Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing

TY - JOUR

T1 - Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing

AU - Heitzer, Ellen

AU - Auer, Martina

AU - Gasch, Christin

AU - Pichler, Martin

AU - Ulz, Peter

AU - Hoffmann, Eva Maria

AU - Lax, Sigurd

AU - Waldispuehl-Geigl, Julie

AU - Mauermann, Oliver

AU - Lackner, Carolin

AU - Höfler, Gerald

AU - Eisner, Florian

AU - Sill, Heinz

AU - Samonigg, Hellmut

AU - Pantel, Klaus

AU - Riethdorf, Sabine

AU - Bauernhofer, Thomas

AU - Geigl, Jochen B

AU - Speicher, Michael R

N1 - ©2013 AACR.

PY - 2013/5/15

Y1 - 2013/5/15

N2 - Circulating tumor cells (CTC) released into blood from primary cancers and metastases reflect the current status of tumor genotypes, which are prone to changes. Here, we conducted the first comprehensive genomic profiling of CTCs using array-comparative genomic hybridization (CGH) and next-generation sequencing. We used the U.S. Food and Drug Administration-cleared CellSearch system, which detected CTCs in 21 of 37 patients (range, 1-202/7.5 mL sample) with stage IV colorectal carcinoma. In total, we were able to isolate 37 intact CTCs from six patients and identified in those multiple colorectal cancer-associated copy number changes, many of which were also present in the respective primary tumor. We then used massive parallel sequencing of a panel of 68 colorectal cancer-associated genes to compare the mutation spectrum in the primary tumors, metastases, and the corresponding CTCs from two of these patients. Mutations in known driver genes [e.g., adenomatous polyposis coli (APC), KRAS, or PIK3CA] found in the primary tumor and metastasis were also detected in corresponding CTCs. However, we also observed mutations exclusively in CTCs. To address whether these mutations were derived from a small subclone in the primary tumor or represented new variants of metastatic cells, we conducted additional deep sequencing of the primary tumor and metastasis and applied a customized statistical algorithm for analysis. We found that most mutations initially found only in CTCs were also present at subclonal level in the primary tumors and metastases from the same patient. This study paves the way to use CTCs as a liquid biopsy in patients with cancer, providing more effective options to monitor tumor genomes that are prone to change during progression, treatment, and relapse.

AB - Circulating tumor cells (CTC) released into blood from primary cancers and metastases reflect the current status of tumor genotypes, which are prone to changes. Here, we conducted the first comprehensive genomic profiling of CTCs using array-comparative genomic hybridization (CGH) and next-generation sequencing. We used the U.S. Food and Drug Administration-cleared CellSearch system, which detected CTCs in 21 of 37 patients (range, 1-202/7.5 mL sample) with stage IV colorectal carcinoma. In total, we were able to isolate 37 intact CTCs from six patients and identified in those multiple colorectal cancer-associated copy number changes, many of which were also present in the respective primary tumor. We then used massive parallel sequencing of a panel of 68 colorectal cancer-associated genes to compare the mutation spectrum in the primary tumors, metastases, and the corresponding CTCs from two of these patients. Mutations in known driver genes [e.g., adenomatous polyposis coli (APC), KRAS, or PIK3CA] found in the primary tumor and metastasis were also detected in corresponding CTCs. However, we also observed mutations exclusively in CTCs. To address whether these mutations were derived from a small subclone in the primary tumor or represented new variants of metastatic cells, we conducted additional deep sequencing of the primary tumor and metastasis and applied a customized statistical algorithm for analysis. We found that most mutations initially found only in CTCs were also present at subclonal level in the primary tumors and metastases from the same patient. This study paves the way to use CTCs as a liquid biopsy in patients with cancer, providing more effective options to monitor tumor genomes that are prone to change during progression, treatment, and relapse.

KW - Colorectal Neoplasms

KW - Comparative Genomic Hybridization

KW - Gene Dosage

KW - Genome

KW - Humans

KW - Mutation

KW - Neoplastic Cells, Circulating

KW - Sequence Analysis, DNA

KW - Single-Cell Analysis

U2 - 10.1158/0008-5472.CAN-12-4140

DO - 10.1158/0008-5472.CAN-12-4140

M3 - SCORING: Journal article

C2 - 23471846

VL - 73

SP - 2965

EP - 2975

JO - CANCER RES

JF - CANCER RES

SN - 0008-5472

IS - 10

ER -