The BioCartis Idylla real-time PCR for MDx

For long-time readers of this blog (and come to think of it, this blog started as a hobby in 2013 so take the term ‘long-time’ with a grain of salt) I want to thank you for finding something valuable here, and for the encouraging feedback I’ve received again and again. As a case in point, I’m standing by the SeraCare exhibit (just a table with a few positioning statements for infectious disease, oncology and non-invasive prenatal screening) at the recent Shenzhen ICG-10 conference, and a person walks right up to me to thank me for the blog and all of its valuable information.

And he was kind enough to ask when I’d be posting again, as a subtle reminder that there’s an audience out there, an audience interested in what is new in the world of genomics or genetics, whether a new application or a new technology.

At the recent Association for Molecular Pathology, a Belgium-based company called BioCartis had a workshop presenting their new system called Idylla™ as well as data produced from it. They called it the ‘First sample-in, results out system for oncology’, to contrast it with existing systems such as Cepheid (I highlighted their new Cepheid Omni here) and the new Roche LIAT™ (Laboratory In A Tube, from an acquisition of IQuum last year) which were both launched last summer for infectious disease.

The Idylla System can be favorably compared to what the Cepheid and Roche systems do: take a sample, do the sample disruption (BioCartis calls this ‘liquefaction’ which reminds me of California earthquakes), nucleic acid purification, addition of reagents, and detection in a single cartridge. Where their system differentiates itself is in how they scale both the assay as well as the system itself.

A new trend

These new-generation real-time instruments start a new trend: getting real-time PCR out of a central laboratory (whether it is a molecular pathology laboratory in a hospital setting or a central laboratory with thousands of samples coming from hundreds of miles away) and into other point-of-care type of environments. This could mean a local clinic, or perhaps even a local pharmacy. The central concept is to remove all the specialized knowledge that comes with working with nucleic acids in preparation for PCR, including laboratory hygiene (i.e. care must be taken not to contaminate the pre-PCR area with amplicons from finished assays) and ability to purify and quantitate both RNA and DNA, which in some cases is easy, and in other cases difficult for even the most experienced technician.

These new systems have the ability to enclose all these steps into a single cartridge, and basically take the purification and nucleic acid handling steps away from the end-user. For the Idylla system, 40-150 minutes of sample-to-result turnaround time, 2 minutes of hands-on time, and up to 30 distinct measurements from a single sample.

Due to the nature of this system (a single sample cartridge), there is not much risk from cross-contamination and their integrated barcode scanning system reduces the chance of sample mix-up.

Under the hood

The ‘up to 30 measurements’ means many fluors; this system has the ability to detect 6 fluors per compartment, and as one fluor is taken up by an internal run control, each compartment can have a five-plex PCR for detection. With six compartments and each compartment analyzing five biomarkers that is where ‘up to 30’ comes from, and their literature states higher multiplexing is under development. This is an important point, as choice of which genetic molecular test and what platform to use (in particular, NGS-based ones versus real-time PCR ones versus Sanger sequencing) is a matter of what to detect, at what allele frequency, and how many mutations are needed to be detected simultaneously.

One important aspect of this system is its ability for sample purification; the liquefaction and cell lysis process includes use of chemicals, enzymes, heat and ‘high intensity focused ultrasound’. The nucleic acid purification is silica-based (no mention of magnetic particles, such as the IQuum LIAT uses). To think that all this takes place in a cartridge that you can hold in your hand is something of a wonder; but when I think about it further this is what the Cepheid GeneXpert cartridges have been doing for years.

Launched assays

BioCartis has launched several oncology-focused assays. Their BRAF for example, detects six BRAF mutations down to 1% variant allele frequency (VAF); their KRAS assay detects the ‘extended KRAS’ of mutations in codon 12 (exon 2), codon 13 (exon 2), codon 59 (exon 3), codon 61 (exon 3), codon 117 (exon 4) & codon 146 (exon 4), for a total of 21 KRAS mutations. The majority of mutations are detected down to 5% or less VAF. Their website indicates a ctBRAF assay ‘under development’.

At their AMP Workshop, Dr. Steffen Jensen (Herlev Hospital, Copenhagen Denmark) presented their work on 85 samples tested with both the BioCartis system and several others (one un-named NGS-based, QIAGEN therascreen RGQ and Entrogen KRAS assays). Their cross-platform observations across 85 samples were 100%. Expanding the therascreen RGQ versus BioCartis, with n=127, there was 100% concordance.

It was of note that 3 out of 85 samples the Idylla ‘errors were observed, but genotyped correctly upon re-analysis’. When I asked about it afterward, apparently the Idylla system will not give a call due to unspecified problems with the sample or the particular result, and was simply run again (and the results were fine).

Their second guest presenter, Dr. Max Schreuer (University Hospital, Brussels Belgium) presented data on examining BRAF V600E mutant cell-free DNA in patients with BRAF mutant metastatic melanoma, and showed results from 36 patient samples with Stage IV melanoma, with time-course samples taken. His results showed very good alignment with this recent publication (using BEAMing instead of real-time PCR for detection of mutatation in ctDNA) and the prognostic value of monitoring BRAF V600E ctDNA for this type of cancer. He also showed data where progression of disease could be detected a full 2 months earlier than existing scanning methods.

Regarding infectious disease, BioCartis has an agreement with Janssen Diagnostics BVBA in Belgium, and they have developed an Idylla Respiratory IFV – RSV Panel, currently for Research Use Only. This panel can identify Influenza A or B, and if A, can discriminate between H1:H3, 2009-H1N1 and H275Y oseltamivi mutation types. In addition, it can identify Respiratory Syncytial Virus (RSV) type A or B. According to this GenomeWeb Premium article (subscription required), Janssen is also working on an Ebola assay for this platform.

An ability to scale

Getting back to the Idylla system, they’ve built a cartridge with six compartments and a unique optical imaging platform that has a small disc that swings out of the cartridge. Thus going up to 30 biomarker assays is plenty of real estate for expanding to higher-complexity assays.

The system is comprised of an Idylla Console and an Idylla Instrument; there can be as many as 8 instruments per console. Thus with a larger system and brief turnaround times, samples can be loaded on an as-needed basis, obviating the need to batch samples increasing the turnaround time for a given sample.

Some concluding thoughts

The Idylla platform had its origins in 2006 at Royal Philips Electronics, and then sold to Swiss firm BioCartis in 2010. It currently is not offered for sale in the US (they are undergoing regulatory submissions now), although their presence at AMP (as well as ASCO earlier in the year) demonstrate their progress and set expectations in the marketplace in 2016.

The case for easier-to-use, completely automated real-time PCR is a relatively easy one to make. Just observing the rapid growth of Cepheid from a specialty thermal-cycler sold for military applications, to today’s very elaborate exhibit (complete with human-like models!) is something of a wonder. A competitive market is a good thing – it drives prices lower, which in turn will help adoption, and grow the entire market overall.