Exome enrichment and SOLiD sequencing of formalin fixed paraffin embedded (FFPE) prostate cancer tissue.
Exome enrichment and SOLiD sequencing of formalin fixed paraffin embedded (FFPE) prostate cancer tissue.
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DOI：
10.3390/ijms13078933
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发表时间：
2012
影响因子：
5.6
通讯作者：
Perner S
中科院分区：
文献类型：
--
作者：
Menon R;Deng M;Boehm D;Braun M;Fend F;Boehm D;Biskup S;Perner S
下一代测序（NGS）技术已经彻底改变了癌症研究，允许使用高通量深度测序方法对癌症进行全面研究。这些方法检测基因组改变、核苷酸取代、插入、缺失和拷贝数改变。SOLiD（通过寡核苷酸连接和检测进行测序，Life Technologies）是产生数十亿个50 bp测序读段的有前途的技术。这种稳健的技术已成功应用于基因鉴定，可能有助于使用福尔马林固定石蜡包埋（FFPE）组织检测与癌症发生和进展相关的新基因。本研究的目的是通过标准化为从同一患者获得的正常前列腺FFPE组织，比较新鲜冷冻与FFPE肿瘤组织的全外显子组测序的有效性。对一个初级新鲜冷冻样品、相应的FFPE前列腺癌样品和匹配的相邻正常前列腺组织进行外显子组测序。对测序的读数进行作图和比较。我们的研究是第一个使用SOLiD测序显示FFPE和相应的新鲜冷冻癌症组织之间的可比外显子组测序结果的研究。先前已经进行了一项研究，比较了使用其他NGS平台对FFPE与新鲜冷冻样本进行测序的有效性。我们的验证进一步证明FFPE材料是用于全外显子组测序的可靠材料来源。
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.
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影响因子：
64.8
作者：
通讯作者：
--
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Berger, Michael F.;Lawrence, Michael S.;Demichelis, Francesca;Drier, Yotam;Cibulskis, Kristian;Sivachenko, Andrey Y.;Sboner, Andrea;Esgueva, Raquel;Pflueger, Dorothee;Sougnez, Carrie;Onofrio, Robert;Carter, Scott L.;Park, Kyung;Habegger, Lukas;Ambrogio, Lauren;Fennell, Timothy;Parkin, Melissa;Saksena, Gordon;Voet, Douglas;Ramos, Alex H.;Pugh, Trevor J.;Wilkinson, Jane;Fisher, Sheila;Winckler, Wendy;Mahan, Scott;Ardlie, Kristin;Baldwin, Jennifer;Simons, Jonathan W.;Kitabayashi, Naoki;MacDonald, Theresa Y.;Kantoff, Philip W.;Chin, Lynda;Gabriel, Stacey B.;Gerstein, Mark B.;Golub, Todd R.;Meyerson, Matthew;Tewari, Ashutosh;Lander, Eric S.;Getz, Gad;Rubin, Mark A.;Garraway, Levi A.
通讯作者：
Garraway, Levi A.
影响因子：
3.4
作者：
Talaulikar, D.;Gray, J. X.;Dahlstrom, J. E.
通讯作者：
Dahlstrom, J. E.
影响因子：
64.8
作者：
Ley, Timothy J.;Mardis, Elaine R.;Ding, Li;Fulton, Bob;McLellan, Michael D.;Chen, Ken;Dooling, David;Dunford-Shore, Brian H.;McGrath, Sean;Hickenbotham, Matthew;Cook, Lisa;Abbott, Rachel;Larson, David E.;Koboldt, Dan C.;Pohl, Craig;Smith, Scott;Hawkins, Amy;Abbott, Scott;Locke, Devin;Hillier, LaDeana W.;Miner, Tracie;Fulton, Lucinda;Magrini, Vincent;Wylie, Todd;Glasscock, Jarret;Conyers, Joshua;Sander, Nathan;Shi, Xiaoqi;Osborne, John R.;Minx, Patrick;Gordon, David;Chinwalla, Asif;Zhao, Yu;Ries, Rhonda E.;Payton, Jacqueline E.;Westervelt, Peter;Tomasson, Michael H.;Watson, Mark;Baty, Jack;Ivanovich, Jennifer;Heath, Sharon;Shannon, William D.;Nagarajan, Rakesh;Walter, Matthew J.;Link, Daniel C.;Graubert, Timothy A.;DiPersio, John F.;Wilson, Richard K.
通讯作者：
Wilson, Richard K.