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

Oncotarget
T Z ParrisK Helou

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 amp...Continue Reading

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Citations

Jul 29, 2020·Cancer Reports·Toshima Z ParrisKeiko Funa
May 28, 2019·BMC Cancer·Alexandria C RutkovskyStephen P Ethier
Nov 4, 2020·Neoplasia : an International Journal for Oncology Research·Sebastien Taurin, Haifa Alkhalifa
Nov 10, 2020·Life Sciences·Ioannis A Voutsadakis

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Datasets Mentioned

BETA
GSE17072
GSE97293

Methods Mentioned

BETA
genotyping
RNA-seq
Exome Sequencing

Software Mentioned

Cufflinks
Circos
DNAcopy
ASCAT
TrimGalore
FusionCatcher
Qual By
STAR
SplitNCigarReads
BEDTools BAMTOFASTQ

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