Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer
Abstract
This project is designed to complement a multi-institutional, NIH-funded study of genetic and epigenetic alterations of pre-invasive DCIS that did or did not progress to invasive breast cancer, with an in-depth analysis of expression data on the entire range of informative RNA categories. During the current reporting period, we have completed an Affymetrix HTA 2.0 array-based comprehensive transcriptome assay of samples from 5 collaborating institutions. A gene set enrichment analysis of differentially expressed genes identified statistically significant enrichment of gene sets in both progressive and nn-progressive DCIS, including immune-related pathways that may be involved in disease progression. All samples have also undergone a comprehensive DNA methylome analysis using the Illumina 450K CpG arrays, that was successfully used to develop DNA copy number variation (CNV) data on the same cohort. The CNV analysis suggests that Ch8q may harbor a protective genetic marker for DCIS progression, and that chr13 and chr18 deletions were more prevalent in non-progressive CIS. We have also continued our collaboration with Dr. C. Perou at UNC to maximize the possibility of a successful RNA sequencing effort, and have obtained encouraging results using the new Illumina TruSeq RNA Access Library Preparation kit followed by RNA sequencing performed using the Illumina HiSeq 2500.
Document Details
- Document Type
- Technical Report
- Publication Date
- Sep 01, 2016
- Accession Number
- AD1032877
Entities
People
- Christopher B Umbricht
Organizations
- Johns Hopkins University