“We wanted to make the world’s simplest sequencer,” remarked Joe Beechem, Ph.D., Senior Vice President of R&D at NanoString. Beechem presented the Hyb & Seq platform with live demonstration during a lunchtime workshop at the 2017 annual meeting of Advances in Genome Biology and Technology (AGBT).

Currently in development, the Hyb & Seq platform is a first of its kind, library-free, amplification-free, single-molecule sequencing technique that uses nucleic acid hybridization cycles of fluorescent molecular barcodes onto native targets. The absence of library preparation reduces hands-on time, and the amplification-free technology removes bias caused by amplification and extensive sample preparation.

To demonstrate the simplistic workflow and quick sample to answer of Hyb & Seq, an AGBT attendee, James Hadfield, Ph.D., Head of Genomics at the Cancer Research UK Cambridge Institute, initiated the run of an FFPE sample on the platform in real-time. The run completed a few (not all) cycles of the sequence throughout the 90-minute event. This was the first time Hadfield had used the instrument and, in fact, it was the first time someone other than a NanoString scientist ran a sample on the Hyb & Seq platform.

Hadfield was in a suite just a few doors down from the ballroom where the presentation was being held, and his progress was shared through a live feed which Beechem cut to throughout his presentation to highlight the simplicity and speed of the process.

As the preparation for the experiment was taking place down the hall, Beechem presented the science and motivation for the Hyb & Seq platform.

The world’s simplest future sequencer:

  • The workflow enables users to prepare an FFPE curl for cancer panel sequencing with <15 minutes of hands-on time and <60 minutes of total sample prep time
  • The target cancer panel sequencing (from sample to result) takes <24 hour to complete
  • Users can sequence both DNA and RNA from the same sample, at the same time, on the same instrument
  • Both long and short reads are achieved with the same Hyb & Seq chemistry
  • Neither library preparation nor amplification are a part of the workflow

The Hyb & Seq chemistry is based off of existing NanoString fluorescent barcode technology but with new shorter barcodes with lengths of 20-50 nm. Six base pairs are determined with each cycle, and a typical cancer panel takes 400 cycles.

The workflow carried out live at AGBT consisted of three steps:

  1. Single-tube deparaffinization and lysis and binding of capture probes; 30 minutes’ total time, 5 minutes’ hands-on time
  2. Removal of particulate using a syringe filter; <5 minutes total time, <5 minutes hands-on time
  3. Capture probe purification; 20 minutes total time, 5 minutes hands-on time

The sample is then ready to load onto the flow cell and place on the sequencer.

For the released system still in development, the goal is to achieve automated sample preparation and purification.

By the end of the presentation, the feed showed a live stream of sequencing results, calling bases in real time. “We went from A-to-Z as we sat here,” Beechem remarked.

calls

Live stream of sequencing results at AGBT 2017

Since the first announcement of Hyb & Seq at AGBT 2016, NanoString promised to make it a transparent process with the genomic community by providing real-time insight into the technology to garner timely feedback. As part of the ongoing development of the Hyb & Seq platform, NanoString is interested in partnering with corporate and academic laboratories to collect real customer data on the sequencer throughout 2017 and 2018.

For more news on this event, please see coverage on Enseqlopedia and Next Generation Technologist.

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Posted by Robin Lynn White