title: A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona.
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 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.
authors.affiliation: Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Thai H
authors.initials: TH
authors.lastname: Ho
authors.affiliation: Department of Urology, Mayo Clinic Hospital, Phoenix, Arizona, United States of America.
authors.forename: Rafael Nunez
authors.initials: RN
authors.lastname: Nateras
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Huihuang
authors.initials: H
authors.lastname: Yan
authors.affiliation: Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Jin G
authors.initials: JG
authors.lastname: Park
authors.affiliation: Department of Chemistry & Biochemistry, The Biodesign Institute-Center for Personalized Diagnostics, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Sally
authors.initials: S
authors.lastname: Jensen
authors.affiliation: Department of Chemistry & Biochemistry, The Biodesign Institute-Center for Personalized Diagnostics, Arizona State University, Tempe, Arizona, United States of America.
authors.forename: Chad
authors.initials: C
authors.lastname: Borges
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America.
authors.forename: Jeong Heon
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Mia D
authors.initials: MD
authors.lastname: Champion
authors.affiliation: Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Raoul
authors.initials: R
authors.lastname: Tibes
authors.affiliation: Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Bryce
authors.affiliation: Division of Hematology and Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Estrella M
authors.initials: EM
authors.lastname: Carballido
authors.affiliation: Division of Anatomic Pathology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Todd
authors.affiliation: Division of Hematology and Oncology, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Richard W
authors.initials: RW
authors.lastname: Joseph
authors.affiliation: Department of Radiation Oncology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: William W
authors.initials: WW
authors.lastname: Wong
authors.affiliation: Departments of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, United States of America.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Parker
authors.affiliation: Department of Laboratory Medicine/Pathology, Mayo Clinic, Scottsdale, Arizona, United States of America.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Stanton
authors.affiliation: Department of Urology, Mayo Clinic Hospital, Phoenix, Arizona, United States of America.
authors.forename: Erik P
authors.initials: EP
authors.lastname: Castle
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001130:Arizona; D018070:Biological Specimen Banks / Q000458:organization & administration*; D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000378:metabolism / Q000473:pathology / Q000601:surgery; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D015723:Gene Library; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology / Q000601:surgery; D008297:Male; D008745:Methylation; D008875:Middle Aged; D010084:Oxidation-Reduction; D011786:Quality Control; D012334:RNA, Neoplasm / Q000737:chemistry / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012709:Serum Albumin / Q000737:chemistry
chemical_list: D006657:Histones; D012334:RNA, Neoplasm; D012709:Serum Albumin