Comparison of Target Enrichment Platforms for Circulating Tumor DNA Detection

Abstract

chow 1* cancer-related mortality of solid tumors remains the major cause of death worldwide. circulating tumor DNA (ctDNA) released from cancer cells harbors specific somatic mutations. Sequencing ctDNA opens opportunities to non-invasive population screening and lays foundations for personalized therapy. in this study, two commercially available platforms, Roche's Avenio ctDNA Expanded panel and QIAgen's QIAseq Human Comprehensive Cancer panel were compared for (1) panel coverage of clinically relevant variants; (2) target enrichment specificity and sequencing performance; (3) the sensitivity; (4) concordance and (5) sequencing coverage using the same human blood sample with ultra-deep next-generation sequencing. Our finding suggests that Avenio detected somatic mutations in common cancers in over 70% of patients while QIAseq covered nearly 90% with a higher average number of variants per patient (Avenio: 3; QIAseq: 8 variants per patient). Both panels demonstrated similar ontarget rate and percentage of reads mapped. However, Avenio had more uniform sequencing coverage across regions with different GC content. Avenio had a higher sensitivity and concordance compared with QIAseq at the same sequencing depth. This study identifies a unique niche for the application of each of the panel and allows the scientific community to make an informed decision on the technologies to meet research or application needs. Cancer is the second leading cause of death worldwide. Cancer-related mortality of most solid tumors remains steady despite intense research on carcinogenesis and significant advancement in effective treatments. It is estimated that 1 in every 6 deaths is related to cancer and late-stage presentation is still very common 1. For cervical and colorectal cancers, population-wide screenings have contributed to the decreasing mortality 2. However, there is still an urgent need for accurate, effective and non-invasive paradigms to reduce cancer-related mortality for other common and deadly cancer types via early diagnosis, personalized therapeutic strategies and disease monitoring. Circulating cell-free DNA (cfDNA) is released into the peripheral blood due to apoptosis, necrosis or active release 3-5. Higher cfDNA level is found in the plasma of cancer patients comparing to healthy controls 6,7. Circulating tumor DNA (ctDNA) from cancer cells harboring a unique set of genetic and epigenetic alterations creates a biological signature. This mutation signature is not only specific to cancer in general when compared to normal tissues but is also highly individual specific 3,8,9. The level of ctDNA, somatic mutations burden, the mutation signature and epigenetic marks are highly correlated with cancer pathophysiology and treatment response 3,10. Unlike traditional biopsy, profiling of somatic mutations via ctDNA is not only minimally invasive but also provides a less localized and biased sampling. Profiling of ctDNA, released from various cells in the tumor, allows a snapshot of somatic mutation burden to provide a more ...

Longitudinal tracking of 97 esophageal adenocarcinomas using liquid biopsy sampling

“…Here we describe the results from a commercially available pancancer mutation panel evaluated with respect to both tumor and white cell cfDNA in a large, prospectively collected and annotated sample cohort from resected EAC. [11][12][13][14][15][16]…”

Patient specific circulating tumor DNA fingerprints to monitor treatment response across multiple tumors

“…Currently, the most prevalent way to analyze ctDNA employs next-generation sequencing (NGS) in combination with multiplex PCR to check a panel of hotspot mutations, which can be either generic to all tumors or specific to a certain cancer type [ 13 , 14 ]. Although low cost and easy to design, ctDNA panels generated these ways can potentially miss important mutational clones in some patients if the mutations are not included in the panel targets, therefore result in inaccurate evaluation of disease status and treatment response.…”

Analytical performance evaluation of a commercial next generation sequencing liquid biopsy platform using plasma ctDNA, reference standards, and synthetic serial dilution samples derived from normal plasma

“…However, TSO500 panel required higher number of sequencing reads due to its larger panel size (500 genes) and required higher cfDNA input (30 ng) making it less economical and clinically feasible in comparison to Avenio assay. A similar study was recently reported by Lam, et al in which the AVENIO platform was compared to Qiagen's QIAseq Human Comprehensive Cancer panel for panel coverage of clinically relevant variants and overall sequencing performance [21]. Detailed results from both comparison studies reveal strengths and shortcomings unique to each of these different assays.…”