By Kevin Davies
June 26, 2012 | Intelligent Biosystems (IBS), a privately held next-gen sequencing (NGS) company based in Waltham, Mass., has been acquired by molecular diagnostics company Qiagen, signaling a concerted move to integrate clinical NGS testing into the German company’s diagnostics portfolio.
Financial terms were not disclosed, although a figure of around $50 million has been rumored.
Qiagen’s ambition, says CEO Peer Schatz, “is to create a new dimension of benefits for these [NGS} technologies by offering workflow solutions for clinical use, particularly to develop new medicines and improve healthcare with advanced diagnostics.” Qiagen also announced a deal with SAP for a bioinformatics capability.
IBS has been developing two models of NGS instrumentation based on technology licensed from the lab of Columbia University professor Jingyue Ju, who co-founded the company with Steven Gordon in 2005.
The first sequencer – the Max-Seq – has been distributed by Azco Biotech, and was unveiled at the International Congress of Human Genetics conference last year. Recently, however, IBS has been focusing on a smaller benchtop sequencer, the Mini-Seq, aimed squarely at the clinical market.
This benchtop sequencer features a carousel that takes the sample to the chemistry, rather than the other way round. In this way, up to 20 samples can be processed independently and sequenced in parallel with great efficiency, without need of bar-coding, in a format that will be familiar to clinical research operations.
“We are very excited to join forces with Qiagen, which is an ideal partner to bring our new ultra-low cost sequencing technologies to the market as part of a complete workflow that will expand our product's use into new areas,” said Gordon, IBS CEO and co-founder, in a prepared statement. (Gordon was traveling and unavailable for additional comment.)
The IBS Mini-Seq instrument is aimed at offering targeted gene or exome sequencing, in areas including but not limited to cancer diagnostics and prenatal testing, for a pricepoint of around $100, according to a briefing Gordon offered Bio-IT World earlier this year.
Gordon believes IBS can deliver those sorts of NGS tests more cost-effectively than other technologies. The instrument is specifically designed like a clinical analyzer, with the ability to run 10-20 samples at a time using a traditional carousel system to move the samples to the reagents. The benchtop instrument accepts individual patient samples without indexing or bar-coding, and keeps them separate. This minimizes delays caused by grouping samples before a run, says Gordon.
The sequencing-by-synthesis chemistry utilized by IBS was developed in the Ju lab at Columbia, and bares some similarities to the chemistry employed by Illumina’s HiSeq and MiSeq platforms.
After the DNA is cleaved and adapters added, amplification can take place either via emulsion PCR or a rolling-circle amplification step, prior to the actual sequencing. The polymerase-based sequencing chemistry relies on custom nucleotides that that feature a cleavable linker between the base and dye moiety. The polymerase only incorporates single nucleotides into the new DNA strand because of the presence of a blocking chemical group. After each cycle and measurement step, a cleaving step removes both the dye and the blocking group.
A hallmark of the IBS system is that it features a tiny concentration of labeled nucleotides in the presence of about 100-fold greater concentrations of the corresponding unlabeled nucleotides to drive the reactions to completion. This results in a significant cost-differential – about 50-fold cheaper – than comparable systems, says Gordon.
IBS was on course to enter beta testing with its Mini-Seq machine in the second half of this year. But the Waltham company, with less than 20 employees, would have faced an uphill challenge to commercialize the platform prior to the Qiagen acquisition.
“We can deliver greater value to our customers from our novel technologies by leveraging QIAGEN's leadership in sample preparation, advanced gene panels and global reach,” Gordon noted. “Our goal is to better address the demands of clinical and core lab customers for complete solutions, since many have been struggling to adapt existing sequencing platforms to their workflows.”
Bring in Bioinformatics
Qiagen intends to launch a first sample-to-result NGS solution next year, utilizing Qiagen’s expertise in automated sample preparation with the IBS platform. To that end, Qiagen is working on a pair of automation workflows from sample to the final result: one workflow integrates the NGS module into the QIAsymphony automation family, the other is based on the QIAcube sample preparation system. The company says it plans to offer eight preconfigured cancer gene panels as well as enable customers to create customized panels for specific molecular pathways and diseases.
Qiagen also announced a new bioinformatics collaboration with SAP to apply the SAP HANA platform in NGS interpretation to reduce the time required for analyzing sequenced data.