After launching the Ion Proton benchtop sequencer in September, Life Technologies officials announced last week that more than 7,000 runs have been completed on systems in the company's laboratory and customer laboratory.
One of the clients, Joe Boland of the National Cancer Institute, reported this week at a seminar at the annual meeting of the American Society of Human Genetics that his laboratory has performed 50 runs on four Proton instruments, usually each The operation can produce 8 Gb-9 Gb of data, and the read length is about 150 bp.
He said that when the instrument was first installed in September, the flux was 4 – 6 Gb and the read length was 100 bp, but the flux quickly increased to 8 Gb and the read length also reached 150 bp. At present, some operations of the research team have exceeded 10 Gb, and it is expected that 9 Gb-11 Gb will be produced by the end of the year.
Boland also mentioned that accuracy has also improved, currently about 99%, which "definitely meets our needs."
NCI's laboratory also has two Illumina HiSeq 2000 instruments, one MiSeq, and six Ion Torrent PGM instruments.
Boland plans to use Proton mainly for rapid exome sequencing, "high-level" amplicon sequencing of 500 – 1,000 samples, and full transcriptome sequencing.
He said that most of NCI's sequencing is exomes. There are two HiSeq instruments in the laboratory, and each instrument can produce 56 exomes every 6-8 days, so "our process is always very full." .
Proton will be used to improve sequencing capabilities and to sequence exomes that require rapid turnaround. In addition, if the sample on HiSeq encounters technical difficulties, it will be sent directly to Proton instead of returning to HiSeq's team.
Boland said the center's first batch of exome operations on Proton used the NimbleGen capture chip to cover 80% of the exome with 20-fold coverage. With the continuous increase of laboratory experience, the coverage ratio of exomes is also constantly improving. At present, the laboratory can cover almost 90% of exomes with 20 times coverage. The average coverage is about 100 times.
The research team also examined the transcriptome sequencing on Proton. Using the second edition of the Ion Total RNA Kit and 5-500 ng of poly-A RNA, he was able to generate 50 million reads for a melanoma sample, compared to only 2.5 million reads using the PGM 316 chip.
Looking to the future, Boland talked about, since Life Tech plans to launch Avalanche sample preparation reagent and Ion Chef system in 2013, he looks forward to sample preparation improvement and automation.
Avalanche is Ion's emulsion-free PCR sample preparation reagent, which is planned to be launched next year. Similar to the company's Wildfire technology for SOLiD systems, Avalanche will be based on isothermal amplification. At the same time, Ion Chef is an automated sample preparation system, which can shorten the time of manual operation, thereby improving the efficiency of chip loading.
When talking about Ion Chef, Boland said: "Consistency will be the key."
In addition, Boland said the laboratory plans to expand to full-genomic sequencing on Proton in mid-2013.
Other users of Proton Instruments have a similar experience. Associate Professor Richard Allcock of the School of Pathology and Laboratory Medicine at the University of Western Australia mentioned that his laboratory received Proton in October.
He said that his laboratory currently produces about 7 Gb of data per run, with a read length of 100-110 bp. The laboratory only carried out 5 runs on the system using the control library generated by Life, and carried out 2 runs using its own library. There are also two PGM instruments in the laboratory. He feels that the data quality of the two instruments is equivalent, but Proton is "more sensitive to process problems." The current PI chip loading efficiency is about 80%. He said that if at least 60% of the sequence Q values ​​reached 20, he would consider the instrument to be accurate. So far, all Proton runs have reached this level. Looking forward to the future, he hopes that reading will improve. He originally expected Proton's reading length to start at the PGM reading length level, "so when hearing the reading length from 100 bp, it will bring a lot of restrictions." In addition to two PGM and one Proton, the laboratory is still Two SOLiD 5500 instruments were running, there was a 454 GS FLX instrument before. He said that in the following year, the laboratory may gradually phase out 5500 instruments and instead run two PGM and one Proton instruments. Allcock plans to run about 200 exomes on Proton in 2013. He also plans to convert the neuromuscular analysis of the 300 genes currently running on SOLiD to Proton. The combination of Proton and PGM will bring "unprecedented flexibility" to sequence everything from small genomes and targeted analysis, to exome and large-scale analysis, and finally to the whole genome.
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