NEW YORK – QuantumCyte, a startup that seeks to increase the availability of biomarkers for metastatic cancer, introduced itself to the world of tumor sequencing at last week's annual meeting of the Association for Molecular Pathology.
The Sunnyvale, California-based firm unveiled its QPrecise "automated microdissection" technology that it says can improve the way tumor DNA and RNA is collected from tissue slides and increase the number of samples that pass quality control for NGS-based testing.
Bearing more similarity to silk-screening a T-shirt than just about any other sample prep method in the clinical lab, QPrecise starts with an image file of a particular tissue section that has been annotated to identify tumor cells or other regions of interest. It then uses that information to lay a "mask" on the slide with an inkjet printer, covering the non-tumor cells and preventing them from being lysed. Thus, nucleic acids are recovered only from the unmasked cells.
In a Wednesday session sponsored by QuantumCyte, Rish Pai, a pathologist at the Mayo Clinic, showed how QPrecise, in combination with his artificial intelligence-based algorithm QuantCRC — was able to ultimately increase the quality of DNA obtained from 55 cancer samples compared to manual microdissection. Along the way, he showed data on proof-of-principle steps, including the ability to obtain DNA from the process and to isolating nucleic acids from small regions of interest for sequencing.
In most samples, QPrecise increased the variant allele frequency (VAF) in a 48-gene panel, Pai's data showed, and helped capture 18 mutations not found with manual preparation. And in samples where tumors made up less than 80 percent of the tissue area, VAF was between one-and-a-half and seven times as high as with manual dissection by a lab technician.
"Between 10 and 22 percent of patient specimens fail clinical molecular oncology testing, with insufficient tumor content contributing to most failures," Pai said. "This technology can rescue a proportion of specimens from being rejected, thereby providing important results to oncologists to help guide subsequent therapy."
At AMP, QuantumCyte announced a partnership with Mayo to develop a test based on Pai's work, though financial and other details were not disclosed. The QuantCRC algorithm can stratify patients by risk of recurrence, leading to intensive treatment and follow-up for high-risk patients and letting low-risk patients avoid chemotherapy, Pai said.
QuantumCyte also has collaborations with researchers at Singapore General Hospital.
Founded in 2014 by genomics industry veteran John Butler, who previously held manufacturing management positions at Applied Biosystems and Pacific Biosciences, QuantumCyte has taken a meandering path to providing its current technology. Butler said he started the company to satisfy an employment requirement to be a visiting scholar at Stanford University and that the firm's early focus was on single-cell analysis. By 2018, the company had turned its attention to solving the issue of low tumor content in tissue slides.
Butler developed the masking approach with Bidhan Chaudhuri, chief technology officer and cofounder of QuantumCyte, who he knew from their days at PacBio. Using off-the-shelf inkjet printing technology, QPrecise can isolate regions as small as 50 microns across and can process 40 slides per hour, he said.
In addition to tumor cell nucleic acids, QuantumCyte is also exploring applications with other diseases and even other biomarkers. The firm has collaborated with Ochre Bio and Reveal Biosciences to study nonalcoholic steatohepatitis, a type of fatty liver disease. Butler said QuantumCyte's technology helped process 2,700 liver samples for RNA sequencing in three weeks, which he estimated would have taken 34 weeks with laser capture microdissection. And the company is working with Mayo's Pai to do proteomics with the method.
QuantumCyte has raised approximately $1 million in a 2017 friends and family financing round and approximately $6 million in a seed financing round, Butler said, adding that he's working on a Series A round. The firm has five employees, including Chief Commercial Officer Bernadine Lim. Butler said he's hoping to add approximately 10 employees over the next year.