Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer

Abstract

Background: Real-time knowledge of the somatic genome can influence management of patients with metastatic castration-resistant prostate cancer (mCRPC). While routine metastatic tissue biopsy is challenging in mCRPC, plasma circulating tumor DNA (ctDNA) has emerged as a minimally invasive tool to sample the tumor genome. However, no systematic comparisons of matched "liquid" and "solid" biopsies have been performed that would enable ctDNA profiling to replace the need for direct tissue sampling.

Methods: We performed targeted sequencing across 72 clinically relevant genes in 45 plasma cell-free DNA (cfDNA) samples collected at time of metastatic tissue biopsy. We compared ctDNA alterations with exome sequencing data generated from matched tissue and quantified the concordance of mutations and copy number alterations using the Fisher exact test and Pearson correlations.

Results: Seventy-five point six percent of cfDNA samples had a ctDNA proportion greater than 2% of total cfDNA. In these patients, all somatic mutations identified in matched metastatic tissue biopsies were concurrently present in ctDNA. Furthermore, the hierarchy of variant allele fractions for shared mutations was remarkably similar between ctDNA and tissue. Copy number profiles between matched liquid and solid biopsy were highly correlated, and individual copy number calls in clinically actionable genes were 88.9% concordant. Detected alterations included AR amplifications in 22 (64.7%) samples, SPOP mutations in three (8.8%) samples, and inactivating alterations in tumor suppressors TP53 , PTEN , RB1 , APC , CDKN1B , BRCA2 , and PIK3R1 . In several patients, ctDNA sequencing revealed robust changes not present in paired solid biopsy, including clinically relevant alterations in the AR, WNT, and PI3K pathways.

Conclusions: Our study shows that, in the majority of patients, a ctDNA assay is sufficient to identify all driver DNA alterations present in matched metastatic tissue and supports development of DNA biomarkers to guide mCRPC patient management based on ctDNA alone.

© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Figures

Figure 1.

Somatic alterations detected in plasma cell-free DNA. A) Schematic showing the proportion of cell-free DNA that was tumor derived (the circulating cell-free tumor DNA [ctDNA] fraction) and the relationship of this variable to select clinical characteristics. The grid provides an overview of metastatic locations in each patient at the time of sampling (green), with filled black circles indicating the region that was subjected to tissue biopsy concomitant to plasma collection. Orange squares denote prior exposure to (and progression on) three major systemic therapies for metastatic castration-resistant prostate cancer (mCRPC) at the time of paired sample collection. B)Matrix of mutations and copy number alterations detected in independent analysis of plasma cell-free DNA (cfDNA) samples. All 72 mCRPC driver genes included in the cfDNA sequencing panel are shown (sorted by chromosome and position). Note that sensitivity of copy number calling is diminished in samples with less than 35% ctDNA. ALP = alkaline phosphatase; cfDNA = cell–free DNA; ctDNA = circulating cell-free tumor DNA; LN = lymph node; PSA = prostate-specific antigen.

Figure 2.

Concordance of mutation calls between solid and liquid biopsies. A) Bar plot showing the variant allele frequencies for driver mutations in selected clinically relevant metastatic castration-resistant prostate cancer (mCRPC) genes. For each mutation, allele frequencies are provided for the solid tissue biopsy (S) and the cell–free DNA (cfDNA) liquid biopsy (L). The circulating cell-free tumor DNA (ctDNA) fraction corresponding to each mutation is shown in the lower panel. B) Variant allele frequencies for somatic mutations shared between matched liquid and solid biopsies, showing broad conservation of mutant allele fraction hierarchy. ctDNA fraction for each liquid biopsy is provided at the bottom. For patient 149, two cfDNA samples obtained at different time points are shown. AF = allele frequency; ctDNA = circulating cell-free tumor DNA.

Figure 3.

Concordance of genome copy number between liquid and solid biopsies. A)Shows representative scatter plots showing the correlation for coverage log ratio across the 72 genes in our targeted panel. Each gene is represented as a single circle. B) Shows the R2 value for this correlation across all samples in the cohort and the relationship to circulating cell-free tumor DNA (ctDNA) fraction. C) Bubble plots showing the concordance for copy number calls across individual genes, and how concordance depends on ctDNA fraction. Discordant calls are indicated in red, with patient ID annotated. ctDNA = circulating cell-free tumor DNA.