Reliability and reproducibility of gene expression measurements using amplified RNA from laser-microdissected primary breast tissue with oligonucleotide arrays

Combined use of microdissection and high-density oligonucleotide arrays is a powerful technique to study in vivo gene expression. Because microdissection generally yields ng quantities of RNA, RNA amplification is necessary but affects array results. We tested the reliability and reproducibility of oligonucleotide array data obtained from small sample amplified RNA isolated from primary tissues via laser capture microdissection, to determine whether gene expression measurements obtained under these now customary conditions are reliable and reproducible enough to detect authentic expression differences between clinical samples. We performed eight U133A Affymetrix GeneChip oligonucleotide array hybridizations using RNA isolated from a single normal human breast specimen: two standard and six small samples prepared using independent microdissections, RNA isolations, and amplifications. We then performed six array hybridizations using RNA obtained similarly from paired normal epithelium and ductal carcinoma in situ from three independent breast specimens. We determined reliability by analysis of hybridization quality metrics, and reproducibility by analysis of the number of more than twofold changed genes, linear regression, and principal components analysis. All amplified RNA generated good quality hybridizations. From the initial specimen, correlations between replicates (r = 0.96 to 0.99) and between small samples (r = 0.94 to 0.98) were high, and between standard and small samples (r = 0.84) were moderate. in contrast, in the three normal cancer pairs, the differences in gene expression were large among the normal samples, the ductal carcinoma in situ samples, and between normal and ductal carcinoma in situ within each pair. These differences were a much larger source of variability than the technical variability introduced by the processes of laser capture microdissection, small sample amplification, and array hybridization. Nanogram quantities of RNA isolated from primary tissue using lasercapture microdissection generates reliable and reproducible gene expression measurements. These measurements do not mirror those obtained using micrograms of RNA. Biological variability in gene expression between independent specimens, and between histologically distinct samples within a specimen, is greater than the technical variability associated with the procedures. Future studies of in vivo gene expression using this approach will identify functionally important differences within or between specimens.