Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays.

Author(s): Dobbin KK, Beer DG, Meyerson M, Yeatman TJ, Gerald WL, Jacobson JW, Conley B, Buetow KH, Heiskanen M, Simon RM, Minna JD, Girard L, Misek DE, Taylor JM, Hanash S, Naoki K, Hayes DN, Ladd-Acosta C, Enkemann SA, Viale A, Giordano TJ

Publication: Clin Cancer Res, 2005, Vol. 11, Page 565-72

PubMed ID: 15701842 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to assess sources of microarray variability among different biological specimens processed and analyzed at four independent laboratories according to standardized protocols. Surplus tissue from surgical resections were frozen before analysis and included primary lung squamous cell carcinoma (two cases), renal cell carcinoma (two cases), adrenal cortical adenoma, gastric adenocarcinoma, gastrointestincal stromal tumor, uterine leiomyoma, ovarian papillary serous adenocarcinoma, large cell lymphoma, a metastatic melanoma to the lymph node, and a normal liver specimen. DNA and RNA samples derived from these twelve tissues specimens were blinded prior to their distribution and analysis.

   Summary of Findings:

   Within-laboratory gene expression profiles exhibited very strong correlations (0.95-0.97) among tissue, cell pellet, and reference RNA specimens; between -laboratory correlations for specimen replicated were somewhat lower (0.93-0.96). Hierarchical cluster analysis revealed clustering by biospecimen type (frozen tissue, frozen cell pellet, RNA) and by tumor type. For frozen tumor sections, of the three sources of variation among gene expression profiles investigated, biological variation among specimens was the largest contributor followed by analytical error, with inter-laboratory variation having the smallest contribution.

   Biospecimens

   • Tissue - Lung
   • Tissue - Stomach
   • Tissue - Ovary
   • Tissue - Liver
   • Tissue - Lymph Node
   • Tissue - Uterus
   • Tissue - Adrenal Gland
   • Tissue - Kidney

   Preservative Types

   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma
   • Neoplastic - Lymphoma
   • Neoplastic - Melanoma
   • Normal

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Biospecimen location	Lung Adrenal gland Stomach Liver Kidney Lymph node Uterus Ovary

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