Abstract
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE) tissue. This study’s aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The sequenced reads were mapped and compared. Our study was the first to show comparable exome sequencing results between FFPE and corresponding fresh-frozen cancer tissues using SOLiD sequencing. A prior study has been conducted comparing the validity of sequencing of FFPE vs. fresh frozen samples using other NGS platforms. Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing.
Highlights
The recent development in generation sequencing (NGS) technologies has revolutionized cancer research [1,2,3,4]
We further evaluated the reproducibility of the sequencing data using two different fixation methods of the same sample, in order to see if formalin fixed paraffin embedded (FFPE) tissue could be used as a promising alternative to fresh frozen samples for SOLiD Next generation sequencing (NGS) technologies
The uniquely mapped reads for each sample were in the range of 43.9 million for FFPE normal prostatic, 42.5 million for FFPE tumor and 51.0 million for fresh frozen tumor
Summary
The recent development in generation sequencing (NGS) technologies has revolutionized cancer research [1,2,3,4]. Generation sequencing (NGS) technologies has revolutionized cancer research by making it possible to comprehensively study the complexity of cancer using high throughput deep sequencing methodologies. These methods enable the detection of genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations [5,6]. Another study described the mutation frequencies observed in advanced and lethal prostate cancer by exome sequencing of xenograft tissue [8] Studies in this field are limited due to the high cost of NGS, and the challenge involved in data analysis, requiring time and bioinformatic expertise [9]. We further evaluated the reproducibility of the sequencing data using two different fixation methods (fresh frozen and FFPE) of the same sample, in order to see if FFPE tissue could be used as a promising alternative to fresh frozen samples for SOLiD NGS technologies
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