High-density SNP arrays improve detection of HER2 amplification and polyploidy in breast tumors

Abstract

BackgroundHuman epidermal growth factor receptor-2 (HER2) overexpression and gene amplification are currently established by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. This study investigates whether high-density single nucleotide polymorphism (SNP) arrays can provide additional diagnostic power to assess HER2 gene status.MethodsDNA from 65 breast tumor samples previously diagnosed by HER2 IHC and FISH analysis were blinded and examined for HER2 copy number variation employing SNP array analysis.ResultsSNP array analysis identified 24 (37%) samples with selective amplification or imbalance of the HER2 region in the q-arm of chromosome 17. In contrast, only 15 (23%) tumors were found to have HER2 amplification by IHC and FISH analysis. In total, there was a discrepancy in 19 (29%) samples between SNP array and IHC/FISH analysis. In 12 of these cases, the discrepancy towards FISH could be attributed to concomitant amplification or deletion of the centromeric region, which harbors the FISH reference probe sequence. In 3 tumors, repeated IHC/FISH analysis revealed that the original IHC/FISH analysis had failed to indicate the correct HER2 expression level. Finally, the SNP array analysis revealed that more than two thirds of the samples exhibited polyploidy that was unrecognized by conventional FISH.ConclusionsCollectively, the data show that determination of HER2 copy number variations by SNP array-based genomic segmentation analysis is an effective supplement to IHC/FISH HER2 analysis that, by providing additional diagnostic sensitivity and accuracy, may elect more women for targeted treatment with HER2 inhibitors.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-015-1035-1) contains supplementary material, which is available to authorized users.

CAncer bioMarker Prediction Pipeline (CAMPP) - A standardised and user-friendly framework for the analysis of quantitative biological data

“…The six genes returned as the most interconnected in this module, were strongly associated with Her2-enriched BC subtype. These genes included ERBB2 (HER2 itself), GRB7 (a Pam50 classifier gene) and MIEN1, CDK12, PGAP3 and TCAP, all of which are ERBB2 amplicon passenger genes (Cancer Genome Atlas, 2012;Hansen, et al, 2015;Plautz, et al, 2014). These results highlight the utility of the complementary R-frameworks implemented in the CAMPP wrapper.…”

Validation of HER2 status in whole genome sequencing data of breast cancers with AI-driven, ploidy-corrected approach

“…Last year, a continuation of the study exploited the borderline cases with excellent concordance [12]. Several other studies have also proven the clinical value of panel NGS for HER2 testing in breast cancer and other solid tumours, using the same strategy of fold change determination, using either Illumina [1–4] or Ion Torrent methodology [5].…”

“…However, changes in ploidy are seldom associated with overexpression of ERBB2 gene, as average global transcript levels remain unchanged. Secondly, the isolated deletion or duplication events of chromosome 17 may influence the ERBB2 transcription [4,5]. The gain of an additional copy of chromosome 17, called polysomy, is correlated with tumour ploidy and is considered its surrogate in the FISH test, but discrepancies between these parameters are in part the reason for inaccuracy in ERBB2 amplification detection [6].…”

Molecular subtyping of breast cancer improves identification of both high and low risk patients

“…Scoring of ER and Ki67 protein were semi quantitative with a positive cutoff point of >1% for ER positive tumor. Scoring of HER2 was performed as described by Hansen et al [32] following the national guidelines (www.dbcg.dk). Online available datasets for comparison of percentage of positive Ki67 protein-cells were downloaded from www.ebi.ac.uk/arrayexpress/ (accession numbers; E-GEOD-43358, -76040 and -76250).…”