NuGEN Introduces Unique Indexing Solutions for Illumina’s High Capacity Sequencing Platforms

02-Oct-2017 Intellasia | BusinessWire | 8:00 PM Print This Post

SAN CARLOS, Calif.–(BUSINESS WIRE)–#allegrotargetedgenotyping–Today NuGEN
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.

About NuGEN Technologies, Inc.

Based in San Carlos, California, NuGEN Technologies, Inc., provides
innovative NGS and genomic sample prep products for a broad range of
sample types including RNA and DNA from whole tissues, FFPE samples,
single cells and liquid biopsies. NuGEN’s products offer rapid and
simple workflows designed to reduce time and cost per sample. NuGEN
products are used by 1000s of customers in basic research, applied
markets and molecular diagnostics. NuGEN products are manufactured under
stringent quality controls (ISO 13485). To learn more about NuGEN visit


Media inquiries:
NuGEN Technologies, Inc.
Richard Fekete,
Ph.D., Vice President of Marketing
[email protected]


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