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Early MiSeq Users Report Good Data Despite a Few Glitches; Uncertain Buying Plans Amid Rapid Changes

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By Monica Heger

Following the launch of the Illumina MiSeq instrument late last year, users are reporting very high data quality, although a number of customers have experienced a few glitches with the machine.

Additionally, users do not quite know what to make of the recent announcements about Illumina's HiSeq 2500 and Life Technologies' Ion Proton machines, saying that the availability of these instruments could affect purchase decisions in the coming year. The recent announcement that Roche intends to purchase Illumina (IS 1/25/2012) further complicates purchasing decisions for many customers (see related story, this issue).

"We're quite excited about the [MiSeq] technology — short runs, fast turnaround," said James Hadfield, head of the genomics core facility at the Cambridge Research Institute. "But our experiences with it have been mixed. When it works, it works great. But there have been the inevitable teething problems."

Jack Gilbert, an environmental microbiologist at the Argonne National Laboratory in Chicago and co-leader of the Earth Microbiome Project, agreed, and said that when the lab received its instrument in September and tried to duplicate runs that Illumina had been doing out of its Cambridge facility, it "suffered some severe problems."

Not Quite Idiot-Proof

Hadfield has had his instrument since December and has completed around 15 runs on the machine. He said that his lab has had hardware, software, and reagent issues with the system, all of which "are to be expected with a new instrument."

Most of the problems have been hardware related — "something stopping during a run or an RFID tag not being present," he said.

"It's nothing we're worried about," he noted. However, "the way the instrument was announced, as being almost idiot-proof, we had hoped not to have these [problems] at all."

While the instrument works, the data quality is very high and the lab has "outperformed what [Illumina] said we would get," Hadfield added.

For instance, Hadfield detailed on his blog that a recent 2x151-base paired end run generated 2.24 gigabases of data, just over the 1.5 gigabases to 2 gigabases Illumina advertises for the system.

Additionally, Hadfield said that the data quality has been as good, if not better, than data from the HiSeq instruments.

He is currently using the instrument primarily for quality control, "where we want to get a quick overview of the quality of a library before doing a whole-genome or whole-exome sequence [on the HiSeq]," he said. His group is also using it for method development, where "we just need to know that the method is an improvement over a previous method."

Those types of projects are ideal, he said, because data can be generated very quickly and the team can run a limited number of samples to test the protocol before doing a much larger experiment.

Additionally, he said that he has been working with groups that are interested in using the MiSeq to develop targeted sequencing panels for cancer diagnosis. The MiSeq will likely "allow us to use sequencing as a diagnostic tool for cancer medicine," he said.

But for now, "we're still bringing it into our normal workflow and educating users [about] what they can do with it," he said.

Similar to Hadfield's experience at the Cambridge Research Institute, the introduction of the MiSeq at Argonne has not gone as smoothly as Gilbert had hoped. He said that prior to buying the instrument, Illumina had provided data that it had generated at its Cambridge facility and the protocols worked fine.

But after the lab received its machine, the team had problems with the analysis, and the motherboard had to be replaced. Gilbert said that while the lab received its instrument in September, the new motherboard did not come until this month.

Gilbert's team is using the MiSeq to do 16S ribosomal RNA sequencing as part of the Earth Microbiome Project, which aims to characterize more than 200,000 microbial samples from around the world (IS 3/29/2011).

"We've been having problems getting the protocol accurately defined," he said, despite the fact that the protocol was working well in the hands of Illumina.

He attributed the problem mainly to communication between the technicians at Illumina and the Argonne laboratory. "If you know how to drive your car, you drive it perfectly every time. You understand the nuances of your machine," he said.

Initially, those nuances were not communicated, but he said the protocols are now working after some "tinkering".

Like Hadfield, Gilbert said that when the machine works properly, the data that is generated is very good quality with "incredibly high accuracy."

Gilbert said that the MiSeq will serve as a complement to the HiSeq and that both will be used for sequencing in the EMP. Because the project involves so many collaborators who have sample sizes ranging from 10 to 2,000, the MiSeq could be used in cases where a collaborator has fewer samples.

"As soon as we have the libraries created, we can run those quickly and get data within weeks, rather than months waiting for enough samples to be run on the HiSeq," he said.

Impact of HiSeq 2500, Proton

Even though the MiSeq has only been in customers' hands for a few months, Illumina has already announced plans to upgrade the machine this year and also plans to launch an entirely new instrument, the HiSeq 2500, that would enable users to sequence an entire genome in a little over one day (IS 1/10/2012).

Additionally, Life Technologies recently announced that it would be launching a new machine, the Ion Proton, which would first enable whole-exome sequencing, and eventually whole-genome sequencing, in a few hours at $1,000 per sample (IS 1/10/2012).

Hadfield said that the rapidly changing landscape is making it difficult to make purchase decisions, particularly for labs that are looking to develop clinical assays.

Even when considering just the MiSeq, that instrument itself is expected to see improvements to read lengths and throughput in the near future.

"It makes it difficult for users to plan assays for use in the clinic," Hadfield said.

Other MiSeq users agree. "There's a new announcement every six months, so I don't know if we should buy capital equipment now, or wait," said Olivier Harismendy, an assistant adjunct professor in the division of genome information sciences at the University of California, San Diego.

Harismendy is developing a targeted sequencing-based cancer panel, UDT-Seq, for which it recently tested the MiSeq platform (CSN 12/21/2011). The UCSD team is now planning a clinical trial of the assay in breast cancer patients and is deciding on what instrument to use.

Harismendy said that he has been "very happy with the data" from the MiSeq. "It's definitely much better quality than the [Genome Analyzer]," he said, but has not yet done a strict comparison between the MiSeq and HiSeq.

Now, however, with Illumina's HiSeq 2500 and the Ion Proton both on the horizon, he said he is reconsidering whether to purchase a MiSeq. Particularly with the HiSeq 2500, he said he wasn't sure if it was worth investing in a MiSeq. Additionally, he said, there have been a number of changes to the Ion Torrent PGM recently, including a paired-end protocol and the ability to do indexing. "All those tiny changes can shift decisions very much," he said.

"Especially in this funding environment where spending on capital equipment is a huge decision, we don't want to spend money on equipment if it's going to be obsolete in a year, or cost twice as much per sample," he said.


Have topics you'd like to see covered by In Sequence? Contact the editor at mheger [at] genomeweb [.] com.

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