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New or disruptive Next Generation Sequencing (NGS) Technologies 

This side presents a list of new NGS technologies. Some of these technologies are based on new enzymes used for sequencing, on microdroplet sequencing, or on electron microscopy (ZS Genetics). Some technologies are based on nanopores and aim to improve existing nanopore sequencing technologies (Genia Technology). The different intentions for developing these new technologies are improving sequencing accuracy, simplification of sequencing and analysis workflows, enabling longer sequencing reads, real time sequencing without prior amplification, or reducing sequencing costs. 

Most of these technologies are still in the development, validation or commercialization status and currently not available for end users. 

Genia Technology

Introduction to Genia Technology NanoTag sequencing

Genia Technology intends to reduce sequencing costs, improve accuracy, increase sequencing speed and simplify workflow by enabling sequencing without complex sample preparation and without the utilization of optical detection.

Improving nanopore technology Genia Technologies Nanopore

The technology is based on protein nanopores that are incorporated into a lipid bilayer membrane. The general principle is based on nanopore sequencing as used in Oxford Nanopore Technologies.

The main difference is that this technology does not measure the changes in conductivity caused by the different nucleotides passing through the pore. Instead each nucleotide (G, A, T, and C) contains a characteristic tag. The figure shows these characteristic tags (conveniently the tags are labelled with G, A, T, and C).

These tags are cleaved by a DNA replication enzyme and captured by the nanopore. If these tags are guided into the nanopore they will cause characteristic changes in the membrane current flow. This is measured before the tag is cleaved of from the nucleotide. 
These tags are engineered to enable maximal distinction in current flow changes. This will improve the sequencing accuracy compared to other nanopore based technologies that measure current changes induced by the different natural occurring nucleotides passing the nanopore.

A major benefit of this sequencing technology is the implementation of standardized semiconductor technology that will markedly reduce sequencing costs.

Genia Technologies was acquired by Roche in June 2014.



Introduction to GenapSys sequencing technology

The aim of the GenapSys technology is to provide a fast and easy to use way to generate low cost and accurate sequence information. The Gene Electronic Nano-Integrated Ultra-Sensitive (GENIUS) fully integrated platform enables a simplified workflow based on the first purely electronic sequencing chip.
Genius is a portable, easy to use intuitive sequencing system.

What is GenapSys sequencing technology?

In general the technology is based on semiconductor chips similar as used in the Ion Torrent technology. The Genius device measures electronic signals during copying of the DNA molecule. Detailed information about the technology are not public available.

GenapSys announced to offer different chips for different sequencing project sizes enabling 1, 10 or 100 giga base data output.

The technology is currently in a testing program called "Join The Club" were users can apply for member chip and become a Genius test user.



Introduction to GnuBIO (Biorad) sequencing platform

GnuBIO offers a fully integrated next generation sequencing system. The platform is designed to reduce hands on time by simplification and integration of workflow steps and data analysis into the system.
By applying microfluidic technology the biochemical reaction for sequencing takes place in nano size droplet microfluidics.

The system is especially developed for targeted sequencing and hotspot analysis such as of rare variants.
It is planned to use the system in the future also for applications such as whole genome sequencing, transcriptome sequencing, or epigenetic studies.



Introduction to Lasergen Lightning Terminators™ sequencing technology

The NGS system is based on cyclic reversible termination (CRT) that enable higher accuracy, longer reads, reduces costs and sequencing time.

How does Lightning Terminators™ technology based sequencing works?

This technology is based on photo cleavable terminator chemistry and reduces the need of enzymes or chemicals for terminator cleavage. The incorporation of lightning terminators is as accurate as the incorporation of natural nucleotides.
The major difference of Lightning Terminators compared to other terminators is the unblocked ribose 3’-OH, this enables an easy incorporation of nucleotides in the growing DNA with commercial available enzymes for sequencing.

In general the technology uses fluorescence light signal generated during the nucleotide incorporation into a growing DNA strand similar as Illumina, Roche 454, or others.

No detailed information are public available about throughput, sequencing time, read length and if the system is chip or flow cell based.


Microdroplet sequencing

Introduction to Microdroplet sequencing from base4

Microdroplet sequencing is a new technology that enables high throughput long read sequencing at low costs without modification of the sample molecules. The sequencing takes place in real time and data will be available with short time delay.

The technology is based on microdroplets. The DNA molecule is guided through a microfluidic channel. In the next step individual nucleotides are released by pyrophosphorolysis. Each individual nucleotide is captured by a oil microdroplet. The microdroplets stream through a microfluidic channel one by one and the nucleotides will be processed by specific reaction cascades resulting in characteristic signals for each nucleotide. The sequence of the fluorescence light signals will be translated into the DNA sequence information.



Introduction to Nabsys sequencing technology

The Nabsys sequencing system aims to provide simultaneously sequence information and information about the location in the genome respectively in the DNA molecule.

How does Nabsys sequencing works?

