A robust method to study cancer heterogeneity in liquid biopsy

Scientists reported the development of a robust and streamlined procedure for whole-genome copy number profiling of circulating tumor cells (CTCs) from a simple blood test. In contrast to existing methods that are complex and costly, the single-tube, single-step protocol is able to detect absolute Copy Number Alterations (CNA) in single cells and maintain accuracy at a lower cost than conventional genomic analysis procedure, opening up to the possibility for genome-driven targeted therapy selection and monitoring of disease progression in liquid biopsy.

The genome of tumor cells goes through multiple aberration events which are intimately connected to the underlying tumor biology and are reflected in the CNA profile of the entire genome. Multiple recent findings across several cancer types have pointed to the fact that these pattern of aberrations are linked to increased response or resistance to different classes of drugs, ranging from classical chemotherapy to PARP-inhibitors and Immune checkpoint inhibitors. "A variety of analytical techniques have been developed to analyze copy-number alterations in the research lab," explained Nicolò Manaresi, Ph.D., lead author of the study. "However, they are not well suited for clinical application on CTCs where reproducibility, robustness and scalability are required. Our approach offers a streamlined, less expensive method for genome-wide CNA profiling of single cancer cells." Dr. Manaresi also serves as Chief Scientific Officer at Menarini-Silicon Biosystems, based in Bologna and Huntingdon Valley, PA. (U.S.)

The study, published in the online scientific journal PLOS ONE, presents the characterization of an innovative workflow -- developed and commercialized by Menarini Silicon Biosystems as Ampli1™ LowPass kit. The method exploits the characteristics of Ampli1 WGA, which is based on ligation mediated-PCR WGA of fragments obtained by digestion on specific restriction sites, to produce, in a single amplification step, sequencing-ready, barcoded DNA libraries suitable for genome-wide CNA profiling by low-pass whole-genome sequencing. This allowed decreasing workflow time and efforts, allowing higher throughput while reducing the cost. The approach is also demonstrated on patient CTCs, isolated by DEPArray™ technology following enrichment from blood using the CELLSEARCH® system*.

"In comparison to aCGH, a widely used and accepted method for screening CNAs in clinical diagnostic, our approach allowed us to decrease the cost of analysis while providing comparable or superior performances," said Dr. Manaresi. "Moreover Ampli1 LowPass has the advantage to determine absolute copy numbers changes and this has important implications for the biological inter¬pretation of cancer samples. As sequencing cost per base is decreasing with advances in NGS technologies, our streamlined workflow will further decrease the cost of copy number analysis in the future and pave the way to a simpler blood test to study cancer heterogeneity in liquid biopsy."

Researchers from the University Hospital of the Heinrich-Heine-University of Dusseldorf, the Medical Oncology Unit of the University Hospital of Bologna, The Institute of Cancer Research, London, and The Royal Marsden NHS Foundation Trust (London) also participated in the study.