Circulating and disseminated tumor cells are of great interest because they provide a minimally invasive window for assessing aspects of cancer biology, including tumor heterogeneity, a means to discover biomarkers of disease behavior, and a way to identify and prioritize therapeutic targets in the emerging era of precision oncology.
However, the rarity of circulating and disseminated tumor cells poses a substantial challenge to the consistent success in analyzing their molecular features, including genomic aberrations. Herein, we describe optimized and robust methods to reproducibly detect genomic copy number alterations in samples of 2 to 40 cells after whole-genome amplification with the use of a high-resolution single-nuclear polymorphism-array platform and refined computational algorithms. We have determined the limit of detection for heterogeneity within a sample as 50% and also demonstrated success in analyzing single cells. We validated the genes in genomic regions that are frequently amplified or deleted by real-time quantitative PCR and nCounter copy number quantification. We further applied these methods to disseminated tumor cells isolated from individuals with advanced prostate cancer to confirm their highly aberrant nature. We compared copy number alterations of disseminated tumor cells with matched metastatic tumors isolated from the same individual to gain biological insight. These developments provide high-resolution genomic profiling of single and rare cell populations and should be applicable to a wide-range of sample sources.
The Journal of molecular diagnostics : JMD. 2015 Nov 19 [Epub ahead of print]
Yu Wu, Jamie R Schoenborn, Colm Morrissey, Jing Xia, Sandy Larson, Lisha G Brown, Xiaoyu Qu, Paul H Lange, Peter S Nelson, Robert L Vessella, Min Fang
Fred Hutchinson Cancer Research Center, Seattle, Washington. , Fred Hutchinson Cancer Research Center, Seattle, Washington. , University of Washington, Seattle, Washington. , Fred Hutchinson Cancer Research Center, Seattle, Washington. , University of Washington, Seattle, Washington. , Puget Sound VA Health Care System, Seattle, Washington. , Fred Hutchinson Cancer Research Center, Seattle, Washington. , University of Washington, Seattle, Washington. , Fred Hutchinson Cancer Research Center, Seattle, Washington; University of Washington, Seattle, Washington. , University of Washington, Seattle, Washington; Puget Sound VA Health Care System, Seattle, Washington. , Fred Hutchinson Cancer Research Center, Seattle, Washington; University of Washington, Seattle, Washington.