A company in Malaysia is offering to map whole-genome sequencing data and call variants in one week’s time for $4,000.
I readily admit that I have not taken sequencing-as-a-service companies very seriously. The idea of sending precious samples off to a third party and getting back the sequence and variants doesn’t appeal to me for a number of reasons. Outsourcing just the analysis of sequence data is even more anathema. Why would anyone want to do that? Analysis is the best part! Then again, I’m fairly biased in this matter because (1) I work at a major genome center with significant in-house sequencing resources, and (2) sequence analysis and variant detection are among my job responsibilities. Obviously I don’t want those to go away.
That said, there seems to be a growing interest in outsourcing sequencing and/or analysis in the wider research community. Complete Genomics had a strong presence at Marco Island this year, and has a growing customer list that includes (perhaps surprisingly) at least two genome centers. Beijing Genomics Institute (BGI) announced a purchase of 128 Illumina HiSeq2000 instruments in January; a month later in Science magazine I saw a full-page ad indicating that they’re open for business as a sequencing provider. No big deal, they’re half a world away, right? So I thought, until I heard whispers of a BGI facility in San Francisco.
Second and third-generation sequencing technologies are bringing about volatile changes in the fields of genetics and genomics. Throughput continues to skyrocket, while the costs of sequencing plummet. It’s now possible to sequence a complete human or mammalian genome to high coverage on a single instrument run at ~$20,000. This has had two effects on the research community:
- Genomes abound. At least a dozen individual human genomes have been published, but NGS technologies are being applied to a wide range of studies – exomes, transcriptomes, model organisms, you name it.
- Everyone wants to sequence. Thanks to a lot of press and some high-profile publications, massively parallel sequencing is known to every corner of the biomedical research world. Suddenly every clinician with a patient cohort wants in, because if they don’t find the disease-causing genes, someone else will.
- Not everyone can buy an NGS instrument. Commercially-available sequencers currently cost a quarter to a half million dollars or more each, which is a significant purchase even for labs flush with ARRA funding. This means that a lot of small labs will not be looking to buy a machine, but rather to rent space from someone who has one. Music, no doubt, to the ears of BGI and Complete Genomics.
One thing is clear. These new sequencers and service providers are going to put high-throughput sequencing into the hands of many investigators. Investigators, I might add, who likely have never dealt with NGS data. I think that’s potentially very exciting, and I hope that the experiences of major genome centers will help newcomers address the challenges of massively parallel sequencing.