Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

Viktor A Adalsteinsson,J Christopher Love,Sarah C Reed,Joshua M Francis,Nancy U Lin,Eric P Winer,Daniel Rosebrock,Joseph F Kramkowski,Mary‐Ellen Taplin ,Gad Getz,Mara Rosenberg,Sara M Tolaney,Sairah Mahmud,Denisse Rotem,Nelly Oliver ,Andrea Saltzman,Rachel Leeson,Rachel Barry ,Rebecca A Santiago,Paz Polak,Atish D Choudhury,Karla Helvie,Coyin Oh,Dimitri Livitz,Jesse S Boehm,Margaret S Merrill,Nikhil Wagle,Chip Stewart,Ofir Cohen,Heather A Parsons,Adrienne G Waks,Justin Rhoades,Gregory Gydush,Seong Ho Jeong ,Daniel G Stover,Ken Chen ,Denis Loginov,Edward O’connor ,Jens G Lohr,Todd R Golub,Cory M Johannessen,Molly Schleicher,Emily Lipscomb,Ignaty Leshchiner,Gavin Ha,L Polácek ,Levi A Garraway,Lori Marini,Lauren C Harshman,Mari Nakabayashi,Jaegil Kim,Eliezer M Van Allen,Samuel S Freeman,Zhenwei Zhang,Huiming Ding,Maxwell R Lloyd ,Matthew Meyerson

doi:10.1038/s41467-017-00965-y

Abstract

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

Highlights

Whole-exome sequencing of cell-free DNA could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain
We found that the size distribution (Supplementary Fig. 1) and yields of cfDNA from metastatic cancer patients and healthy donors (HD) were consistent with previous reports[18, 19] (Supplementary Data 1)
Our study has overcome three major hurdles for making Whole-exome sequencing (WES) of cfDNA a routine possibility for patients with metastatic cancer: (1) efficient screening for tumor content prior to WES; (2) comprehensive benchmarking of cfDNA and conventional biopsies; (3) applicability to many patients with metastatic cancer

Summary

Introduction

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. We provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing. We hypothesized that being able to estimate tumor fraction from 0.1× sequencing coverage (ultralow-pass whole-genome sequencing, ULP-WGS) could enable cost-effective screening for the existence of a significant amount of tumor-derived cfDNA in a substantial fraction of patients with metastatic cancer and calibrate the application of WES. Further examination of 1439 blood samples from 520 patients with metastatic breast or prostate cancer using ichorCNA reveals >30% of blood samples and >40% of patients to have sufficient tumor fraction for standard depths of WES of cfDNA

Methods

Results

Conclusion