ArticleScientific reports2016
Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin-Embedded Tumors by Next Generation Sequencing.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 41 citations in OpenAlex.
- Identification of actionable targets using DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded tissues followed by shallow whole-genome sequencing.The Journal of pathology · 2026Article
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- Clonality assessment and detection of clonal diversity in classic Hodgkin lymphoma by next-generation sequencing of immunoglobulin gene rearrangements.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples.Bio-protocol · 2022Article
- Molecular analysis of bovine leukemia virus in early epidemic phase in Japan using archived formalin fixed paraffin embedded histopathological specimens.The Journal of veterinary medical science · 2022Article
- Tumor cell enrichment by tissue suspension enables detection of mutations with low variant allele frequency and estimation of germline mutations.Scientific reports · 2022Article
- Detection of Lung Cancer Cells in Solutions Using a Terahertz Chemical Microscope.Sensors (Basel, Switzerland) · 2021Article
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- Whole-genome sequencing of single circulating tumor cells from neuroendocrine neoplasms.Endocrine-related cancer · 2021Article
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- Somatic Focal Copy Number Gains of Noncoding Regions of Receptor Tyrosine Kinase Genes in Treatment-Resistant Epilepsy.Journal of neuropathology and experimental neurology · 2021Article
- Enriched transcriptome analysis of laser capture microdissected populations of single cells to investigate intracellular heterogeneity in immunostained FFPE sections.Computational and structural biotechnology journal · 2021Article
- Biosensors Based on Mechanical and Electrical Detection Techniques.Sensors (Basel, Switzerland) · 2020Review
- Targeted Sequencing of Sorted Esophageal Adenocarcinoma Cells Unveils Known and Novel Mutations in the Separated Subpopulations.Clinical and translational gastroenterology · 2020Article
- Precise detection of genomic imbalances at single-cell resolution reveals intra-patient heterogeneity in Hodgkin's lymphoma.Blood cancer journal · 2019Article
- Visualisation of HER2 homodimers in single cells from HER2 overexpressing primary formalin fixed paraffin embedded tumour tissue.Molecular medicine (Cambridge, Mass.) · 2019Article
- Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development.British journal of cancer · 2019Article
- DEPArray™ system: An automatic image-based sorter for isolation of pure circulating tumor cells.Cytometry. Part A : the journal of the International Society for Analytical Cytology · 2018Review
- Genomic profiles of primary and metastatic esophageal adenocarcinoma identified via digital sorting of pure cell populations: results from a case report.BMC cancer · 2018Article
- Identification of novel mutations in FFPE lung adenocarcinomas using DEPArray sorting technology and next-generation sequencing.Journal of applied genetics · 2018Article
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Authors and funding
19 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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