The technology uses electronic detection based on semiconductor measurements.
Long DNA molecules will be sequence specific tagged with molecules that enable characteristic measurements in the nano detector (see also Genia Technology and Stratos Genomics). These tagged DNA molecules pass through the nano detector controlled by electrophoretic and hydrodynamic forces. The velocity can reach over 1 million bases per second.
Detailed information about the nano detector and the process of DNA tagging are currently not published by Nabsys.

Nabsys technology can be applied especially for analysis of structural variants, de novo sequencing of genomes, validation of contigs, or for sample heterogeneity characterization.

In March 2016, Nabsys underwent a restructuring of its company. Currently (April 2016), there are no information about development and validation status of the technology or about product launch dates available.


Stratos Genomics Technology

Introduction to Stratos Genomics Sequencing Technology

Stratos Genomics sequencing technology is based on combining nanopore sequencing technology with expandable nucleotide (X-NTP™) tagged DNA.
The aim of Stratos Genomics is to set new standards for ultra-low cost single molecule sequencing.

How does Stratos Genomics sequencing works? StratosGenomicsSeq

The technology combines nanopore sequencing with Stratos sequencing by Expansion™” (SBX) method. The development of a specific polymerase enzyme enables the translation of the nucleotide sequence information into a highly measurable molecule called Xpandomer. An Xpandomer is a sequence of high signal reporter molecules called expandable nucleotide (X-NTP™). Each nucleotide of the DNA template is replaces by one specific X-NTP™.
During sequencing, the Xpandomer passes through a nanopore and a highly specific read out will be measured for each X-NTP™ sequentially passing through the nanopore.
For general explanation of nanopore sequencing technology we refer to the Oxford Nanopore Technologies website.

In 2014 Roche invested in Stratos Genomics leading to a research collaboration.


SIMDEQ™ (SIngle-molecule Magnetic DEtection and Quantification)

Introduction to SIMDEQ™ sequencing technology

SIMDEQ™ (SIngle-molecule Magnetic DEtection and Quantification) technology is provides by PicoSeq. The aim of PicoSeq´s sequencing technology is to provide sequence and epigenetic information with one system at low costs and with high accuracy. The new technology does not require sample amplification and is not based on fluorescence detection.

How does SIMDEQ™ technology works?

The technology is based on artificial generated DNA or RNA hairpin libraries. One DNA/ RNA strand end of the hairpin is tagged with a biotin the other end is tagged with a digoxigenin. The DNA hairpin is fixed on a coverslip via the digoxigenin the other end is attached to a magnetic bead via a biotin-streptavidin bond.
The DNA hairpin is unzipped by a magnetic forces applied from above the coverslip. These forces are periodically modified to open and close the hairpins in a solution containing different oligonucleotides that are complementary to sections in the hairpins. The different oligonucleotides can hybridize to the open hairpin. This will lead to a difference in hairpin’s end-to-end distance (extension) by blocking of the original hairpin structure during unzipping of the hairpin. The distance can be measured for each hairpin during each unzip/ zip step. With this method the binding position of the oligonucleotide can be recorded.
By repeating the steps in different solutions containing different oligonucleotides the sequence of the hairpin DNA/ RNA fragment can be determined.
For more detailed information we refer to the publication Single-molecule mechanical identification and sequencing.

High Throughput can be realized by processing millions of hairpin/ bead complexes in parallel. The technology can be performed on 25kb long fragments.
This technology is especially useful for investigation of complex DNA regions with repeats, insertions or deletions as well as for detection of genetic fingerprints and for DNA identification.
The platform is already validated and is currently in the optimization and commercialization phase.



Q-SEQ™ Whole Genome Sequencing
Alongside QuantuMDx's novel sequencing by synthesis (SBS) DNA sequencing chemistry deployed on its nanowire FET biosensors, QMDx is also developing a novel DNA sequencing technology named Q-SEQ™. This device will perform single molecule, direct read (i.e. no need for reagents or expensive fluorescent detectors), long DNA sequencing reads and is presently at the prototyping stage. Q-SEQ™ is also being developed to undertake rapid sample to result low cost sequencing of whole genomes, integrating front end technologies developed by QuantuMDx's for its Q-POC™ device.
Source: quantumdx


ZS Genetics

Introduction to ZS Genetics sequencing technology

The technology of ZS Genetics is based on electron microscopy. The aim of ZS Genetics is to offer highest accuracy for long read single molecule DNA sequencing.

How does ZS Genetics sequencing technology works?

The system is based on the ability to recognize individual heavy atoms that mark the location and identity of specific DNA base pairs. This is enabled by atomic resolution imaging using electron microscopy. The DNA template of interest is denatured in single strand DNA and afterwards the second strand will be generated by labelling each nucleotide of the template DNA strand with a specific heavy atom.

The technology will focus on long DNA read sequencing without amplification steps. The company aspires to enable read length between 20 -50 k base pairs (publishing data 2012).

It has to be stated that the set up, maintenance and working on electron microscopes is still complex and the technology is relative expensive.