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1.
Sci Rep ; 6: 20944, 2016 Feb 11.
Article in English | MEDLINE | ID: mdl-26864208

ABSTRACT

Precision medicine in oncology requires an accurate characterization of a tumor molecular profile for patient stratification. Though targeted deep sequencing is an effective tool to detect the presence of somatic sequence variants, a significant number of patient specimens do not meet the requirements needed for routine clinical application. Analysis is hindered by contamination of normal cells and inherent tumor heterogeneity, compounded with challenges of dealing with minute amounts of tissue and DNA damages common in formalin-fixed paraffin-embedded (FFPE) specimens. Here we present an innovative workflow using DEPArray™ system, a microchip-based digital sorter to achieve 100%-pure, homogenous subpopulations of cells from FFPE samples. Cells are distinguished by fluorescently labeled antibodies and DNA content. The ability to address tumor heterogeneity enables unambiguous determination of true-positive sequence variants, loss-of-heterozygosity as well as copy number variants. The proposed strategy overcomes the inherent trade-offs made between sensitivity and specificity in detecting genetic variants from a mixed population, thus rescuing for analysis even the smaller clinical samples with low tumor cellularity.


Subject(s)
Cell Separation/methods , Flow Cytometry/methods , High-Throughput Nucleotide Sequencing , Microarray Analysis/methods , Neoplasms/diagnosis , Cell Separation/instrumentation , DNA Copy Number Variations , Fixatives , Flow Cytometry/instrumentation , Formaldehyde , Genetic Variation , Humans , Microarray Analysis/instrumentation , Mutation , Neoplasms/genetics , Neoplasms/pathology , Paraffin Embedding , Sensitivity and Specificity , Sequence Analysis, DNA , Tissue Fixation
2.
EMBO Mol Med ; 6(11): 1371-86, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25358515

ABSTRACT

Several hundred clinical trials currently explore the role of circulating tumor cell (CTC) analysis for therapy decisions, but assays are lacking for comprehensive molecular characterization of CTCs with diagnostic precision. We therefore combined a workflow for enrichment and isolation of pure CTCs with a non-random whole genome amplification method for single cells and applied it to 510 single CTCs and 189 leukocytes of 66 CTC-positive breast cancer patients. We defined a genome integrity index (GII) to identify single cells suited for molecular characterization by different molecular assays, such as diagnostic profiling of point mutations, gene amplifications and whole genomes of single cells. The reliability of > 90% for successful molecular analysis of high-quality clinical samples selected by the GII enabled assessing the molecular heterogeneity of single CTCs of metastatic breast cancer patients. We readily identified genomic disparity of potentially high relevance between primary tumors and CTCs. Microheterogeneity analysis among individual CTCs uncovered pre-existing cells resistant to ERBB2-targeted therapies suggesting ongoing microevolution at late-stage disease whose exploration may provide essential information for personalized treatment decisions and shed light into mechanisms of acquired drug resistance.


Subject(s)
Breast Neoplasms/diagnosis , Genomics/methods , Neoplastic Cells, Circulating/pathology , Pathology, Molecular/methods , Single-Cell Analysis/methods , Female , Humans
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