Abstract 5014: Analytical validation of a complete system for detection and characterization of genomic aberrations in circulating tumor DNA
Authors: Stamper Ericca , Shen Weiming , Pruthi Aman , Nagel Casey , Piechota Marcin , Tomala Katarzyna , Wei Qi , Willoughby David 
Published: March 2024

Cell-free DNA (cfDNA) fragments are readily detected at a low concentration in the human blood stream. In healthy patients cfDNA is primarily derived from apoptosis of hematopoietic cells. In cancer patients circulating DNA derived from tumor cells (ctDNA) undergoing apoptosis, shedding, and necrosis contribute to total cfDNA. Next generation sequencing (NGS) of cfDNA isolated from patient plasma can be used to fully characterize cancer driven changes in the tumor DNA including the relative contribution of cfDNA, single nucleotide variants (SNVs), small insertions and deletions (Indels), larger deletions, regions of amplified DNA, and structural rearrangements.

Frontage has developed a complete lab system for analysis of circulating cfDNA including automated sample extraction, preparation and sequencing of libraries targeting exon sequences of 293 oncology-related genes, and a bioinformatic reporting system. The Frontage sample extraction process uses a post-extraction size selection step to remove high molecular weight DNA derived from lysed blood cells in the plasma sample to increase the sensitivity of detection of ctDNA. The NGS platform couples hybridization-based selection of genomic DNA fragments derived from protein-coding exons with deep sequencing to ~4,000X gross coverage on the NextSeq 2000. The bioinformatic pipeline integrates unique molecular barcode-based generation of consensus reads for each template molecule, somatic variant calling with GATK Mutect2 and FreeBayes, and removal of false positive variants by comparison to a 60 samples healthy patient data set.

Analytical validation was performed for each component of the system. For verification of the sample extraction process, cfDNA was extracted in duplicate from four lots of pooled K2 EDTA plasma of healthy patients as well as individual K2 EDTA plasma of colorectal cancer (CRC) patients in four independent extraction runs. The mean yields of cfDNA from healthy samples ranged from 2.3 - 4.2 nanograms per ml plasma and all 32 of the isolated cfDNA aliquots from healthy patient plasma showed a prominent peak around 167 nt with minimal contamination from high molecular weight DNA. For validation of the NGS and bioinformatics platform a set of 8 different reference cfDNAs were processed through four independent runs of library preparation, sequencing, and analysis. For each of the validation runs, greater than 97% of 208 SNVs and Indels with expected allele frequencies (AF) between 2-3% were detected by the platform with higher levels of accuracy for variants at above 3% AF. Two or less false positive variants per run were detected out of 278,000 nucleotides of verified non-mutated sequence that overlapped with the 293 gene panel. Four known DNA amplification events were detected in each of the validation runs. Data from characterization of CRC and other clinical samples with the system will be presented.

Citation Format: Ericca Stamper, Weiming Shen, Aman Pruthi, Casey Nagel, Marcin Piechota, Katarzyna Tomala, Qi Wei, David Willoughby. Analytical validation of a complete system for detection and characterization of genomic aberrations in circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5014.