A multidisciplinary biospecimen bank of renal cell carcinomas compatible with discovery platforms at Mayo Clinic, Scottsdale, Arizona

Thai H. Ho, Rafael Nunez Nateras, Huihuang Yan, Jin Park, Sally Jensen, Chad Borges, Jeong Heon Lee, Mia D. Champion, Raoul Tibes, Alan H. Bryce, Estrella M. Carballido, Mark A. Todd, Richard W. Joseph, William W. Wong, Alexander S. Parker, Melissa L. Stanton, Erik P. Castle

Research output: Contribution to journalArticle

6 Citations (Scopus)

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 (bymass 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 frombanked 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.

Original languageEnglish (US)
Article numbere0132831
JournalPLoS One
Volume10
Issue number7
DOIs
StatePublished - Jul 16 2015

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kidney cells
Renal Cell Carcinoma
carcinoma
Cells
RNA
Genes
Atlases
Chromatin Immunoprecipitation
Chromatin
Genome
chromatin
Plasmas
genome
Workflow
Nucleic Acids
Albumins
nucleic acids
neoplasms
albumins
Tissue

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

A multidisciplinary biospecimen bank of renal cell carcinomas compatible with discovery platforms at Mayo Clinic, Scottsdale, Arizona. / Ho, Thai H.; Nateras, Rafael Nunez; Yan, Huihuang; Park, Jin; Jensen, Sally; Borges, Chad; Lee, Jeong Heon; Champion, Mia D.; Tibes, Raoul; Bryce, Alan H.; Carballido, Estrella M.; Todd, Mark A.; Joseph, Richard W.; Wong, William W.; Parker, Alexander S.; Stanton, Melissa L.; Castle, Erik P.

In: PLoS One, Vol. 10, No. 7, e0132831, 16.07.2015.

Research output: Contribution to journalArticle

Ho, TH, Nateras, RN, Yan, H, Park, J, 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 2015, 'A multidisciplinary biospecimen bank of renal cell carcinomas compatible with discovery platforms at Mayo Clinic, Scottsdale, Arizona', PLoS One, vol. 10, no. 7, e0132831. https://doi.org/10.1371/journal.pone.0132831
Ho, Thai H. ; Nateras, Rafael Nunez ; Yan, Huihuang ; Park, Jin ; Jensen, Sally ; Borges, Chad ; Lee, Jeong Heon ; Champion, Mia D. ; Tibes, Raoul ; Bryce, Alan H. ; Carballido, Estrella M. ; Todd, Mark A. ; Joseph, Richard W. ; Wong, William W. ; Parker, Alexander S. ; Stanton, Melissa L. ; Castle, Erik P. / A multidisciplinary biospecimen bank of renal cell carcinomas compatible with discovery platforms at Mayo Clinic, Scottsdale, Arizona. In: PLoS One. 2015 ; Vol. 10, No. 7.
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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 (bymass 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 frombanked 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.",
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AU - Jensen, Sally

AU - Borges, Chad

AU - Lee, Jeong Heon

AU - Champion, Mia D.

AU - Tibes, Raoul

AU - Bryce, Alan H.

AU - Carballido, Estrella M.

AU - Todd, Mark A.

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