[HTML][HTML] Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy

DH Hovelson, CJ Liu, Y Wang, Q Kang, J Henderson… - Oncotarget, 2017 - ncbi.nlm.nih.gov
DH Hovelson, CJ Liu, Y Wang, Q Kang, J Henderson, A Gursky, S Brockman, N Ramnath
Oncotarget, 2017ncbi.nlm.nih.gov
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology
workflows are typically limited to targeted and/or disease-specific applications. In advanced
cancer, disease burden and cfDNA tumor content are often elevated, yielding unique
precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer,
rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision
oncology screening strategy via ultra-low coverage (~ 0.01 x) tumor content determination …
Abstract
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~ 0.01 x) tumor content determination through genome-wide copy number alteration (CNA) profiling. We applied PRINCe to a retrospective cohort of 124 cfDNA samples from 100 patients with advanced cancers, including 76 men with metastatic castration-resistant prostate cancer (mCRPC), enabling cfDNA tumor content approximation and actionable focal CNA detection, while facilitating concordance analyses between cfDNA and tissue-based NGS profiles and assessment of cfDNA alteration associations with mCRPC treatment outcomes. Therapeutically relevant focal CNAs were present in 42 (34%) cfDNA samples, including 36 of 93 (39%) mCRPC patient samples harboring AR amplification. PRINCe identified pre-treatment cfDNA CNA profiles facilitating disease monitoring. Combining PRINCe with routine targeted NGS of cfDNA enabled mutation and CNA assessment with coverages tuned to cfDNA tumor content. In mCRPC, genome-wide PRINCe cfDNA and matched tissue CNA profiles showed high concordance (median Pearson correlation= 0.87), and PRINCe detectable AR amplifications predicted reduced time on therapy, independent of therapy type (Kaplan-Meier log-rank test, chi-square= 24.9, p< 0.0001). Our screening approach enables robust, broadly applicable cfDNA-based precision oncology for patients with advanced cancer through scalable identification of therapeutically relevant CNAs and pre-/post-treatment genomic profiles, enabling cfDNA-or tissue-based precision oncology workflow optimization.
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