Study

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

Study ID Alternative Stable ID Type
EGAS00001000737 Other

Study Description

Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable resource for clinical research. However, nucleic acids extracted from FFPE tissues are fragmented and chemically modified making them challenging to use in molecular studies. We analysed 23 fresh-frozen (FF), 35 FFPE and 38 paired FF/FFPE specimens, representing six different human tissue types (bladder, prostate and colon carcinoma; liver and colon normal tissue; reactive tonsil) in order to examine the potential use of FFPE samples in next-generation sequencing (NGS) based retrospective and prospective clinical studies. Two methods for DNA and three methods for RNA extraction from FFPE tissues were compared and were found to affect nucleic acid quantity and quality. DNA and RNA from selected FFPE and paired FF/FFPE specimens were used for exome and transcriptome analysis. Preparations of DNA Exome-Seq libraries was more challenging (29.5 % success) than that of RNA-Seq libraries, presumably because of modifications to FFPE tissue-derived DNA. Libraries could still be prepared from RNA isolated from two-decade old ... (Show More)

Study Datasets 7 datasets.

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Dataset ID Description Technology Samples
EGAD00001000829
NA
Illumina HiSeq 2000 16
EGAD00001000830
NA
Illumina HiSeq 2000 14
EGAD00001000831
NA
Illumina HiSeq 2000 30
EGAD00001000832
NA
Illumina HiSeq 2000 16
EGAD00001000833
NA
Illumina HiSeq 2000 10
EGAD00001000834
NA
Illumina HiSeq 2000 20
EGAD00001000835
NA
Illumina HiSeq 2000 8

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