Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis

摘要: Background: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalinfixed and paraffin-embedded (FFPE) their use would open up access to a variety clinical trials. However, FFPE incompatible many down-stream molecular biology techniques such PCR based amplification methods gene expression studies. Methodology/Principal Findings: Here we investigated sample quality requirements tissues for massively parallel short-read sequencing approaches. We evaluated key variables pre-fixation, fixation related post-fixation processes that occur in routine medical service (e.g. degree autolysis, duration storage). also influence tissue storage time by using material was 18 years old. Finally, analyzed normal tumor breast Sequencing Synthesis technique (Illumina Genome Analyzer, Solexa) simultaneously localize genome-wide copy number alterations detect genomic variations substitutions point-deletions and/or insertions samples. Conclusions/Significance: The application second generation small amounts opens possibility analyze have been collected during work well context This particular important since amply available surgical resections histopathological diagnosis, comprise precursor lesions, primary tumors, lymphogenic hematogenic metastases. Large-scale studies this will result better prediction prognosis cancer patients early identification respond therapy.