TY - JOUR
T1 - Exome enrichment and SOLiD sequencing of formalin fixed paraffin embedded (FFPE) prostate cancer tissue
AU - Menon, Roopika
AU - Deng, Mario
AU - Boehm, Diana
AU - Braun, Martin
AU - Fend, Falko
AU - Boehm, Detlef
AU - Biskup, Saskia
AU - Perner, Sven
N1 - Copyright:
Copyright 2015 Elsevier B.V., All rights reserved.
PY - 2012/7
Y1 - 2012/7
N2 - 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 Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing.
AB - 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 Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing.
UR - http://www.scopus.com/inward/record.url?scp=84864351002&partnerID=8YFLogxK
U2 - 10.3390/ijms13078933
DO - 10.3390/ijms13078933
M3 - Journal articles
C2 - 22942743
AN - SCOPUS:84864351002
SN - 1661-6596
VL - 13
SP - 8933
EP - 8942
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
IS - 7
ER -