Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer
Abstract
This project is designed to complement an ongoing a multi-institutional, NIH-funded study of genetic and epigenetic alterations of pre-invasive DCIS and no previous or concurrent invasive breast cancer (IBC) that either progressed to IBC (cases) or had no further breast cancer events (controls), with an in-depth analysis of expression data on the entire range of informative RNA categories, including mRNA, miRNA, and lnc RNA, as well as their splice variants. During the current reporting period, we have completed the accrual, initial characterization and processing of samples from 5 collaborating institutions. Among 229 patient tissues processed for the discovery phase, a total of 196 samples, 98 cases and controls, passed Q/C for both DNA and RNA extracts. All samples have undergone a comprehensive DNA methylome analysis using the Illumina 450K CpG arrays, with excellent call rates, the bioinformatics analysis is ongoing. Because of the high failure rate in generating high quality libraries for RNA Sequencing from our limited samples, we proceeded with a pilot study of the newly released Affymetrix HTA 2.0 arrays, with excellent results, and have begun our comprehensive transcriptome analysis using this platform. We have also initiated a collaboration with Dr. C. Perou at UNC to maximize the possibility of a successful RNA Sequencing effort.
Document Details
- Document Type
- Technical Report
- Publication Date
- Sep 01, 2015
- Accession Number
- AD1002597
Entities
People
- Christopher B Umbricht
Organizations
- Johns Hopkins University