Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma

Salomon Manier ,C J Liu,J Park,Viktor A Adalsteinsson ,Sarah C Reed ,Marzia Capelletti ,Gavin Ha ,Laurent Garderet ,Samuel S Freeman ,Adriana Perilla-Glen ,Eliezer M Van Allen ,Mark Bustoros ,Shaji Kumar ,Gregory Gydush ,J Christopher Love ,Justin Rhoades ,Karma Z Salem ,Claudia Freymond ,Gad Getz ,Denisse Rotem ,Amir Yosef ,Daisy Huynh ,Irène M Ghobrial

doi:10.1038/s41467-018-04001-5

Abstract

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM.

Highlights

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA have enabled minimally invasive characterization of many cancers, but are rarely analyzed together
We added the CD138-selection step to enrich CTCs without flow cytometry sorting (Supplementary Fig. 1). This process involves using ichorCNA to detect somatic copy number alterations (SCNAs) and estimate tumor fraction from ultra-low pass wholegenome sequencing (ULP-WGS) data, and enables informed selection of samples for whole-exome sequencing (WES) based on tumor content
For CTCs, the tumor fraction corresponds to the fraction of clonal cells present within the normal mononuclear cells isolated during the CD138+ bead selection used to enrich for the tumor cells

Summary

Introduction

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. We reasoned that ultra-low pass wholegenome sequencing (ULP-WGS) can provide a rapid and affordable screening and monitoring tool to detect tumor fraction and copy number alterations (CNAs) in cfDNA and CTCs, while whole-exome sequencing (WES) of matched CTCs, cfDNA, and bone marrow biopsies from patients with MM would help to resolve the clonal relatedness and role of liquid biopsies in the genomic monitoring of patients with MM. If concordant genome-wide SSNVs and SCNAs could be derived from cfDNA and CTCs in patients with MM, it could be possible to use CTCs and cfDNA interchangeably for comprehensive profiling of MM If both provide different yet complementary information regarding clonal heterogeneity, performing studies on both fractions of liquid biopsy could possibly replace the need for bone marrow biopsies in future clinical applications. We hypothesized that some patients may harbor higher tumor fraction in the CD138-selected CTCs than cfDNA or vice versa—due to technical or biological reasons—but that analyzing both may help to broaden the applicability of WES to patients with MM, if CTCs and cfDNA exhibit concordant genomic profiles

Methods

Results

Conclusion