Who are your customers? Which do they value more, cost or speed?
Dr. Gao: Most of our approximately 100 samples per week come from our internal university users. Fewer than 10% are from outside organizations. Cost, turnaround time, and data quality are all important for the researchers we serve.
Regarding speed, filling a flow cell for a particular run takes time. We can fill one flow cell easily for a short, single-read 40 bp run by combining miRNA-seq and ChiP-seq samples. It takes longer to obtain enough sample for a PE 2 x 100 bp run. It would be great to be able to run each lane independently, for example with SOLiD 5500xl.
The turnaround depends on the technology and application. For the Illumina PE 2 x 100 bp, turnaround time is normally 8 days, or 11 days when we’re running 2 flow cells simultaneously. The Oxford Nanopore technology will change the field completely with fast turnaround—about 15 minutes per human genome, and the cost is expected to be less than $1,000. This system is supposed to be available by the end of this year.
Dr. Green: Our customers are largely affiliated with the University of Illinois and include both faculty and research physicians. In addition, external customers typically include microbial ecologists looking for amplicon sequencing, genome, metagenome, and metatranscriptome sequencing. Typically, but not always, cost is more important for my customers than speed. This varies from project to project, and some projects are highly time sensitive (particularly those supporting grants).
Because of the diverse types of samples and projects, it is hard to provide an approximate throughput as this varies significantly. We are currently a rather small facility, processing, for example, only a few Ion Torrent samples per week.
Our facility provides a variety of services to address a range of scientific endeavors—from medical to environmental research. By maintaining an Ion Torrent, we have the ability to rapidly produce sequence data for small to medium projects, and collaborate with other sequencing facilities for the largest projects. Through this approach, we are able to match the appropriate sequencing platform to meet the cost and time constraints of our customers.
Dr. Jafari: We mostly provide services to our internal users at Northwestern University and its affiliates. Both speed and cost are important to our investigators, but current budget issues have put more strain on researchers from the cost perspective.
Kingham: Our customers are largely University of Delaware investigators, or investigators with ties to the university. The rapidly growing field of translational research has connected us with many clinical researchers employed by regional healthcare systems. Most investigators are looking for a balance between cost, amount of data, data quality, and turnaround time. This balance can fluctuate based on the project. For example, turnaround time is critical for obtaining preliminary data for an upcoming grant, while data accuracy is more important for the targeted sequencing of an oncogene. Our HiSeq 2000 runs at about 75–80% capacity; we are still validating the PacBio RS.
Dr. Kiss: Our customers are members of the Miami University community. Cost and speed are both factors for them, but I would say cost is more of a concern. We currently process very few samples as we do not currently have instrumentation on site. In addition to the two facilities mentioned earlier, for large genome sequencing projects we recommend the facilities at Ohio State University’s Plant-Microbe Genomics Facility. Despite its name, this facility conducts all types of sequencing.
Dr. Lyons: We have roughly 100 distinct next-gen client laboratories, virtually all of whom are at our own university. We are willing to accept projects from outside users, but are required to add a surcharge to their recharge rates. In practice, few outsiders opt to send samples for next-generation sequencing here—unlike our Sanger services.
It is impossible to express throughput in terms of either samples or projects, due to the extreme diversity of the projects we handle. For one project, we’ve done over 1,000 human genomes in the past year, with 3,000 more to be completed by mid-2012. Other clients occupy a single lane, yet require disproportionately higher effort on our part. Sample counts are misleading, too. Sometimes a single sample will occupy numerous lanes, while other times a single lane could have up to 96 samples in it.
In my opinion, clients are somewhat more concerned with cost right now than with speed. A close third consideration, though, is flexibility and availability of options. We try to accommodate clients with urgent needs or nonstandard protocols when we can.
Dr. Thomas: We organize sequencing primarily for research groups at the University of New Hampshire. These researchers are primarily environmental biologists and microbiologists, with a few biochemists; both speed and cost are issues for them. We have wait times in excess of six months and sometimes as long as one year. This is specific to the Illumina platform, which is the most popular and cost-effective. But every run is two weeks long. This is a major issue as there is not sufficient infrastructure in the U.S. to meet sequencing research needs. It is also a problem for us because we have to go outside for this service.