ABSTRACT
Gene expression profiling using microarray platforms allows interrogation of expression levels of essentially all known genes in the tumor cells. Different microarray platforms use DNA probes of various lengths (ranging from 22-mer oligonucleotide in Affymetrix GeneChip, 60-mer oligonucleotides for Agilent arrays, and average 1 kilobase for cDNA arrrays) representing different positions in each gene between the arrays. Sensitivity and dynamic range for measuring a specific gene could be widely different among different array platforms. Preoperative systemic therapy trials provide unique opportunities to assess sensitivity of tumor cells to systemic therapy in vivo while treatment is ongoing. Numerous studies have demonstrated the correlation of subsequent polymerase chain reaction (pCR) and long-term outcome in breast cancer patients, potentially eliminating the need for long-term followup. Despite the fact that gene expression data alone have not been shown to be able to predict pCR with high accuracy, gene expression profiling can be still important in patients treated with neoadjuvant chemotherapy.
