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We are analyzing https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-12-124.

Title:
Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues | BMC Cancer | Full Text
Description:
Background With over 20 million formalin-fixed, paraffin-embedded (FFPE) tissue samples archived each year in the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of cancer. Technologies have recently been introduced for whole-transcriptome amplification and microarray analysis of degraded mRNA fragments from FFPE samples, and studies of these platforms have only recently begun to enter the published literature. Results The Emerging Technologies for Translational Bioinformatics symposium on gene expression profiling for archival tissues featured presentations of two large-scale FFPE expression profiling studies (each involving over 1,000 samples), overviews of several smaller studies, and representatives from three leading companies in the field (Illumina, Affymetrix, and NuGEN). The meeting highlighted challenges in the analysis of expression data from archival tissues and strategies being developed to overcome them. In particular, speakers reported higher rates of clinical sample failure (from 10% to 70%) than are typical for fresh-frozen tissues, as well as more frequent probe failure for individual samples. The symposium program is available at http://www.hsph.harvard.edu/ffpe . Conclusions Multiple solutions now exist for whole-genome expression profiling of FFPE tissues, including both microarray- and sequencing-based platforms. Several studies have reported their successful application, but substantial challenges and risks still exist. Symposium speakers presented novel methodology for analysis of FFPE expression data and suggestions for improving data recovery and quality assessment in pre-analytical stages. Research presentations emphasized the need for careful study design, including the use of pilot studies, replication, and randomization of samples among batches, as well as careful attention to data quality control. Regardless of any limitations in quantitave transcriptomics for FFPE tissues, they are often the only biospecimens available for large patient populations with long-term history and clinical follow-up. Current challenges can be expected to remain as RNA sequencing matures, and they will thus motivate ongoing research efforts into noise reduction and identification of robust, translationally relevant biological signals in expression data from FFPE tissues.
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Keywords {🔍}

ffpe, expression, tissues, profiling, data, cancer, samples, studies, sample, analysis, gene, symposium, clinical, rna, article, bmc, study, quality, assay, archival, tissue, microarray, illumina, nugen, development, simpson, affymetrix, breast, published, amplification, presented, pilot, central, rnaseq, cookies, information, technologies, waldron, challenges, failure, control, large, planning, technical, williams, provided, panel, biostatistics, authors, privacy,

Topics {✒️}

springer nature author information authors ffpe tissue samples abbreviations ct giovanni parmigiani & curtis huttenhower tissue samples archived require additional planning long-term clinical follow dana-farber cancer institute clinical sample failure author correspondence state privacy rights enabled post-hoc identification pre-publication history tissue storage tissue type expression-based diagnostic assay accurate disease classification earliest rt-pcr studies sample failure frequent probe failure long-term health studies formalin-fixed paraffin-embedded gene expression profiling open access article ffpe expression profiles bmc cancer 12 activated b-cell information long-term history rights smaller-scale studies privacy choices/manage cookies ffpe expression studies poor sample quality authors scientific editing ffpe expression data ffpe expression profiling candidate gene panel wg-dasl® assay technologies enabling rna-seq housekeeping gene proved breast cancer res archival tissues remain sample characteristics introduced nugen sample preparation patient characterization center clinical ffpe tissues 800-gene panel assayed genome-dasl assay

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WebPage:
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         description:With over 20 million formalin-fixed, paraffin-embedded (FFPE) tissue samples archived each year in the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of cancer. Technologies have recently been introduced for whole-transcriptome amplification and microarray analysis of degraded mRNA fragments from FFPE samples, and studies of these platforms have only recently begun to enter the published literature. The Emerging Technologies for Translational Bioinformatics symposium on gene expression profiling for archival tissues featured presentations of two large-scale FFPE expression profiling studies (each involving over 1,000 samples), overviews of several smaller studies, and representatives from three leading companies in the field (Illumina, Affymetrix, and NuGEN). The meeting highlighted challenges in the analysis of expression data from archival tissues and strategies being developed to overcome them. In particular, speakers reported higher rates of clinical sample failure (from 10% to 70%) than are typical for fresh-frozen tissues, as well as more frequent probe failure for individual samples. The symposium program is available at http://www.hsph.harvard.edu/ffpe . Multiple solutions now exist for whole-genome expression profiling of FFPE tissues, including both microarray- and sequencing-based platforms. Several studies have reported their successful application, but substantial challenges and risks still exist. Symposium speakers presented novel methodology for analysis of FFPE expression data and suggestions for improving data recovery and quality assessment in pre-analytical stages. Research presentations emphasized the need for careful study design, including the use of pilot studies, replication, and randomization of samples among batches, as well as careful attention to data quality control. Regardless of any limitations in quantitave transcriptomics for FFPE tissues, they are often the only biospecimens available for large patient populations with long-term history and clinical follow-up. Current challenges can be expected to remain as RNA sequencing matures, and they will thus motivate ongoing research efforts into noise reduction and identification of robust, translationally relevant biological signals in expression data from FFPE tissues.
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      headline:Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues
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         Health Promotion and Disease Prevention
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