Nanopore sequencing

An exciting wave of newly released DNA sequencing instruments and technology will soon be available to researchers. From DNA sequencers the size of a cell phone to platforms that turn short reads into long-range information, these new sequencing technologies will be available on Genohub as services that can be ordered. Below is a summary of the technology you can expect in Q1 of 2016:

10X Genomics GemCode Platform

The GemCode platform from 10X Genomics partitions long DNA fragments up to 100 kb with a pool of ~750K molecular barcodes, indexing the genome during library construction. Barcoded DNA fragments are made such that all fragments share the same barcode. After several cycling and pooling steps, >100K barcode containing partitions are created. GemCode software then maps short Illumina read pairs back to the original long DNA molecules using the barcodes added during library preparation. With long range information, haplotype phasing and improved structural variant detection are possible. Gene fusions, deletions and duplications can be detected from exome data.

Ion Torrent S5, S5 XL

The S5 system was developed by Ion to focus on the clinical amplicon-seq market. While the wait for delivery of Proton PII chips continues, Ion delivered a machine with chip configurations very much similar to past PGM and Proton chips. 520/530 chips offer 200-400 bp runs with 80M reads and 2-4 hour run times. Using Ion’s fixed amplicon panels, data analysis can be completed within 5 hours. The Ion chef is required to reduce hands on library prep time, otherwise libraries and chip loading needs to be performed manually. Ion looks to have positioned their platform toward clinical applications. With stiff competition from Illumina and their inability to deliver similar read lengths and throughput, this is a smart decision by Ion. Focusing their platform on a particular application likely means future development (longer and higher throughput reads) has been paused indefinitely.

Pacific Biosciences Sequel System

Announced in September 2015, the Sequel System uses the same Single Molecule, Real Time (SMRT) technology as the RSII,   but boasts several tech advancements. At around one third the cost of a RSII, the Sequel offers 7x more reads with 1M zero –mode waveguides (ZMWs) per SMRT cell versus the previous standard of 150K. The application of Iso-Seq or full length transcript sequencing is especially promising as 1M reads crosses into the threshold where discovery and quantitation of transcripts becomes interesting. By providing full length transcript isoforms, it’s no longer necessary to reconstruct transcripts or infer isoforms based on short read information. Of course, the Sequel is ideal for generating whole genome de novo assemblies. We’l follow how the Oxford Nanopore’s ONT MinIon competes with the Sequel system in 2016.

Oxford Nanopore’s (ONT) MinIon

In 2014, Oxford Nanopore started it’s MinIon Access Program (MAP) delivering over 1,000 MinIons to users who wanted to test the technology. These users have gone on to publish whole E. Coli and Yeast genome assemblies. Accuracy of the device is up to 85% per raw base and there are difficulties in dealing with high G+C content sequences. There remains a lot of work left to improve the technology before widespread adoption. The workflow is simple and uses typical library construction steps of end-repair and ligation. Once the sample is added to the flow cell, users can generate long reads >100 kb and can analyze data in real time. Median reads are currently in the 1-2 kb length. Combined alongside with MiSeq reads, publications have shown MinIon output can enhance contiguity of de novo assembly. Lower error rates generated by Two Direction reads produced with recent updated MinIon chemistry does give cause for optimism that greatly reduced error rates can be achieved in the near future. This along with a low unit cost and the ability to deploy the USB sized device in the field make this a very exciting technology.

Illumina HiSeq X

While HiSeq X services have been available on Genohub for over a year, Illumina’s announcement of its expansion to non-human whole genomes was well received. However there are still several unanswered questions. Illumina states,

“The updated rights of use will allow for market expansion and population-scale sequencing of non-human species in a variety of markets, including plants and livestock in agricultural research and model organisms in pharmaceutical research. Previously, it has been cost prohibitive to sequence non-human genomes at high coverage.”

You can now sequence mouse, rat and other relatively large sized genomes economically on the HiSeq X. This makes the most sense for high coverage applications, e.g. 30x or above. While smaller sized and medium sized genomes can be sequenced on a HiSeq X, the low level of barcoding and high coverage you’d obtain makes these applications less attractive. According to Illumina, as of 12/20/2015, metagenomic whole genome sequencing was not a compatible application on the HiSeq X. The instrument is still restricted to WGS only. RNA-Seq, Exome-seq and ChIP-Seq applications will have to wait. Perhaps by the time the HiSeq X One is released access will be opened to these non-WGS applications.

While these new instruments make their way onto Genohub’s Shop by Project page, you can make inquiries and even order services by placing a request on our consultation page.