The challenge of gene expression profiling in heterogeneous clinical samples.
Almost all samples used in tumor biology, such as tissues and bodily fluids, are heterogeneous, i.e., consist of different cell types. Evaluating the degree of heterogeneity in samples can increase our knowledge on processes such as clonal selection and metastasis. In addition, generating expression profiles from specific sub populations of cells can reveal their distinct functions. Tissue heterogeneity also poses a challenge, as it can confound the interpretation of gene expression data. This chapter will (1) give a brief overview on how heterogeneity may influence gene expression profiling data and (2) describe the methods that are currently available to assess transcriptional biomarkers in a heterogeneous cell population.
Department of Medical Oncology, Josephine Nefkens Institute and Cancer Genomics Centre, Erasmus Medical Center, Rotterdam, The Netherlands.
F German
FG
Rodrıguez-Gonzalez
Dana A M
DA
Mustafa
Bianca
B
Mostert
Anieta M
AM
Sieuwerts
D000818:Animals; D000951:Antigens, Neoplasm / Q000235:genetics / Q000378:metabolism; D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D001943:Breast Neoplasms / Q000378:metabolism* / Q000473:pathology; D015815:Cell Adhesion Molecules / Q000235:genetics / Q000378:metabolism; D000071858:Epithelial Cell Adhesion Molecule; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009360:Neoplastic Cells, Circulating / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D059010:Single-Cell Analysis
D000951:Antigens, Neoplasm; D014408:Biomarkers, Tumor; D015815:Cell Adhesion Molecules; C499379:EPCAM protein, human; D000071858:Epithelial Cell Adhesion Molecule; D012313:RNA