title: Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays.
abstract: We recently developed a sensitive and flexible gene expression profiling system that is not dependent on an intact poly-A tail and showed that it could be used to analyze degraded RNA samples. We hypothesized that the DASL (cDNA-mediated annealing, selection, extension and ligation) assay might be suitable for the analysis of formalin-fixed, paraffin-embedded tissues, an important source of archival tissue material. We now show that, using the DASL assay system, highly reproducible tissue- and cancer-specific gene expression profiles can be obtained with as little as 50 ng of total RNA isolated from formalin-fixed tissues that had been stored from 1 to over 10 years. Further, tissue- and cancer-specific markers derived from previous genome-wide expression profiling studies of fresh-frozen samples were validated in the formalin-fixed samples. The DASL assay system should prove useful for high-throughput expression profiling of archived clinical samples.
authors.affiliation: Genetic Analysis, Illumina, Inc., 9885 Towne Center Drive, San Diego, CA 92121, USA.
authors.forename: Marina
authors.initials: M
authors.lastname: Bibikova
authors.forename: Dimitri
authors.initials: D
authors.lastname: Talantov
authors.forename: Eugene
authors.initials: E
authors.lastname: Chudin
authors.forename: Joanne M
authors.initials: JM
authors.lastname: Yeakley
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.forename: Dennis
authors.initials: D
authors.lastname: Doucet
authors.forename: Eliza
authors.initials: E
authors.lastname: Wickham
authors.forename: David
authors.initials: D
authors.lastname: Atkins
authors.forename: David
authors.initials: D
authors.lastname: Barker
authors.forename: Mark
authors.initials: M
authors.lastname: Chee
authors.forename: Yixin
authors.initials: Y
authors.lastname: Wang
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
mesh_terms: D000465:Algorithms; D001940:Breast / Q000473:pathology; D001943:Breast Neoplasms / Q000473:pathology; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D003106:Colon / Q000473:pathology; D003110:Colonic Neoplasms / Q000473:pathology; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000378:metabolism; D005557:Formaldehyde / Q000494:pharmacology; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D005557:Formaldehyde; D012313:RNA; D012343:RNA, Transfer