Sun, 20 Jul 2008 13:38:36 BST CiteULike: jyuh ffpe http://www.citeulike.org/user/jyuh/tag/ffpe CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/3008394 <i>Human mutation (12 June 2008)</i><br /><br />Highly accurate and high-throughput SNP genotyping platforms are increasingly popular but the performance of suboptimal DNA samples remains unclear. The aim of our study was to determine the best platform, amplification technique, and loading concentration to maximize genotype accuracy and call rate using degraded samples. We amplified high-molecular weight genomic DNA samples recently extracted from whole blood and degraded DNA samples extracted from 50-year-old patient sera. Two whole-genome amplification (WGA) methodologies were used: an isothermal multiple displacement amplification method (MDA) and a fragmentation-PCR-based method (GenomePlex((R)) [GPLEX]; Sigma-Aldrich, St. Louis, MO). Duplicate runs were performed on genome-wide dense SNP arrays (Nsp-Mendel; Affymetrix) and custom SNP platforms based on molecular inversion probes (Targeted Genotyping [TG]; Affymetrix) and BeadArray technology (Golden Gate [GG]; Illumina). Miscalls and no-calls on Mendel arrays were correlated with each other, with confidence scores from the Bayesian calling algorithm, and with average probe intensity. Degraded DNA amplified with MDA gave low call rates and concordance across all platforms at standard loading concentrations. The call rate with MDA on GG was improved when a 5 x concentration of amplified DNA was used. The GPLEX amplification gave high call rate and concordance for degraded DNA at standard and higher loading concentrations on both TG and GG platforms. Based on these analyses, after standard filtering for SNP and sample performance, we were able to achieve a mean call rate of 99.7% and concordance 99.7% using degraded samples amplified by GPLEX on GG technology at 2 x loading concentration. These findings may be useful for investigators planning case-control association studies with patient samples of suboptimal quality. Hum Mutat 0, 1-7, 2008. (c) 2008 Wiley-Liss, Inc. Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms. Simon Mead Mark Poulter John Beck James Uphill Chris Jones Cheng Eng Ang Charles A Mein John Collinge doi:10.1002/humu.20782 Human mutation (12 June 2008) 2008-07-16T12:44:40-00:00 2008 Human mutation 1098-1004 ffpe microaray snp wga http://www.citeulike.org/user/jyuh/article/2997796 <i>International journal of legal medicine (2 July 2008)</i><br /><br />In forensic science, the unequivocal identification of the cellular origin of crime scene samples used for DNA profiling can provide crucial information for crime scene reconstruction. We have previously shown that various mRNA markers from genes with expression patterns specific for blood and saliva can be established from whole-genome expression analysis of time-wise degraded samples and were stable enough to specifically identify blood and saliva stains up to 180 days of age. Here, we showed that nine blood-specific and five saliva-specific mRNA markers can be amplified successfully and reliably in much older blood (13-16 years) and saliva (2-6 years) stains, respectively, suggesting their suitability for tissue identification in forensic case work. Moreover, our findings imply that forensic RNA testing can be reliable and robust if degraded samples are considered in the marker ascertainment procedure, with promising expectations beyond tissue identification purposes. New markers for old stains: stable mRNA markers for blood and saliva identification from up to 16-year-old stains. Dmitry Zubakov Mieke Kokshoorn Ate Kloosterman Manfred Kayser doi:10.1007/s00414-008-0249-z International journal of legal medicine (2 July 2008) 2008-07-14T02:42:35-00:00 2008 International journal of legal medicine 0937-9827 blood ffpe microarray saliva http://www.citeulike.org/user/jyuh/article/2427774 <i>Laboratory Investigation, Vol. aop, No. current.</i> Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays Maria Ravo Margherita Mutarelli Lorenzo Ferraro Olì Ornella Paris Roberta Tarallo Alessandra Vigilante Daniela Cimino Michele De Bortoli Ernesto Nola Luigi Cicatiello Alessandro Weisz doi:10.1038/labinvest.2008.11 Laboratory Investigation, Vol. aop, No. current. 2008-02-26T01:28:14-00:00 Laboratory Investigation 0023-6837 aop current Nature Publishing Group ffpe microarray http://www.citeulike.org/user/jyuh/article/1594812 <i>J Histochem Cytochem, Vol. 54, No. 6. (June 2006), pp. 739-743.</i><br /><br />A satisfactory protocol of protein extraction has been established based on the heat-induced antigen retrieval (AR) technique widely applied in immunohistochemistry for archival formalin-fixed, paraffin-embedded (FFPE) tissue sections. Based on AR, an initial serial experiment to identify an optimal protocol of heat-induced protein extraction was carried out using FFPE mouse tissues. The optimal protocol for extraction of proteins was then performed on an archival FFPE tissue of human renal carcinoma. FFPE sections were boiled in a retrieval solution of Tris-HCl containing 2% SDS, followed by incubation. Fresh tissue taken from the same case of renal carcinoma was processed for extraction of proteins by a conventional method using radioimmunoprecipitation assay solution, to compare the efficiency of protein extraction from FFPE tissue sections with extraction from fresh tissue. As a control, further sections of the same FFPE sample were processed by the same procedure without heating treatment. Evaluation of the quality of protein extracted from FFPE tissue was done using gel electrophoresis and mass spectrometry, showing most identified proteins extracted from FFPE tissue sections were overlapped with those extracted from fresh tissue. Protein extraction from formalin-fixed, paraffin-embedded tissue sections: quality evaluation by mass spectrometry. SR Shi C Liu BM Balgley C Lee CR Taylor doi:10.1369/jhc.5B6851.2006 J Histochem Cytochem, Vol. 54, No. 6. (June 2006), pp. 739-743. 