes or targets in future studies, the company said.

New England Biolabs this week released the NEBNext Microbiome DNA Enrichment Kit.

The new kit uses a novel method to separate microbial DNA from host DNA, thereby reducing the high cost of sequencing microbiome DNA to a more practical level, the company said.

Microbiome samples are commonly dominated by host DNA (up to 99 percent), complicating their genetic analyses — particularly total microbiome DNA sequencing studies, NEB said. Since only a small percentage of sequencing reads pertain to the microbes of interest, obtaining sufficient sequence coverage of the microbiome DNA can become cost-prohibitive or even technically infeasible.

The NEBNext Microbiome DNA Enrichment Kit uses the MBD2-Fc protein, which binds to CpG-methylated DNA (including human genomic DNA) with very high specificity. The MDB2-Fc protein is attached to Protein A-coated magnetic beads, enabling quick and easy removal of the contaminating host DNA in about 30 minutes. The microbial DNA-enriched sample is then ready to be processed for multiple downstream applications, including next-generation sequencing, qPCR, and endpoint PCR, the company said.

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