Abstract
Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.
Highlights
Cancer is a generic term for a large group of malignant diseases that can affect any part of the body
We developed an analysis pipeline that incorporates various open-source tools, such as TopHat, RSEM, SNPiR, ANNOVAR, and custom filters to produce gene expression and single nucleotide variant calls from Formalin-Fixed Paraffin-Embedding (FFPE) RNA sequencing data that are highly correlated and concordant with RNA sequencing data from patient-matched fresh frozen tumor samples (Figure S1)
These results suggest that reads mapping to the intronic regions may have contributed to the abnormal GC-content peak in FFPE samples
Summary
Cancer is a generic term for a large group of malignant diseases that can affect any part of the body. Large-scale efforts are underway to characterize somatic mutations across a number of different cancers so that comprehensive knowledge can be constructed to advance personalized medicine. At present these efforts rely on samples stored as fresh frozen (FF) tissues[6,7,8,9,10,11]. We used SNPiR bioinformatics tool and customer filters to analyze sequence variations from RNA-sequencing and used DNA-sequencing data for verification purpose These analyses indicate the feasibility of performing comprehensive genomic characterization of tumor samples from archived FFPE samples
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