Abstract 3183: Breast Cancer MethylSeq: Analysis of bisulfite converted breast cancer genomes using microdroplet-based targeted sequencing

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Targeted sequencing using microdroplet-based PCR provides a method to selectively and uniformly amplify thousands of genomic regions of interest (ROIs) for efficient next generation sequencing (NGS). Recently, this approach has been adapted for the analysis of bisulfite-treated DNA, enabling strand-specific determination of cytosine methylation status with single-base pair resolution. This droplet PCR-based targeted approach significantly reduces cost and improves sequencing depth compared to whole-genome sequencing, allowing researchers to power larger studies to discover and validate how methylation and genomic aberrations affect cancer development. Here we report results from our ongoing work using a breast cancer targeted panel (Breast Cancer MethylSeq Panel) for sequence specific analysis of both epigenomic methylation and genomic mutation in breast tumor samples. The panel includes PCR primer pairs designed to target ∼2,700 ROIs, leaving room for an additional 1,300 target ROIs of interest to be added by individual researchers. Use of this single panel will provide information about CpG methylation and genomic sequence enabling analysis of multiple content types including: A) cell subtype; B) genomic mutation; C) surrogate gene expression subtypes using promoter CpG islands or other methylation markers; D) copy-number variation (CNV); E) Loss of Heterozygosity (LOH); F) methylation-mediated gene silencing and loss of imprinting. The Breast Cancer MethylSeq microdroplet library, comprising individual primer pairs for PCR in droplets, will be tested and validated using a set of 64 bisulfite-converted samples including 8 breast cancer cell lines, a range of ER positive and negative tumors and TCGA samples, and a set of 8 metastatic tumors from a single individual. We will report overall sequencing success metrics, as well as concordance with metadata on the various ROI classes (A-F above). The deep and comprehensive breast tumor sequencing enabled by this targeting panel will allow researchers to identify epigenomic alterations and genomic mutations across a range of assay types using just one assay. The goal for development and validation of this panel is to provide the breast cancer research community a unique tool for identifying and correlating cancer subtypes with clinical outcomes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3183. doi:1538-7445.AM2012-3183