title: Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing.
abstract: 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.
authors.affiliation: Institute of Human Genetics, Medical University of Graz, Graz, Austria.
authors.forename: Ellen
authors.initials: E
authors.lastname: Heitzer
authors.forename: Martina
authors.initials: M
authors.lastname: Auer
authors.forename: Christin
authors.initials: C
authors.lastname: Gasch
authors.forename: Martin
authors.initials: M
authors.lastname: Pichler
authors.forename: Peter
authors.initials: P
authors.lastname: Ulz
authors.forename: Eva Maria
authors.initials: EM
authors.lastname: Hoffmann
authors.forename: Sigurd
authors.initials: S
authors.lastname: Lax
authors.forename: Julie
authors.initials: J
authors.lastname: Waldispuehl-Geigl
authors.forename: Oliver
authors.initials: O
authors.lastname: Mauermann
authors.forename: Carolin
authors.initials: C
authors.lastname: Lackner
authors.forename: Gerald
authors.initials: G
authors.lastname: Höfler
authors.forename: Florian
authors.initials: F
authors.lastname: Eisner
authors.forename: Heinz
authors.initials: H
authors.lastname: Sill
authors.forename: Hellmut
authors.initials: H
authors.lastname: Samonigg
authors.forename: Klaus
authors.initials: K
authors.lastname: Pantel
authors.forename: Sabine
authors.initials: S
authors.lastname: Riethdorf
authors.forename: Thomas
authors.initials: T
authors.lastname: Bauernhofer
authors.forename: Jochen B
authors.initials: JB
authors.lastname: Geigl
authors.forename: Michael R
authors.initials: MR
authors.lastname: Speicher
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology; D055028:Comparative Genomic Hybridization / Q000379:methods*; D018628:Gene Dosage; D016678:Genome; D006801:Humans; D009154:Mutation; D009360:Neoplastic Cells, Circulating / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis