In April 2014, OncoDNA, a clinical NGS provider affiliated with the Institute of Pathology and Genetics in Gosselies, Belgium, announced that it was providing targeted sequencing of metastatic breast cancer patients for a large international effort called AURORA, led by the Breast International Group, a non-profit organisation that facilitates breast cancer research.
As the testing provider for AURORA: Aiming to Understand the Molecular Aberrations in Metastatic Breast Cancer, which was funded by grants from the Breast Cancer Research Foundation, the Luxembourg Cancer Foundation, Belgium’s national lottery, and individual donors, OncoDNA was dedicated to analysing samples from around 1,300 patients with metastatic breast cancer using its OncoDEEP Clinical Plus test.
The first results from the AURORA study have now been published in Nature Breast Cancer, including the chief technology officer from OncoDNA as an author. While they show that profiling is feasible in a large international study, the data from the first 41 patients enrolled highlight some serious concerns.
Sequencing results were only obtained in 63% of patients, and at least one actionable mutation was found in 73% of those (or 46% of the enrolled population).
In comparing the OncoDEEP Ion Torrent results to those from the Illumina platform, there was only a 66% concordance of substitution calls per patient and a 59% concordance between their copy number aberrations and the benchmark of single nucleotide polymorphism arrays. The Illumina NGS platform outperformed the Ion Torrent technology when compared to the same SNP arrays.
The authors of the paper found these results somewhat sobering. While the higher background error rate of the Ion Torrent NGS technology could be a contributing factor, further investigation is warranted of this NGS platform and the accompanying circulating tumour DNA test.
Given the poor agreement with solid benchmarks, the authors agreed that the results presented do not support, at least for now, the use of the Ion Torrent NGS platform in a clinical setting.
The Caris 592-gene NGS offering uses a hybrid-capture based Illumina NGS platform to provide full exon coverage to an average depth of >750x. Our platform has been fully validated by NYSDOH for all 592 genes and our MSI test, which is the highest quality standard available.
- Maetens M, Brown D, Irrthum A, et al. The AURORA pilot study for molecular screening of patients with advanced breast cancer–a study of the breast international group. NPJ Breast Cancer. 2017;3:23.