Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples
نویسندگان
چکیده
Formalin fixed paraffin embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas) including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.
منابع مشابه
Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing.
Most tumor samples available for clinical genotyping are formalin-fixed and paraffin-embedded (FFPE), but there has been relatively little published on the suitability of such samples for next-generation sequencing approaches. A new study by Wagle and colleagues shows that a combination of hybridization-capture and deep sequencing yields high-quality data from FFPE specimens.
متن کاملQuantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays.
We recently developed a sensitive and flexible gene expression profiling system that is not dependent on an intact poly-A tail and showed that it could be used to analyze degraded RNA samples. We hypothesized that the DASL (cDNA-mediated annealing, selection, extension and ligation) assay might be suitable for the analysis of formalin-fixed, paraffin-embedded tissues, an important source of arc...
متن کاملReliable microRNA profiling in routinely processed formalin-fixed paraffin-embedded breast cancer specimens using fluorescence labelled bead technology
BACKGROUND During the last years the analysis of microRNA expression patterns has led to completely new insights into cancer biology. Furthermore, these patterns are a very promising tool for the development of new diagnostic and prognostic markers. However, most human tumour samples for which long term clinical records are available exist only as formalin-fixed paraffin-embedded specimens. The...
متن کاملMolecular Identification of Mycobacterium Tuberculosis Complex in Formalin-Fixed, Paraffin-Embedded Tissue Blocks of Extra Pulmonary Speciemens using Genomics Extraction
Background: Tuberculosis has been detected in some extra pulmonary ecological niches. Although extra pulmonary tuberculosis (EPTB) is less frequent than Pulmonary Tuberculosis (PTB), its incidence has increased worldwide. The aim of this study was to investigate the presence of EPTB and MDR-EXPT in Formalin-fixed, paraffin-embedded tissue blocks among different samples in Kerma...
متن کامل