Abstract 1833: Identification of abnormally expressed lincRNAs in breast cancer using high-density SNP arrays

Background: The intergenic portion of the human genome is pervasively transcribed to produce large numbers of long intergenic non-coding RNAs (lincRNAs), which are tentatively defined as RNA molecules of more than 200 nucleotides. LincRNAs participate in and regulate a wide array of transcriptional and posttranscriptional processes in both physiological and disease conditions. While dysregulation of lincRNAs expression has been observed in some cancers, their expression signatures in breast cancer are poorly characterized. Here, we established a novel genome-wide approach, employing high-density SNP arrays, to globally identify lincRNA genes whose expression is altered in breast cancers. Methods: Both genomic DNA (gDNA) and double-stranded cDNA (ds-cDNA) samples from primary breast tumor and matched adjacent normal cells were hybridized onto Illumina HumanOmni5 BeadChips. This platform includes a total of 2,435,915 SNP loci dispersed at an average interval of ∼700 nt through the intergenic region of the human genome. We mapped annotated lincRNA genes or the linc-transcriptome to a subset of 332,539 or 8,661 SNP loci, which were included in our analysis for five tumor-normal paired primary human mammary epithelial cells (HMECs). Using gDNA intensity signals as a reference, differential expression of lincRNAs between tumor and normal samples were obtained through normalization, filtering and statistical analysis using paired t-tests. Results: We found 47 lincRNA transcripts that were dysregulated in tumors (P