Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA.
OBJECTIVE
The expanding number of targeted therapeutics for non-small cell lung cancer (NSCLC) necessitates real-time tumor genotyping, yet tissue biopsies are difficult to perform serially and often yield inadequate DNA for next-generation sequencing (NGS). We evaluated the feasibility of using cell-free circulating tumor DNA (ctDNA) NGS as a complement or alternative to tissue NGS.


METHODS
A total of 112 plasma samples obtained from a consecutive study of 102 prospectively enrolled patients with advanced NSCLC were subjected to ultra-deep sequencing of up to 70 genes and matched with tissue samples, when possible.


RESULTS
We detected 275 alterations in 45 genes, and at least one alteration in the ctDNA for 86 of 102 patients (84%), with EGFR variants being most common. ctDNA NGS detected 50 driver and 12 resistance mutations, and mutations in 22 additional genes for which experimental therapies, including clinical trials, are available. Although ctDNA NGS was completed for 102 consecutive patients, tissue sequencing was only successful for 50 patients (49%). Actionable EGFR mutations were detected in 24 tissue and 19 ctDNA samples, yielding concordance of 79%, with a shorter time interval between tissue and blood collection associated with increased concordance (P = 0.038). ctDNA sequencing identified eight patients harboring a resistance mutation who developed progressive disease while on targeted therapy, and for whom tissue sequencing was not possible.


CONCLUSIONS
Therapeutically targetable driver and resistance mutations can be detected by ctDNA NGS, even when tissue is unavailable, thus allowing more accurate diagnosis, improved patient management, and serial sampling to monitor disease progression and clonal evolution. Clin Cancer Res; 22(23); 5772-82. ©2016 AACR.
Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Jeffrey C
JC
Thompson
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Stephanie S
SS
Yee
Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Andrea B
AB
Troxel
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Samantha L
SL
Savitch
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Ryan
R
Fan
Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
David
D
Balli
Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
David B
DB
Lieberman
Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania.
Jennifer D
JD
Morrissette
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Tracey L
TL
Evans
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Joshua
J
Bauml
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Charu
C
Aggarwal
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
John A
JA
Kosteva
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Evan
E
Alley
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Christine
C
Ciunci
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Roger B
RB
Cohen
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Stephen
S
Bagley
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Susan
S
Stonehouse-Lee
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Victoria E
VE
Sherry
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Elizabeth
E
Gilbert
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Corey
C
Langer
Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Anil
A
Vachani
Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania. erical@upenn.edu.|Abramson Family Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
Erica L
EL
Carpenter
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D000074141:Circulating Tumor DNA / Q000235:genetics*; D004273:DNA, Neoplasm / Q000097:blood* / Q000235:genetics*; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005260:Female; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D009154:Mutation / Q000235:genetics*; D011446:Prospective Studies
D014408:Biomarkers, Tumor; D000074141:Circulating Tumor DNA; D004273:DNA, Neoplasm