title: High-Resolution Genomic Profiling of Disseminated Tumor Cells in Prostate Cancer.
abstract: Circulating tumor cells and disseminated tumor cells (DTCs) 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 tumor cells and DTCs 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 DTCs isolated from individuals with advanced prostate cancer to confirm their highly aberrant nature. We compared copy number alterations of DTCs 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.
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Jamie R
authors.initials: JR
authors.lastname: Schoenborn
authors.affiliation: Department of Urology, University of Washington, Seattle, Washington.
authors.forename: Colm
authors.initials: C
authors.lastname: Morrissey
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Jing
authors.initials: J
authors.lastname: Xia
authors.affiliation: Department of Urology, University of Washington, Seattle, Washington.
authors.forename: Sandy
authors.initials: S
authors.lastname: Larson
authors.affiliation: Department of Urology, Puget Sound VA Health Care System, Seattle, Washington.
authors.forename: Lisha G
authors.initials: LG
authors.lastname: Brown
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Qu
authors.affiliation: Department of Urology, University of Washington, Seattle, Washington.
authors.forename: Paul H
authors.initials: PH
authors.lastname: Lange
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Urology, University of Washington, Seattle, Washington.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Nelson
authors.affiliation: Department of Urology, University of Washington, Seattle, Washington; Department of Urology, Puget Sound VA Health Care System, Seattle, Washington.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Vessella
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Urology, University of Washington, Seattle, Washington. Electronic address: mfang@fhcrc.org.
authors.forename: Min
authors.initials: M
authors.lastname: Fang
mesh_terms: D000368:Aged; D000465:Algorithms; D014408:Biomarkers, Tumor / Q000097:blood / Q000235:genetics*; D001859:Bone Neoplasms / Q000235:genetics / Q000556:secondary; D045744:Cell Line, Tumor; D055028:Comparative Genomic Hybridization / Q000379:methods; D056915:DNA Copy Number Variations / Q000235:genetics*; D018628:Gene Dosage / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D057230:Limit of Detection; D008113:Liver Neoplasms / Q000235:genetics / Q000556:secondary; D008207:Lymphatic Metastasis / Q000235:genetics; D008297:Male; D009360:Neoplastic Cells, Circulating / Q000473:pathology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011470:Prostatic Hyperplasia / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D011471:Prostatic Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D014408:Biomarkers, Tumor