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Clin Cancer Res DOI:10.1158/1078-0432.CCR-12-1915

Expression profiling of archival tumors for long-term health studies.

Publication TypeJournal Article
Year of Publication2012
AuthorsWaldron, L, Ogino, S, Hoshida, Y, Shima, K, Reed, AEMcCart, Simpson, PT, Baba, Y, Nosho, K, Segata, N, Vargas, ACristina, Cummings, MC, Lakhani, SR, Kirkner, GJ, Giovannucci, E, Quackenbush, J, Golub, TR, Fuchs, CS, Parmigiani, G, Huttenhower, C
JournalClin Cancer Res
Date Published2012 Nov 15
KeywordsBreast Neoplasms, Colorectal Neoplasms, Female, Fixatives, Follow-Up Studies, Formaldehyde, Gene Expression Profiling, Humans, Oligonucleotide Array Sequence Analysis, Paraffin Embedding, Quality Control, Reference Values, Reproducibility of Results, RNA, Messenger, Tissue Fixation, Transcriptome

PURPOSE: More than 20 million archival tissue samples are stored annually in the United States as formalin-fixed, paraffin-embedded (FFPE) blocks, but RNA degradation during fixation and storage has prevented their use for transcriptional profiling. New and highly sensitive assays for whole-transcriptome microarray analysis of FFPE tissues are now available, but resulting data include noise and variability for which previous expression array methods are inadequate.

EXPERIMENTAL DESIGN: We present the two largest whole-genome expression studies from FFPE tissues to date, comprising 1,003 colorectal cancer (CRC) and 168 breast cancer samples, combined with a meta-analysis of 14 new and published FFPE microarray datasets. We develop and validate quality control (QC) methods through technical replication, independent samples, comparison to results from fresh-frozen tissue, and recovery of expected associations between gene expression and protein abundance.

RESULTS: Archival tissues from large, multicenter studies showed a much wider range of transcriptional data quality relative to smaller or frozen tissue studies and required stringent QC for subsequent analysis. We developed novel methods for such QC of archival tissue expression profiles based on sample dynamic range and per-study median profile. This enabled validated identification of gene signatures of microsatellite instability and additional features of CRC, and improved recovery of associations between gene expression and protein abundance of MLH1, FASN, CDX2, MGMT, and SIRT1 in CRC tumors.

CONCLUSIONS: These methods for large-scale QC of FFPE expression profiles enable study of the cancer transcriptome in relation to extensive clinicopathological information, tumor molecular biomarkers, and long-term lifestyle and outcome data.


Alternate JournalClin. Cancer Res.
PubMed ID23136189
PubMed Central IDPMC3500412
Grant ListP01 CA087969 / CA / NCI NIH HHS / United States
P01 CA055075 / CA / NCI NIH HHS / United States
R01 CA151993 / CA / NCI NIH HHS / United States
P01 CA55075 / CA / NCI NIH HHS / United States
U19 CA148065 / CA / NCI NIH HHS / United States
P50 CA127003 / CA / NCI NIH HHS / United States