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Cancer Diagnosis Program (CDP) — Biorepositories & Biospecimen Research Branch (BBRB) Cancer Diagnosis Program (CDP) Biorepositories & Biospecimen Research Branch (BBRB)
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Last Updated: 06/30/22

BPV Analytical Platforms

Highly annotated biospecimens were collected for the Biospecimen Pre-analytical Variables (BPV) program through an organized and well-controlled infrastructure of Biospecimen Source Sites (BSS). Various analytical platforms were used by BSS to determine pre-analytical variable effects on a wide range of studies including DNA methylation, copy number variation, genotyping, mRNA expression, miRNA expression and protein expression.

BSS receive in-person training on the proper use of standard operating procedures developed by NCI to ensure that uniform collection and handling procedures are used across all sites. All BPV biospecimens are collected using kits provided by the Comprehensive Biospecimen Resource (CBR), a centralized site that assembles collection and shipping kits, receives most biospecimens from the BSSs for processing and storage, and ships biospecimens from the BSSs to the processing and analysis facilities.

BSS use a web-based interface (the Comprehensive Data Resource- CDR) to enter data regarding collection, processing, and handling of donor biospecimens and clinical information as well as pathological evaluation of the tumor. Over 300 common data elements are collected in CDR for each case, which are reviewed by data quality managers. BPV specimens are tracked via specimen IDs and unique barcodes using the Laboratory Information Management System (LIMS).

Figure 1. Analysis, cancer type and platforms used in the BPV program

Study Cancer Type Platform and Analysis
DNA Methylation Kidney MethyLight- methylation-specific PCR amplification of methylation markers
Copy Number Variation Kidney Genome e-wide CNV evaluation by array-based genomic hybridization (aCGH)
Genotyping Kidney, Colon, Ovary Whole exome sequencing by NGS
RNA Expression Kidney, Colon, Ovary Transcriptome profiling by NGS
miRNA Expression Kidney, Ovary Human miRNA profiling by WaferGen SmartChip (Human miRNA Panel)
miRNA Expression Kidney Oncopanel evaluation by TaqMan Open Array
miRNA Expression Kidney Cold-ischemic biomarker expression by TaqMan
miRNA Expression Kidney, Colon, Ovary Expression biomarkers by RNA in-situ hybridization (RNAscope)
Protein Expression (Tissue) Kidney, Colon, Ovary Cancer specific biomarker expression by Immunohistochemistry (IHC) assay
Protein Expression (Tissue) Kidney, Colon, Ovary Total protein and phosphoprotein expression by MassSpec
Protein Expression (Plasma) Kidney, Colon, Ovary, Lung Targeted protein expression by multiplexed Multiple Reaction Monitoring (MRM) assay
Protein Expression (Plasma) Kidney, Colon, Ovary, Lung Cancer specific protein expression by Luminex assay (HumanMap)
Metabolite Profile (Plasma) Kidney, Colon, Ovary, Lung Global metabolite profiling by MassSpec

Biospecimen Pre-analytical Variables (BPV)