Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay

被引：75

作者：

Abramovitz, Mark ^{[2
]}

Ordanic-Kodani, Maja

Wang, Yuefang

Li, Zhenhong ^{[2
]}

Catzavelos, Charles ^{[3
]}

Bouzyk, Mark ^{[4
]}

Sledge, George W., Jr. ^{[5
]}

Moreno, Carlos S. ^{[1
]}

Leyland-Jones, Brian

机构：

[1] Emory Univ, Dept Pathol & Lab Med, Sch Med, Winship Canc Inst, Atlanta, GA 30322 USA

[2] VM Inst Res, Montreal, PQ, Canada

[3] McGill Univ, Dept Pathol, St Marys Hosp, Montreal, PQ, Canada

[4] Emory Univ, Sch Med, Ctr Med Genom, Atlanta, GA 30322 USA

[5] Indiana Univ, Ctr Canc, Indianapolis, IN 46204 USA

来源：

BIOTECHNIQUES | 2008年 / 44卷 / 03期

关键词：

D O I：

10.2144/000112703

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Formalin-fixed paraffin-embedded (FFPE) breast tumor tissues are readily available and represent a largely untapped, vast resource for molecular profiling of clinical samples with long-term follow-up data. We have optimized the conditions and parameters that result ill the preparation of total RNA that is of the necessary quality,for use ill the DASL (cDNA-mediated annealing, selection, extension, and ligation) assay ill which expression of 502 genes are analyzed simultaneously using as little as 100 ng of input RNA.

引用

页码：417 / +

页数：5

共 8 条

[1] Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays [J].

Bibikova, M ;

Talantov, D ;

Chudin, E ;

Yeakley, JM ;

Chen, J ;

Doucet, D ;

Wickham, E ;

Atkins, D ;

Barker, D ;

Chee, M ;

Wang, YX ;

Fan, JB .

AMERICAN JOURNAL OF PATHOLOGY, 2004, 165 (05) :1799-1807

[2] Expression signatures that correlated with Gleason score and relapse in prostate cancer [J].

Bibikova, Marina ;

Chudin, Eugene ;

Arsanjani, Amir ;

Zhou, Lixin ;

Garcia, Eliza Wickham ;

Modder, Joshua ;

Kostelec, Monica ;

Barker, David ;

Downs, Tracy ;

Fan, Jian-Bing ;

Wang-Rodriguez, Jessica .

GENOMICS, 2007, 89 (06) :666-672

[3] Optimization of recovery of RNA from formalin-fixed, paraffin-embedded tissue [J].

Chung, Joon-Yong ;

Braunschweig, Till ;

Hewitt, Stephen M. .

DIAGNOSTIC MOLECULAR PATHOLOGY, 2006, 15 (04) :229-236

[4] A versatile assay for high-throughput gene expression profiling on universal array matrices [J].

Fan, JB ;

Yeakley, JM ;

Bibikova, M ;

Chudin, E ;

Wickham, E ;

Chen, J ;

Doucet, D ;

Rigault, P ;

Zhang, BH ;

Shen, R ;

McBride, C ;

Li, HR ;

Fu, XD ;

Oliphant, A ;

Barker, DL ;

Chee, MS .

GENOME RESEARCH, 2004, 14 (05) :878-885

[5] Transcriptional profiling of degraded RNA in cryopreserved and fixed tissue samples obtained at autopsy [J].

Haller, Andrew ;

Kanakapalli, Deepa ;

Walter, Rosemarie ;

Alhasan, Samir ;

Eliason, James ;

Everson, Richard .

BMC CLINICAL PATHOLOGY, 2006, 6

[6] Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples [J].

Masuda, N ;

Ohnishi, T ;

Kawamoto, S ;

Monden, M ;

Okubo, K .

NUCLEIC ACIDS RESEARCH, 1999, 27 (22) :4436-4443

[7] RNA expression analysis of formalin-fixed paraffin-embedded tumors [J].

Penland, Shannon K. ;

Keku, Temitope O. ;

Torrice, Chad ;

He, Xiaping ;

Krishnamurthy, Janakiraman ;

Hoadley, Katherine A. ;

Woosley, John T. ;

Thomas, Nancy E. ;

Perou, Charles M. ;

Sandler, Robert S. ;

Sharpless, Norman E. .

LABORATORY INVESTIGATION, 2007, 87 (04) :383-391

[8]

RUPP GM, 1988, BIOTECHNIQUES, V6, P56

← 1 →