Phoenix in Mythology and Sequencing

  • Like a Phoenix, Helicos Sequencing is Being Reborn
  • Direct Genomics in China to Launch the Genocare Clinical Sequencer
  • SeqLL in the USA to Launch Benchtop tSMS Sequencer

A phoenix as depicted by F.J. Bertuch (1747–1822). Taken from Wikipedia.org

In ancient Greek mythology, a phoenix is a bird that is cyclically regenerated or reborn by arising from the ashes of its predecessor, which dies in a show of flames and combustion. In contrast to a phoenix, modern biotech methods generally “die” in utility by being displaced with faster, better, and/or cheaper methods rather than undergoing “rebirth” in the context of a new application. However, a method developed by a company named Helicos (scarily close to Helios associate with a phoenix) may prove to be a rare exception. Perhaps this is destiny, but I digress…

Helicos Sequencing

Successful Sanger sequencing of a human genome in the early 2000s spawned numerous efforts to develop faster, better, and/or cheaper methodology to enable genomic analysis on a routine basis. Among the early contenders there was Helicos BioSciences, which was founded in 2003 by several principals including then—and still—uber-famous Stephen Quake.

Helicos sequencing technology, which is depicted below and outlined elsewhere, was especially attractive because it was “true” single-molecule sequencing (i.e. sample prep did not require prior PCR or other amplification, thus greatly simplifying the workflow). Moreover, the technology uniquely allowed direct RNA sequencing, thus obviating the need to first convert RNA into cDNA.

Main steps for primer(P)-based, single-color (Cy3 dye) Helicos sequencing, in this example using two passes. Taken from Harris et al. Science (2008)

3’-Unblocked reversible terminator. Taken from Chen et al. (2013)

Details for how this sequencing-by-synthesis occurs can read in various proof-of-concept publications. However, it’s worth noting here that the 3’-unblocked reversible terminator nucleotide triphosphate monomers have a cleavable linker attached to a detectable dye. Helicos referred to these as “Virtual Terminator” nucleotides since they are efficiently incorporated by a polymerase yet block incorporation of a second nucleotide on a homopolymer template.

So, with these methodological advantages going for it, why did Helicos file for bankruptcy in 2012? Press coverage at that time stated ‘rough financial sledding and tough competition from rival next-generation sequencing companies.’ In my humble opinion, this lack of commercial success was primarily due to the HeliScope Genetic Analysis System (pictured below) being way too big (think upright freezer-refrigerator), far too expensive ($1,350,000), and its ~35-base reads too short on performance—pun intended.

Two Phoenix-Like Versions of Helicos Sequencing

Fast forwarding about five years from the 2012 bankruptcy filing by Helicos brings us to recent reports of two independent efforts to bring back Helicos sequencing in commercially viable formats and contexts, think Phoenix rising from the ashes.

Jiankui He and the GenoCare sequencer (credit Xinjie Tian). Taken from Cyranoski Nature Biotechnology (2016)

The first of these is led by Jiankui He, Founder/CEO of Direct Genomics in Shenzhen, Guangdong, China, as well as Associate Professor at South University of Science and Technology of China in Shenzhen. He, coincidentally, was a postdoc with Helicos cofounder Stephen Quake, who is reported to lead the scientific advisory board for this new company.

The company’s website homepage states the following:

“Direct Genomics is providing physicians with the first single molecule sequencer built exclusively for the clinic. The technology simplifies genome sequencing by reading individual DNA and RNA molecules directly from patient’s blood or tissue samples, which delivers significant improvement in cost and speed. Together with clinicians, Direct Genomics is making genetics an affordable part of everyday patient care.”

Perusal of scant technical information on the company’s website suggests to me that a smaller sized, TIRF-optics-enabled instrument running Helicos-type sequencing has been developed. A story about Direct Genomics by David Cyranoski in Nature Biotechnology states that $100 “clinical sequencing” is being targeted, with a blood-draw to report turnaround time of 20 hours. A very recent publication I found provides details for resequencing the Escherichia coli genome by the Direct genomics platform named GenoCare.

The company’s website lists the following clinical applications:

  • Non-invasive prenatal testing (NIPT)
  • Tumor diagnosis
  • Early-stage cancer prediction
  • Pre-implantation genetic diagnosis (PGD)

The second Phoenix-like rebirth of Helicos sequencing has been developed by SeqLL, which was co-founded in 2013 by William St. Laurent and Daniel Jones, who previously held various technical positions at Helicos. Statements and a video on SeqLL’s website indicate to me that the sequencing technology is essentially that originally developed and patented by Helicos, which is still trademarked as True Single Molecule Sequencing (tSMS™).

William St. Laurent. /   Daniel Jones. Taken seqll.com

SeqLL has been operating as a tSMS™ service provider, but in October 2016 announced the launch of the tSMS™ System Early Access Program giving researchers access to its new benchtop system “designed to deliver unparalleled quantitative RNA and specialty DNA sequencing results to both academic and industry research partners.” I should add that a big, strong bench is needed given that the physical specs are 30 x 30 x 60 inches and 1,000 pounds! Nevertheless, SeqLL recently announced an SBIG grant for improving its direct RNA sequencing technology, which I think could prove to be a driver for adoption.

In conclusion, I think it’s very interesting to see Helicos sequencing coming back to life, if you will, in not one but two different commercial contexts, both of which will hopefully be successful. This despite current ‘tough competition from rival next-generation sequencing companies,’ as observed in the 2012 bankruptcy story about Helicos mentioned above. First and foremost, among that competition is Oxford Nanopore, which I’ve blogged about previously, and whom offers single-molecule sequencing that seems to me to be faster, better, and cheaper for both DNA and RNA, directly.

As usual, your comments are welcomed.

Postscript

After this blog was written, it was reported in GenomeWeb that Direct Genomics plans to deliver 50 instruments this year to SinoTech Genomics, a startup based in Shanghai that offers both clinical and research sequencing services. Direct Genomics CEO Jiankui He is quoted as saying that ‘SinoTech Genomics [is] committed to ultimately purchasing 700 GenoCare platforms,’ and that Direct Genomics ‘has the capacity of producing around 1,000 GenoCare instruments per year,’ which would be very impressive based on past operational experience with manufacturing Sanger sequencers at ABI.

The piece went on to report that Direct Genomics also ‘aims to launch GenoCare in the US in September.’ Regarding what’s inside the box, so to speak, ABI veteran Bill Efcavitch, who previously served as chief technology officer of Helicos, is quoted as saying that ‘the main difference between the former Helicos technology and the GenoCare platform is in the hardware. It’s completely different engineering.’ He added, however, that it still uses Helicos’ virtual terminator chemistry.