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10.1371/journal.pone.0132831 http://scihub22266oqcxt.onion/10.1371/journal.pone.0132831 C4504486!4504486 !26181416     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=26181416 &cmd=llinks): Failed to open stream: HTTP request failed! 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A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona |pdf=|usr=}}{{26181416 }} gab.com Text A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona JO: PLoS One http://www.kidney.de/pget.php?&tw=1&pmid=26181416 #FOAvip To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes and nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms, by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25 °C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91% to 95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing; after genome alignment, only 0.2% to 0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line that was prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between Mayo Clinic vs TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes. Twit Text FOAVip A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona ????PLoS One http://www.kidney.de/pget.php?&tw=1&pmid=26181416 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=26181416 #FOAvip English Wikipedia <ref>{{Cite pmid|26181416 }}</ref> A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona #MMPMID26181416 Ho TH ; Nateras RN ; Yan H ; Park JG ; Jensen S ; Borges C ; Lee JH ; Champion MD ; Tibes R ; Bryce AH ; Carballido EM ; Todd MA ; Joseph RW ; Wong WW ; Parker AS ; Stanton ML ; Castle EP PLoS One 2015[]; 10 (7 ): e0132831 PMID26181416 show ga To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes and nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms, by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25 °C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91% to 95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing; after genome alignment, only 0.2% to 0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line that was prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between Mayo Clinic vs TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes. |*Gene Expression Regulation, Neoplastic [MESH] |Adult [MESH] |Aged [MESH] |Aged, 80 and over [MESH] |Arizona [MESH] |Biological Specimen Banks/*organization & administration [MESH] |Carcinoma, Renal Cell/*genetics/metabolism/pathology/surgery [MESH] |Cell Line, Tumor [MESH] |Chromatin Immunoprecipitation [MESH] |Female [MESH] |Gene Library [MESH] |Histones/*genetics/metabolism [MESH] |Humans [MESH] |Kidney Neoplasms/*genetics/metabolism/pathology/surgery [MESH] |Male [MESH] |Methylation [MESH] |Middle Aged [MESH] |Oxidation-Reduction [MESH] |Quality Control [MESH] |RNA, Neoplasm/chemistry/*genetics [MESH] |Sequence Analysis, DNA [MESH] |Sequence Analysis, RNA [MESH]A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatib(epmc).pdf DeepDyve Pubget Overpricing