Comparison of Target Enrichment Platforms for Circulating Tumor DNA Detection

So Ngo Lam,Ching Man Foo,Po Yi Lee,Ying Chun Zhou,Yee Man Chan,Wing Yeung Mok,Jun Yuan Huang,Chun Kin Chow,Kit Yee Wong,Yan Yee Fung,Wing Sum Wong

doi:10.1038/s41598-020-60375-x

Abstract

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 on-target 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.

Highlights

Cancer is the second leading cause of death worldwide
Both panels aim for the detection of somatic mutations via deep sequencing, the development, design and technologies of the panels and kits are substantially different
By comparing 2 commercialized cancer panels that use different target enrichment technologies, this study demonstrated the performance of both commercial kits for identifying highly diluted Circulating tumor DNA (ctDNA) in plasma

Summary

Introduction

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. Commercial platforms including Roche’s Avenio ctDNA Expanded panel and QIAgen’s QIAseq Human Comprehensive Cancer panel are currently available for minimal invasive ctDNA detection These platforms fall into two categories based on their enrichment technologies, probe-based solution hybridization and amplicon-based enrichment. While making an educated choice of which commercial platforms and technologies to choose for detection of ctDNA to suit specific application or research needs, several factors including the price, size and design of the region of interest, sensitivity, accuracy and sequencing uniformity are worth careful considerations. Most of these questions are still left unanswered. We evaluated several key parameters, including (1) panel coverage of clinically relevant variants; (2) target enrichment specificity and sequencing performance; (3) the sensitivity; (4) concordance and (5) sequencing coverage

Methods

Results

Conclusion