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Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue
Department of Prostate Cancer Research, Institute of Pathology, University Hospital of Bonn, Bonn 53127, Germany
Department of Hematology and Oncology, University Hospital of Tuebingen, Tuebingen 72076, Germany
Center for Genomics and Transcriptomics, CeGaT GmbH, Paul-Ehrlich-Str.17, Tuebingen 72076, Germany
* Author to whom correspondence should be addressed.
Received: 11 April 2012; in revised form: 29 May 2012 / Accepted: 9 July 2012 / Published: 17 July 2012
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.
Keywords: exome sequencing; SOLiD4; prostate cancer; next-generation sequencing
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Menon, R.; Deng, M.; Boehm, D.; Braun, M.; Fend, F.; Boehm, D.; Biskup, S.; Perner, S. Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue. Int. J. Mol. Sci. 2012, 13, 8933-8942.
Menon R, Deng M, Boehm D, Braun M, Fend F, Boehm D, Biskup S, Perner S. Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue. International Journal of Molecular Sciences. 2012; 13(7):8933-8942.
Menon, Roopika; Deng, Mario; Boehm, Diana; Braun, Martin; Fend, Falko; Boehm, Detlef; Biskup, Saskia; Perner, Sven. 2012. "Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue." Int. J. Mol. Sci. 13, no. 7: 8933-8942.