Multiplex analysis of Copy Number Variation in liquid biopsy using dPCR: preliminary data from patients with solid tumors

Powerful liquid biopsy: from multianalytes to ultrasensitive cfDNA analysis

A series of three liquid biopsy webinars about how you can get a complete picture by stabilizing and isolating multiple analytes from the same blood draw – to generate insights otherwise undetectable in single analytes. You will learn how to get started with multianalyte studies and how to analyze cfDNA using NGS and dPCR techniques.

Webinar 3:

Somatic genetic alterations in solid tumors have clinical relevance, predicting response to therapies. Among them, mutations and copy number variations (CNVs) have been extensively investigated. CNVs include amplifications and deletions of a particular segment of chromosomal DNA.

Traditionally methods for the detection of CNVs include fluorescent in situ hybridization (FISH), multiplex ligation dependent probe amplification (MLPA), comparative genomic hybridization microarrays, and SNP arrays. However, these techniques have disadvantages such as high cost and tissue availability.

Nowadays, digital PCR (dPCR) technologies are available for molecular characterization of solid tumors. dPCR is a valid technique and, due to its capability of highly-sensitive quantification of fold change in CNV, it provides the possibility to monitor patients and their treatment response over time.

Moreover, the molecular evaluation using liquid biopsy based on circulating free DNA (cfDNA) offers the opportunity to track the genomic evolution of tumors, and is often used to assess tumor molecular profile.

The present study aims to detect CNVs in cfDNA from patients with solid tumors. Plasma samples from patients with solid tumors will be tested. cfDNA will be extracted from 3 ml of plasma using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). Samples will be screened on the dPCR QIAcuity dPCR system (QIAGEN) using the CNVs Assay for EGFR, MET, KRAS and MYC genes (QIAGEN).

Results will be shown during the webinar.

About the speaker

Stefania Crucitta, PhD, Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine

University of Pisa, Pisa, Italy

Stefania Crucitta is a Junior Researcher and Resident in Clinical Pharmacology and Toxicology at the University of Pisa. She graduated in Medical and Pharmaceutical Biotechnology at the University of Florence in 2015 and pursued a PhD in Clinical and Translational Science at the University of Pisa in 2018 with a thesis focused on the analysis of the androgen receptor splice variants in liquid biopsy to monitor resistance to treatment in castration-resistant prostate cancer. During her PhD at the U.O. Clinical Pharmacology and Pharmacogenetics, Stefania had the opportunity to carry out a 6-month traineeship at the Erasmus Medical Center in Rotterdam.Her research focuses on the analysis of biomarkers predictive of response, resistance and toxicity to pharmacological treatments in patients with solid tumors using pharmacogenetic approaches.