2007-08-26T13:37:12-00:00 2006 J Histochem Cytochem 0022-1554 54 6 739 743 ffpe http://www.citeulike.org/user/jyuh/article/935649 <i>J Histochem Cytochem, Vol. 54, No. 11. (November 2006), pp. 1229-1237.</i><br /><br />Microarrays have been used to simultaneously monitor the expression of thousands of genes from biological samples, an approach that can potentially uncover previously unrecognized functions of genes. Microarray analyses can rarely be conducted retrospectively because of the requirement for RNA to be obtained from fresh or unfixed frozen tissues. Archived pathology specimens would need to be used for retrospective analyses, and these are typically preserved as formalin-fixed, paraffin-embedded (FFPE) tissue. Formalin-fixed tissues have been shown to yield compromised RNA compared with that obtained from frozen tissue. To begin to assess the performance of RNA extracted from FFPE samples on a microarray format, we compared RNA from a model system of pelleted lipopolysaccharide-stimulated human bone marrow stromal cells that were snap frozen with RNA from FFPE cells. RNA integrity and Affymetrix quality control parameters were assessed, and differentially regulated genes were analyzed with Ingenuity Pathway Analysis software. Results demonstrate that both snap-frozen and FFPE samples yielded intact RNA suitable for amplification prior to Affymetrix GeneChip analysis. Although some transcriptional information was lost with RNA extracted from the FFPE samples, Ingenuity Pathway Analysis revealed that the major pathways identified as affected by drug treatment were similar. Results show that FFPE samples are amenable to Affymetrix GeneChip analysis, expanding the possibility for expression profiling on archived tissue blocks in pathology laboratories. Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. MS Scicchitano DA Dalmas MA Bertiaux SM Anderson LR Turner RA Thomas R Mirable RW Boyce doi:10.1369/jhc.6A6999.2006 J Histochem Cytochem, Vol. 54, No. 11. (November 2006), pp. 1229-1237. 2006-11-07T18:23:23-00:00 2006 J Histochem Cytochem 0022-1554 54 11 1229 1237 ffpe http://www.citeulike.org/user/jyuh/article/1462861 <i>J Proteome Res, Vol. 6, No. 4. (April 2007), pp. 1295-1305.</i><br /><br />Formalin fixation, generally followed by paraffin embedding, is the standard and well-established processing method employed by pathologist. This treatment conserves and stabilizes biopsy samples for years. Analysis of FFPE tissues from biopsy libraries has been, so far, a challenge for proteomics biomarker studies. Herein, we present two methods for the direct analysis of formalin-fixed, paraffin-embedded (FFPE) tissues by MALDI-MS. The first is based on the use of a reactive matrix, 2,4-dinitrophenylhydrazine, useful for FFPE tissues stored less than 1 year. The second approach is applicable for all FFPE tissues regardless of conservation time. The strategy is based on in situ enzymatic digestion of the tissue section after paraffin removal. In situ digestion can be performed on a specific area of the tissue as well as on a very small area (microdigestion). Combining automated microdigestion of a predefined tissue array with either in situ extraction prior to classical nanoLC/MS-MS analysis or automated microspotting of MALDI matrix according to the same array allows the identification of both proteins by nanoLC-nanoESI and MALDI imaging. When adjacent tissue sections are used, it is, thus, possible to correlate protein identification and molecular imaging. These combined approaches, along with FFPE tissue analysis provide access to massive amounts of archived samples in the clinical pathology setting. Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections. R Lemaire A Desmons JC Tabet R Day M Salzet I Fournier doi:10.1021/pr060549i J Proteome Res, Vol. 6, No. 4. (April 2007), pp. 1295-1305. 2007-07-17T15:45:26-00:00 2007 J Proteome Res 1535-3893 6 4 1295 1305 ffpe http://www.citeulike.org/user/jyuh/article/1104586 <i>Laboratory Investigation, Vol. aop, No. current.</i> RNA expression analysis of formalin-fixed paraffin-embedded tumors Shannon Penland Temitope Keku Chad Torrice Xiaping He Janakiraman Krishnamurthy Katherine Hoadley John Woosley Nancy Thomas Charles Perou Robert Sandler Norman Sharpless doi:10.1038/labinvest.3700529 Laboratory Investigation, Vol. aop, No. current. 2007-02-13T07:49:15-00:00 Laboratory Investigation 0023-6837 aop current Nature Publishing Group ffpe microarray http://www.citeulike.org/user/jyuh/article/1339234 <i>Laboratory Investigation, Vol. aop, No. current.</i> "Tissue surrogates" as a model for archival formalin-fixed paraffin-embedded tissues Carol Fowler Robert Cunningham Timothy O'Leary Jeffrey Mason doi:10.1038/labinvest.3700596 Laboratory Investigation, Vol. aop, No. current. 2007-05-28T20:22:08-00:00 Laboratory Investigation 0023-6837 aop current Nature Publishing Group ffpe