Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages.

Xiaoyang Ruan,Jean-Pierre A Kocher,Lisa Boardman,Hongfang Liu,Amanda Ewart Toland

doi:10.1371/journal.pone.0095783

Abstract

Studies have shown concurrent loss of heterozygosity (LOH) in breast infiltrating ductal carcinoma (IDC) and adjacent or distant normal tissue. However, the overall extent of LOH in normal tissue and their significance to tumorigenesis remain unknown, as existing studies are largely based on selected microsatellite markers. Here we present the first autosome-wide study of LOH in IDC and distant normal tissue using informative loci deduced from SNP array-based and sequencing-based techniques. We show a consistently high LOH concurrence rate in IDC (mean = 24%) and distant normal tissue (m = 54%), suggesting for most patients (31/33) histologically normal tissue contains genomic instability that can be a potential marker of increased IDC risk. Concurrent LOH is more frequent in fragile site related genes like WWOX (9/31), NTRK2 (10/31), and FHIT (7/31) than traditional genetic markers like BRCA1 (0/23), BRCA2 (2/29) and TP53 (1/13). Analysis at arm level shows distant normal tissue has low level but non-random enrichment of LOH (topped by 8p and 16q) significantly correlated with matched IDC (Pearson r = 0.66, p = 3.5E-6) (topped by 8p, 11q, 13q, 16q, 17p, and 17q). The arm-specific LOH enrichment was independently observed in tumor samples from 548 IDC patients when stratified by tumor size based T stages. Fine LOH structure from sequencing data indicates LOH in low order tissues non-randomly overlap (∼67%) with LOH that usually has longer tract length (the length of genomic region affected by LOH) in high order tissues. The consistent observations from multiple datasets suggest progressive LOH in the development of IDC potentially through arm-specific pile up effect with discernible signature in normal tissue. Our finding also suggests that LOH detected in IDC by comparing to paired adjacent or distant normal tissue are more likely underestimated.

Highlights

Loss of heterozygosity (LOH) has been shown to be an important genetic event in most types of cancer, and used to infer the genomic location of cancer-related genes [1,2]
Using informative loci deduced from SNP array-based technique, analysis shows at autosome level non-random LOH concurrence in infiltrating ductal carcinoma (IDC) and distant normal tissue
The observation is in line with previous finding of LOH in IDC adjacent and distant normal tissue [9,11], indicating histologically normal tissues at a distance from IDC foci are genetically abnormal

Summary

Introduction

Loss of heterozygosity (LOH) has been shown to be an important genetic event in most types of cancer, and used to infer the genomic location of cancer-related genes [1,2]. Cavalli L. et al [9] detected LOH at BRCA1 locus in both IDC and adjacent normal tissue by comparing to peripheral blood in informative patients (i.e. heterozygote in blood) through microsatellite markers. Reis-Filho JS et al [4] reviewed several independent studies that reported LOH in normal tissue from breast cancer patients. It can be implied from the existing studies that detecting LOH in breast malignant or pre-malignant lesion by comparing to the allelic status in adjacent or even distant normal tissue may underestimate the amount of LOH since LOH may already be present in the normal tissue. There is still a lack of high-resolution view of the extent and frequency of LOH in normal breast tissues from IDC patients and how they might be related to tumorigenesis

Methods

Results

Conclusion