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Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

Journal article
Authors Toshima Z Parris
Elisabeth Werner Rönnerman
Hanna Engqvist
Jana Biermann
Katarina Truvé
Szilard Nemes
Eva Forssell-Aronsson
Giovanni Solinas
Anikó Kovács
Per Karlsson
Khalil Helou
Published in Oncotarget
Volume 9
Issue 35
Pages 24140-24154
ISSN 1949-2553
Publication year 2018
Published at Wallenberg Laboratory
Institute of Clinical Sciences, Department of Radiation Physics
Institute of Clinical Sciences, Department of Oncology
Core Facilities, Bioinformatics
Institute of Clinical Sciences, Department of Orthopaedics
Pages 24140-24154
Language en
Links dx.doi.org/10.18632/oncotarget.2532...
www.ncbi.nlm.nih.gov/entrez/query.f...
Subject categories Basic Medicine

Abstract

Genomic instability contributes to the neoplastic phenotype by deregulating key cancer-related genes, which in turn can have a detrimental effect on patient outcome. DNA amplification of the 8p11-p12 genomic region has clinical and biological implications in multiple malignancies, including breast carcinoma where the amplicon has been associated with tumor progression and poor prognosis. However, oncogenes driving increased cancer-related death and recurrent genetic features associated with the 8p11-p12 amplicon remain to be identified. In this study, DNA copy number and transcriptome profiling data for 229 primary invasive breast carcinomas (corresponding to 185 patients) were evaluated in conjunction with clinicopathological features to identify putative oncogenes in 8p11-p12 amplified samples. Illumina paired-end whole transcriptome sequencing and whole-genome SNP genotyping were subsequently performed on 23 samples showing high-level regional 8p11-p12 amplification to characterize recurrent genetic variants (SNPs and indels), expressed gene fusions, gene expression profiles and allelic imbalances. We now show previously undescribed chromothripsis-like patterns spanning the 8p11-p12 genomic region and allele-specific DNA amplification events. In addition, recurrent amplification-specific genetic features were identified, including genetic variants in the HIST1H1E and UQCRHL genes and fusion transcripts containing MALAT1 non-coding RNA, which is known to be a prognostic indicator for breast cancer and stimulated by estrogen. In summary, these findings highlight novel candidate targets for improved treatment of 8p11-p12 amplified breast carcinomas.

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