Today NuGEN Technologies announces a new line of indexing solutions designed to enable researchers to take full advantage of the latest generation of Illumina sequencers. The three new enhancements include the launch of 96 unique dual index pairs to address index hopping, the incorporation of molecular tags to accurately measure PCR duplication levels, and the release of a new Metaplex Module designed to scale multiplexing to thousands of samples per flow cell.
The “index hopping” or “barcode hopping” phenomenon, which happens more frequently on patterned flow cells of the NovaSeq and HiSeq 3000/4000 platforms, is a low frequency event whereby a barcode that has been added to one library ends up on a fragment of a different library. This leads to mis-assignment of that read to a different sample. The addition of unique dual index pairs to the library enables software to recognize when barcode hopping has occurred and eliminate the read from the analysis. “The use of unique dual index pairs is particularly critical when working with applications that require a high degree of sensitivity, such as detecting mutations in cell-free DNA or rare transcripts in any RNA sample,” stated NuGEN’s Chief Scientific Officer, Doug Amorese. “With the addition of unique dual index pairs to NuGEN’s DNA and RNA library preparation kits greater confidence can be achieved for all samples.” The 96 unique dual indexes (192 different sequences) are currently available for NuGEN’s Ovation® Ultralow System V2 for DNA-Seq library preparation, and for the Universal Plus mRNA-Seq and Trio RNA-Seq system for preparation of RNA-Seq libraries. Solutions for the Methyl-Seq product line will also be available soon.
To further enhance sensitivity, use of molecular tags located adjacent to the barcode or integrated in the insert can be used to accurately distinguish true duplicate molecules from those duplicated during PCR amplification. This feature is included in NuGEN’s Ovation SoLo RNA-Seq System, designed for single-cell-level total RNA inputs and will soon be included in the Ovation Ultralow System V2 for DNA library preparation.
The release of Illumina’s NovaSeq has led to a significant increase in the number of reads obtained in a single sequencing run. While this has reduced the cost of sequencing it presents a challenge to researchers since a large number of samples must be pooled to realize these benefits. NuGEN’s third innovation, the Metaplex Module, when used in concert with the Allegro Targeted Genotyping system, can enable scaling up to over 3000 samples in a single lane. Davide Scaglione from IGA Technology Services, an applied Genomics solutions provider based in Udine, Italy states “We have used Allegro across a range of different sample types for fine mapping and association studies. The ability to scale across hundreds to thousands of samples that are often a part of such studies is a requirement for us to be able to provide a cost-effective solution to our customers.” The Allegro Targeted Genotyping system Metaplex Module is currently available for multiplexing up to 3072 samples in a single sequencing lane and additional barcodes will shortly be added to further increase this capacity.
Following the launches of three new products in 2017, Universal Plus mRNA-Seq, Trio RNA-Seq system, and Allegro Targeted Genotyping, these three indexing innovations create novel solutions for a wide array of NGS applications on all Illumina platforms.
Source – BusinessWire