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. 

Why is rare variant detection and discovery from cfDNA so challenging?
Studies have shown that both cfDNA and ctDNA correlate with disease progression and reoccurrence and assist in therapy guidance. But cfDNA is highly fragmented, unstable in biofluids and at low concentrations in non-advanced, non-metastatic cancers. Meanwhile, ctDNA represents just 1–2% of total cfDNA. Add in sequencing reaction errors, enrichment biases and false positives, and you will need a lower limit of detection (LOD) of about 0.1% variant allele frequency (VAF) to find those valuable insights. To be confident in your rare variant identification, cfDNA requires highly sensitive and specific techniques.

Join us for a webinar discussing the newest technology for reliable detection of ultra-rare variants at a 0.1% VAF from cfDNA and go from sample to sequencing-ready library in just 8 hours. We will discuss the following:

• The biggest challenges in liquid biopsy variant detection
• Our new QIAseq chemistry and workflow
• Simplified data analysis with our integrated bioinformatics pipeline

Explore how our new QIAseq Targeted cfDNA Ultra Panels can help you unlock the potential in your liquid biopsy samples. 

Adeno-associated virus (AAV) has emerged as the primary vector for in vivo gene therapy applications. AAV samples are measured and dosed via DNA concentration, traditionally determined by quantitative PCR (qPCR). qPCR is gradually being replaced by the more precise digital PCR method, which achieves absolute quantification of target sequences without standard curves. A precise AAV titration method is critical for the entire drug development journey, from preclinical studies, through process development and clinical dosing.

This webinar will cover:

• Development of well-controlled AAV titration methods
• Comparison of multiple digital PCR platforms for AAV titration
• Strategies for bridging legacy qPCR methods to improved digital PCR platforms

Adeno-associated virus (AAV) has emerged as the primary vector for in vivo gene therapy applications. AAV samples are measured and dosed via DNA concentration, traditionally determined by quantitative PCR (qPCR). qPCR is gradually being replaced by the more precise digital PCR method, which achieves absolute quantification of target sequences without standard curves. A precise AAV titration method is critical for the entire drug development journey, from preclinical studies, through process development and clinical dosing.

This webinar will cover:

• Development of well-controlled AAV titration methods
• Comparison of multiple digital PCR platforms for AAV titration
• Strategies for bridging legacy qPCR methods to improved digital PCR platforms