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.
Is “Hercus” in the news “Colin Hercus”, the key person behind novoalign? Personally I am quite impressed by his product and believe he can deliver satisfactory services. I think data-processing-as-a-service is indeed the future. But on the other hand, there are some potential concerns. Most importantly, when you do not do the data processing by yourself, you may be unaware of artifacts and biases in the data processing which will be propagated to the final conclusion. Actually if we compare the several whole-genome resequencing papers, they are not all consistent. Furthermore, while I trust novocraft group, I do not for many other service providers. What is the quality of their results? Can they provide evidence that they do better, at least as good as, big genome centers? At this point, I more trust BGI as they have published high-profile papers. In addition, although MGRC claim they can process 30X data in a week, data transfer is probably much slower. I think they should try to bundle sequencing services as soon as possible. The typical model is sequencing and data analyses happen at the same place/company.
Sequencing as a service makes sense at a high level, and particularly (as you note) for smaller sites, but it gets tougher once you get into the details, at least for grant-funded organizations. The existing funding mechanisms and organizational cultures make it attractive to acquire instruments, the in-house services are typically subsidized at a level commercial providers can’t compete with. Perhaps more importantly, there is a critical dialogue and education that goes on between the services and the researchers with respect to designing experiments in front of a sequencing run, and analyzing them after the run. While it’s not impossible for that to happen with an external service, my impression is that it’s not at the same level as with an internal service. There are also the concerns MB notes around artifacts and bias in the data processing, and I would add in the chemistry.
Theoretically true about in-house benefits, but I see the “critical dialogue” you mention between investigators and sequencers shutting down at the biggest centers (too busy, too many collaborations, too much self-importance).
If you are one of the few chosen as a collaborator, your emails will not be returned or you’ll get a terse, snotty reply. Meanwhile, work-flow will be determined by who just wrote the largest check. “You only have $500,000? Chump change! Get lost!”
Faced with this country-club attitude, investigators will vote with their feet. Even if the service is inferior at a commercial shop at least you get what you pay for.
If you step back a little bit and analyze it from a different perspective, service-driven biology has been growing steadily for decades now and is poised to become an even larger cornerstone of modern research. Regardless of how you feel about it this is the undeniable truth. Labs are not equipped or do not have the expertise to stay abreast with every current trend and new technology but do have access to resources which can give them access to data they would otherwise have been excluded from. There is ALWAYS the issue of data reliability and fidelity as you are not doing the experiments yourself and in many cases are not savvy enough to even spot a problem with your data if one did indeed exist.
Look at a dying yet still existing field of microarrays. Investigators have no qualms about outsourcing chip experiments to the milieu of commercial enterprises in existant but
If you step back a little bit and analyze it from a different perspective, service-driven biology has been growing steadily for decades now and is poised to become an even larger cornerstone of modern research. Regardless of how you feel about it this is the undeniable truth. Labs are not equipped or do not have the expertise to stay abreast with every current trend and new technology but do have access to resources which can give them access to data they would otherwise have been excluded from. There is ALWAYS the issue of data reliability and fidelity as you are not doing the experiments yourself and in many cases are not savvy enough to even spot a problem with your data if one did indeed exist.
Look at a dying yet still existing field of microarrays. Investigators have no qualms about outsourcing chip experiments to the milieu of commercial enterprises in existence. How is this any different than sequencing? Most investigators who have a microarray done do not have the capacity to understand the underlying bioinformatics and potential limitations of the technology but it certainly hasn’t stopped the service.
Bottom-line, the service industry is a cut-throat business regardless of what services you are providing. If your service is subpar, you will no longer be in business. If these companies put out some bogus data analyses, it will soon be discovered and they will ease to exist. The good ones will float to the top and the chaff will be discarded.
What is more shocking to me is that WashU is listed as a client! Is that for real?
Maybe some clinical investigator outside of the genome center is involved?