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The NCI Biospecimen Research Network
Author(s) -
Gillespie John,
Moore Helen,
Dang Hien,
Player Audrey,
Wang Yonghong,
David Kerstin,
Spangenberg Joerg,
Vaught Jim,
Schneider Julie,
Erickson Heidi,
Barker Anna,
Compton Carolyn
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.5.a388-a
Subject(s) - rna , gene expression , housekeeping gene , gene , real time polymerase chain reaction , biology , microbiology and biotechnology , computational biology , biochemistry
Since access to high‐quality human biospecimens is a critical resource to support genomic‐ and proteomic‐base studies, the NCI established the Office of Biorepositories and Biospecimen Research (OBBR) to coordinate biospecimen research‐related policies and practices. The NCI Biospecimen Research Network (BRN) of the OBBR is conducting bimolecular studies for the development of data‐driven, evidence‐based protocols for various specimen types and molecular analysis platforms. Two current projects examine the effects of pre‐analytical variables on downstream gene expression. The first project examines the effect of intra‐operative ischemic times from 20 to 50 minutes on gene expression profiles in colon cancer tissues. Tissue samples were microdissected, RNA purified, and quantity/quality determined. After RNA amplification and labeling, differential gene expression for ischemia were determined using Affymetrix Human Genome U133 GeneChips. Genes differentially expressed will be validated using quantitative RT‐PCR. The second project compares histology and recovery of RNA for frozen, FineFix‐fixed, paraffin‐embedded (FiFPE), ethanol‐fixed, paraffin‐embedded (EFPE), and formalin‐fixed, paraffin‐embedded (FFPE) kidney and prostate tissue. Histological quality is comparable for FiFPE, EFPE, and FFPE tissue and is superior to frozen tissue. By RT‐PCR for beta actin, RNA recovery is comparable for frozen and FiPE and are both superior to EFPE and FFPE. RNA recovery will be further assessed by qRT‐PCR for cyclophilin A, beta actin, HPRT, and GAPDH.