Skip to main content
Premium Trial:

Request an Annual Quote

Rarity Bioscience Building Oncology Test Portfolio on Highly Sensitive 'SuperRCA' Technology


NEW YORK – Rarity Bioscience is using a recent cash infusion to further develop its SuperRCA cell-free and genomic DNA detection technology and scale up the production of targeted mutation assay kits with plans to begin releasing some of them by the end of the year for oncology research applications.

In addition, the Uppsala University spinout hopes to eventually tap into the clinical oncology testing market with both research-use-only (RUO) and in vitro diagnostic (IVD) versions of its assays in both the EU and US.

Rarity currently has roughly 250 assays, from single-mutation tests up to 40-plex assays, said Rarity CEO Linus Bosaeus. The company has so far focused largely on demonstrating SuperRCA's utility in minimal residual disease (MRD) testing in leukemias, which Bosaeus said is a logical early application as the technology is designed to work with flow cytometers that are readily available in most labs and part of most hematology workflows.

"I think that's a huge advantage from a user perspective," he said.

However, Bosaeus said that the company is also developing panels for colorectal and lung cancers and is exploring other uses of the SuperRCA method, such as looking for druggable mutations and monitoring treatment efficacy.

"This is a technology not exclusively for MRD," Bosaeus said, "but very suitable for MRD because of [its] high sensitivity."

SuperRCA, which was initially published in Nature Communications in 2022, combines padlock probes and consecutive rolling circle amplification reactions to enable the detection of extremely low levels of cell-free and genomic DNA. Padlock probes are oligonucleotides that become circularized by DNA ligation in the presence of an appropriate DNA or RNA target sequence.

"We are using the concept of padlock probes and rolling circle amplifications, which are well published, but we are combining [them] in a way that can allow us to get much higher sensitivity," Bosaeus said.

Limited cycles of high-fidelity PCR followed by padlock probe-facilitated DNA ligation and rolling circle amplification helps keep the PCR error rate low.

"This is the downside of PCR," Bosaeus said. "Any PCR at 30 or 40 cycles would eventually self-introduce the sequence that you're looking for. That was what we saw with Covid –– if you ran [PCR] high enough, everyone was testing positive."

SuperRCA generates DNA clusters, where each molecule is essentially a "long necklace" of identical copies. This, Bosaeus said, is critical for genotyping, wherein a high density of fluorescence-labeled hybridization probes bind each of the mutant- or wild-type-specific products, enabling a high degree of sensitivity and efficient counting via standard flow cytometry.

Using a high number of probes to interrogate each SuperRCA molecule, Bosaeus said, drives the method's overall sensitivity because an occasional target misidentification by an allele-specific padlock probe remains undetectable as long as the majority of the SuperRCA copies are accurately genotyped.

"So instead of doing error suppressing after the fact, I'm relying on 100 probes to do the same job as one," Bosaeus said.

Bosaeus explained that this methodology enables better sensitivity than standard next-generation sequencing (NGS) or Droplet Digital PCR (ddPCR) at a lower cost and with a faster turnaround time. Although Bosaeus acknowledged that NGS can be adapted to detect lower frequency mutations, doing so incurs a greater cost with similar long turnaround times.

The exact sensitivity of SuperRCA varies depending on the sequence one is looking for, Bosaeus explained, "but we typically say that we can find one [single-nucleotide variant] in 100,000."

Jake Chabon, CEO and cofounder of Foresight Diagnostics — one of many potential competitors to Rarity — commented that while rolling circle amplification is a well-developed and sensitive DNA amplification method, past applications have sometimes struggled to disambiguate spontaneous mutations from single-nucleotide variations that naturally occur in cells.

Foresight develops MRD assays based on a method called PhasED-seq, which makes use of the improbability of two or more mutations occurring on the same circulating tumor DNA (ctDNA) fragment as a way to increase sensitivity while reducing sequencing errors.

"We do see variations, where some mutations naturally occur in healthy cells," Bosaeus said, but explained that these can be resolved through multiple measurements, as occurs in serial MRD testing.

Chabon also noted that in many clinical settings, even a sensitivity of one in 100,000 would be insufficient, and a sensitivity of one in 1 million or better would be needed.

Bosaeus countered that the scientific consensus remains unsettled regarding how best to consider such low mutation levels, partly because "it has not been possible to study such low levels."

The SuperRCA reaction occurs all in a single tube, with a relatively large amount of starting DNA, which Bosaeus says enables a simpler protocol with better sampling. "We typically input 660 nanograms in one hematology assay, whereas digital PCR is limited to roughly 100 [nanograms]," he noted.

Bosaeus said that optimizing SuperRCA to function within a single tube has been the biggest development since the Nature Communications publication.

Meanwhile, Rarity is also working to scale up its production capabilities.

The company moved into a new facility in Uppsala in February, where both kit production and R&D will take place, and the company is now planning the release of its first kits.

These will initially be RUO, while the company first pursues IVDR certification in the EU and then US regulatory clearance. Bosaeus declined to offer a timeline for IVDR certification, citing ongoing uncertainty surrounding the relatively new process.

Rarity also plans to present data from retrospective studies in AML cohorts at the European Society for Clinical Cell Analysis conference in September and at the American Society of Hematology conference in December.

"Our technology is cancer agnostic as long as you know the mutations to track," Bosaeus said. "As soon as someone figures out what they can do [with it], there's a new opportunity."