Will the real $1,000 genome please stand up?

Illumina's HiSeq X Ten is designed to sequence a human genome for $1,000.
Illumina's HiSeq X Ten genome sequencing system

This month, Illumina ($ILMN) announced it had achieved the elusive $1,000 genome. Critics have taken issue with that math--and now startup-minded researchers in Japan are readying an "ultra-low cost" genome sequencing system for the market next year.

On Jan. 14, Illumina unveiled its HiSeq X Ten sequencing system. Since then, observers have pointed out additional costs that may in fact bring Illumina's cost per sample above $2,000. Enter Quantum Biosystems. The unheralded Japanese firm showed up at the Personalized Medicine World Conference in Mountain View, CA, this week with single-read raw sequence data it represents as a breakthrough in single-molecule electrical sequencing of DNA.

Quantum, founded just a year ago with technology spun out from Osaka University, has built a sequencer that uses nanometer gaps and picoamp level currents to sequence single-stranded DNA and RNA. The founders say it cuts the cost of sample preparation. Reagents used in sample prep account for most of the costs in Illumina's system--an estimated $800 per genome.

Hiseq X Ten is priced at $10 million up front. Quantum's sequencer will cost less than $10,000 to make, the company told GenomeWeb Tuesday. The disposable silicon devices it uses can be manufactured for under one dollar apiece.

In data announced Tuesday, Quantum used its prototype sequencer to generate reads of about 20 base pairs form short oligonucleotides, according to GenomeWeb. The company reports accuracy of more than 99% in nonhomopolymer regions and 90% in regions with homopolymers.

"We want to see how this initial data release is received publicly," Nava Whiteford, Quantum's executive officer for informatics, told GenomeWeb. "Our hope is that we'll get some engagement from the community, and the fact that we're trying to make an effort to be open will be well received. If everything goes well, we'll release more data in the coming weeks."

To get a genome that truly costs $1,000, an ultra-low cost sequencing system may be needed. AllSeq quibbled with Illumina's $65 per sample estimate for library prep, saying it would call for workers who are "extremely efficient and extremely cheap." And life sciences blogger Todd Smith argues the true cost may be double. He points to a December opinion piece in the National Review of Genetics that contends samples must be sequenced more than once to get accurate data.

On top of that, high-performance computing blogger Glenn Lockwood pointed to the data storage and processing costs of handling all that data: "I'm nervous that the 'new era' will really be one in which the net rate of discovery is finally not limited by sequencing technology, but by available computing capacity."

Illumina may have set a record pace with their HiSeq announcement, but the race to a $1,000 genome looks like it could still be undecided, for now.

- read Quantum's release
- check out the GenomeWeb interview
- here's AllSeq's take
- read Todd Smith's post
- more: Glenn Lockwood on computing costs

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