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posted on 2023-03-31, 20:23 authored by Giulia Siravegna, Andrea Sartore-Bianchi, Rebecca J. Nagy, Kanwal Raghav, Justin I. Odegaard, Richard B. Lanman, Livio Trusolino, Silvia Marsoni, Salvatore Siena, Alberto Bardelli Digital Sequencing-based ctDNA assay workflow. (a) cfDNA is extracted from stabilized peripheral whole blood, (b) labeled with oligonucleotide barcodes at high efficiency, and (c) up to 30ng is used for library preparation. (d) Sequencing libraries are enriched using hybrid capture and sequenced to an average depth of ~15,000x. (e) Individual unique input molecules are then bioinformatically reconstructed using barcode and sequence data to suppress analytical error modes. (f) Somatic variants are deconvoluted from germline and reported by clinical priority with both treatment and clinical trial annotations.
Funding
European Community's Seventh Framework
H2020
IMI
AIRC
Fondazione Piemontese per la Ricerca
TACTIC
Roche per la ricerca
Fondazione Oncologia
Colorectal Cancer
History
ARTICLE ABSTRACT
ERBB2 (HER2) amplification is an emerging biomarker in colon cancer, conferring sensitivity to combination anti-HER2 therapy. Measurement of HER2 copy number is typically performed using surgical specimens, but cell-free circulating tumor DNA (ctDNA) analysis may be a noninvasive alternative. We determined the sensitivity of plasma copy number (pCN) for detecting ERBB2 amplifications and whether pCN correlated with tissue-detected copy number. We also assessed response to HER2-targeted therapy based on pCN and suggest a pCN threshold predictive of response.
Forty-eight pretreatment and progression plasma samples from 29 HER2-positive patients in the HERACLES A clinical trial were tested using the Guardant360 cfDNA assay. We correlated ERRB2 pCN with progression-free survival (PFS) and best objective response (BOR) and applied an adjustment method based on tumor DNA shedding using the maximum mutant allele fraction as a surrogate for tumor content to accurately determine the pCN threshold predictive of response.
Forty-seven of 48 samples had detectable ctDNA, and 46 of 47 samples were ERBB2-amplified on the basis of cfDNA [2.55–122 copies; 97.9% sensitivity (95% confidence interval, 87.2%–99.8%)]. An adjusted ERBB2 pCN of ≥25.82 copies correlated with BOR and PFS (P = 0.0347).
cfDNA is a viable alternative to tissue-based genotyping in the metastatic setting. The cfDNA platform utilized correctly identified 28 of 29 (96.6%) of pretreatment samples as ERBB2-amplified and predicted benefit from HER2-targeted therapy. In this study, an observed pCN of 2.4 and an adjusted pCN of 25.82 copies of ERBB2 are proposed to select patients who will benefit from HER2-targeted therapy.
