A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona

RESEARCH ARTICLE A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona Thai H. Ho1*, Rafael Nunez Nateras2, Huihuang Yan3, Jin G. Park4, Sally Jensen5, Chad Borges5, Jeong Heon Lee6, Mia D. Champion7, Raoul Tibes1, Alan H. Bryce1, Estrella M. Carballido1, Mark A. Todd8, Richard W. Joseph9, William W. Wong10, Alexander S. Parker11, Melissa L. Stanton12, Erik P. Castle2 OPEN ACCESS Citation: Ho TH, Nateras RN, Yan H, Park JG, Jensen S, Borges C, et al. (2015) A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona. PLoS ONE 10(7): e0132831. doi:10.1371/journal.pone.0132831 Editor: Xifeng Wu, MD Anderson Cancer Center, UNITED STATES Received: February 5, 2015 Accepted: June 19, 2015 Published: July 16, 2015 Copyright: © 2015 Ho et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: T.H.H. was supported by funding from the Mayo Clinic Center for Individualized Medicine Epigenomics Program; a K12 grant CA90628 from the National Institutes of Health; a Career Development Award from the Fraternal Order of Eagles; and a Kathryn H. and Roger Penske Career Development Award to Support Medical Research. H. Y., J.H.L., and M.D.C. were supported by funding from the Mayo Clinic Center for Individualized Medicine Epigenomics Program. The funders had no 1 Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America, 2 Department of Urology, Mayo Clinic Hospital, Phoenix, Arizona, United States of America, 3 Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America, 4 Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America, 5 Department of Chemistry & Biochemistry, The Biodesign Institute-Center for Personalized Diagnostics, Arizona State University, Tempe, Arizona, United States of America, 6 Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America, 7 Division of Biomedical Statistics and Informatics, Mayo Clinic, Scottsdale, Arizona, United States of America, 8 Division of Anatomic Pathology, Mayo Clinic, Scottsdale, Arizona, United States of America, 9 Division of Hematology and Oncology, Mayo Clinic, Jacksonville, Florida, United States of America, 10 Department of Radiation Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America, 11 Departments of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America, 12 Department of Laboratory Medicine/Pathology, Mayo Clinic, Scottsdale, Arizona, United States of America * Abstract 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 PLOS ONE | DOI:10.1371/journal.pone.0132831 July 16, 2015 1 / 20 Multidisciplinary Renal Cell Carcinomas Biobank role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. 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. Introduction To support medical research, institutional biobanking efforts have encompassed archived formalin-fixed, paraffin-embedded (FFPE) tissue blocks, frozen tissues, peripheral blood, questionnaires, and medical records [1–4]. Genitourinary diseases are heterogeneous and range from benign to malignant conditions [5,6]. The construction of a biobank encompassing both benign and malignant genitourinary diseases may yield clues regarding molecular progression of disease. In 2010, Mayo Clinic (Scottsdale, Arizona) initiated the Multidisciplinary Genitourinary Diseases Biospecimen Bank to prospectively collect biospecimens from patients with genitourinary diseases and to support health-related research. Herein, we report our experience with frozen banking protocols for renal cell carcinoma (RCC) biospecimens that are compatible with standard clinical practices. The Cancer Genome Atlas (TCGA) Research Network has analyzed the DNA, RNA, and protein from various human tumors to generate molecular profiles, identify recurrent molecular aberrations, and create public data portals to support medical research [7–11]. Currently, TCGA integrates data from DNA methylation at CpG islands, microarray-based measurement of copy number, whole-exome sequencing, RNA sequencing, and reverse-phase protein arrays. The development of next-generation DNA, RNA, chromatin immunoprecipitation (ChIP) sequencing, and high-throughput protein analyses provides an opportunity for institutions to characterize genomic, transcriptomic, and proteomic alterations. However, the application of established and emerging platforms for molecular (...truncated)