The Breast Duct: Pilot Study of Genomic Sequencing of Exfoliated Ductal Cells Obtained Through Endoscopy and Lavage

The objective of this study is to determine whether we can use minimally invasive techniques to gain access to exfoliated ductal epithelial cells for whole genome sequencing. 1. To examine women with nipple aspiration, ductoscopy and ductal lavage and collect exfoliated cells from two ducts per woman. 2. To collect a blood sample at the time of the examination in order to obtain the woman's baseline genomic sequence. 3. De-identified samples will then have DNA and RNA extracted and whole genome sequencing and transcriptome analysis performed by Covance and Illumina. 4. Comparisons will be made within a breast (two ducts) and between the duct and blood as well as between women.

Despite the lack of anatomical clarity in the literature, Tibor Tot has postulated that breast cancer and DCIS are a lobar disease as the simultaneously or asynchronously appearing, often multiple in situ tumor foci are localized within a single "sick" lobe. This theory has some resonance in the molecular studies that have been done in the breast demonstrating that there are large "patches" of clonality even in normal breast tissue. Most of this work was based on microdissection, however, and assumes that adjacent duct profiles belong to the same lobe. In fact both Cooper and Going have shown intertwining of arborizing ducts from different independent lobes. This sets the stage for errors of interpretation in micro-dissected tissue. Ductal lavage allows the cannulation and lavage of individual ducts and collection of 1,000- over 10,000 exfoliated cells that can be studied for molecular and genetic changes. Ductoscopy adds the ability to confirm that the duct has not been perforated and to brush the lining of the duct to increase cell yield. Real-time ultrasound can be used to confirm the ductal anatomy. With the combination of these minimally invasive techniques it is now possible to collect the cells needed to apply new genetic techniques and investigate the genome of the ductal epithelial cell. While the methods for obtaining the ductal epithelial cells have been being developed similar advances have been made in whole genome sequencing technology. Knome®, a for-profit company, is now able to analyze ductal cells against blood to identify variants, including single nucleotide polymorphisms (SNP's), short and long insertions and deletions (indels), inversions, translocations, fusion genes and copy number variations (CNVs). Ingenuity Pathway Analysis can identify mRNA networks that can be driving pre-cancerous hyperplasia. Covance Genomics Laboratory (CAL) will perform DNA and RNA extraction, DNA QC and Next-Generation Sequencing on the Illumina platform. With the combination of these minimally invasive techniques and Next-Generation Sequencing we will be able to test our hypothesis that it is now possible to interrogate the genetic sequence of a single normal duct and to compare it to the sequence in the blood to identify early epithelial mutations. In addition by comparing the sequence of two ducts in one breast we can gain insight into whether each duct is clonal or the whole breast shares the same genetic pattern. And finally, understanding the pathways that are activated in pre-cancerous duct lesions can provide targets for intraductal treatment programs.