Comparison of Target Enrichment Platforms for Circulating Tumor DNA Detection.

Scientific Reports
So Ngo LamChun Kin Chow

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 ...Continue Reading

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Citations

Aug 3, 2020·Journal of Translational Medicine·Jiaping LiYanhong Deng
Dec 29, 2020·Annals of Oncology : Official Journal of the European Society for Medical Oncology·E OcocksE Smyth
Jun 13, 2021·International Journal of Clinical Oncology·Ryoji KatoKazuhiko Nakagawa

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Datasets Mentioned

BETA
PRJNA577992

Methods Mentioned

BETA
CAPP-seq
PCR
biopsies
biopsy
Assay

Software Mentioned

Avenio ctDNA
QIAseq open sources
QIAseq
Avenio
SomaticSniper
MuSE
Mutect2
Varscan2

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