Abstract
Over the last few years the increasing usage of “-omic” platforms, supported by next-generation sequencing, in the analysis of breast cancer samples has tremendously advanced our understanding of the disease. New driver and passenger mutations, rare chromosomal rearrangements and other genomic aberrations identified by whole genome and exome sequencing are providing missing pieces of the genomic architecture of breast cancer. High resolution maps of breast cancer methylomes and sequencing of the miRNA microworld are beginning to paint the epigenomic landscape of the disease. Transcriptomic profiling is giving us a glimpse into the gene regulatory networks that govern the fate of the breast cancer cell. At the same time, integrative analysis of sequencing data confirms an extensive intertumor and intratumor heterogeneity and plasticity in breast cancer arguing for a new approach to the problem. In this review, we report on the latest findings on the molecular characterization of breast cancer using NGS technologies, and we discuss their potential implications for the improvement of existing therapies.
Highlights
Next-generation sequencing (NGS) has opened up new avenues to understanding and battling cancer through the detailed characterization of the cancer genome and epigenome
The reasoning behind this association is that each mutational process leaves a signature on the cancer genome that is a specific combination of mutation types, which is defined by the mechanisms of DNA damage and repair involved
Triple-negative breast cancers (TNBCs) were most distinct from other tumor subtypes due to up-regulation of the mir-17-92 cluster [65], and this finding was confirmed by a later study that reported miRNA expression data from 24 triple-negative breast cancers and 14 adjacent normal tissues [67]
Summary
Next-generation sequencing (NGS) has opened up new avenues to understanding and battling cancer through the detailed characterization of the cancer genome and epigenome. Optimal exploitation of all these data through integrated analyses will lead to a comprehensive understanding of the genetic events that lie at the basis of tumor development and evolution, offering new options for cancer diagnosis and treatment. The breast cancer biomedical research community has benefited from the application of NGS in the study of this extremely heterogeneous and complex disease. Large-scale initiatives examining hundreds of patients have led to the discovery of new breast cancer-associated genes, the dissection of the heterogeneity of individual tumors and the unraveling of the mutational processes involved. We overview some of the most recent comprehensive genome-wide breast cancer studies and discuss the contribution of NGS in investigating breast cancer biology and therapeutics
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