Positive results from a pilot study that aimed to determine the feasibility of large-scale molecular screening, including targeted gene sequencing (TGS) to detect changes in tumour markers in patients with metastatic breast cancer, were presented at the IMPAKT Breast Cancer Conference held 7–9 May 2015 in Brussels, Belgium.
Marion Maetens, Breast Cancer Translational Research Laboratory, Institute Jules Bordet, Brussels, Belgium presented findings on behalf of the Breast International Group (BIG) on the AURORA molecular screening programme during a session on Mutations and Therapy Resistance: Impact of Mutations in the Clinic.
The molecular characterisation of tumours in breast cancer has mostly been done on primary lesions to determine the type of targeted therapy to use in the clinical setting. Growing awareness that metastasis brings with it an evolution of tumour markers and also that tumours become increasingly heterogeneous over time has made the molecular characterisation of tumours throughout the course of disease important to consistently deliver optimal treatment.
However, implementing a screening programme is a huge undertaking that would benefit from preliminary feasibility data and information on the variability of results among the various participating laboratories.
The author discussed findings from a pilot study that began prior to the launch of the AURORA Initiative in 2014, to investigate the feasibility in terms of logistics and timelines.
Secondary aims of the pilot study included comparing somatic mutation calls between two TGS platforms and somatic copy number aberrations (SCNA) calls obtained from TGS and single nucleotide polymorphism (SNP) oligonucleotide arrays.
This pilot study enrolled 41 patients from four European centres. In order to be included in the TGS platforms, patients were required to have at least one representative metastatic biopsy, availability of a whole blood sample, and less than 10% tumour cellularity (upon central pathological review).
Analysis of tumour and normal DNA was done by TGS of cancer-related genes using the Ion Torrent and Illumina platforms. SCNA calls obtained from normalised coverage of TGS data were compared to the output of the ASCAT algorithm on Affymetrix OncoScan formalin fixed paraffin embedded (FFPE) array data.
Most targeted gene sequencing results were obtained with good turnaround times
Biopsies were performed in 35 (85%) patients. The metastatic sites most often biopsied included the liver in 43% of patients, followed by the breast in 20% of cases. Biopsies were obtained less frequently from the lymph node and skin in 14% of patients each, the lung in 6%, and bone in 3% of patients. The tumour cellularity ranged from 10 to 85%.
TGS results were obtained for 26 (74%) of the 35 patients and were reported in a median turnaround time of 9 working days, within a range of 5 to 17 working days. Most frequently mutated genes were PIK3CA (50%), TP53 (27%), and ESR1 (15%).
Somatic mutations were called in exons covered at >100X based on a fixed threshold of 10% variant allele frequency in the cancer sample. The median number of mutations per patient identified from Ion Torrent was 7 (range: 0 to 29). Overall mutation detection rate was 69% and overall “actionable” mutation detection rate was 54%.
Concordance between Ion Torrent and Illumina among mutations for all common target regions was 83% and for clinically “actionable” mutations 100%. However, Ion Torrent has a higher rate of variant detection in term of higher coverage, false positives, and non-exhaustively.
Concordance analysis between Ion Torrent TGS and SNP arrays is ongoing. The investigators are focusing on ERBB2, FGFR1, FGFR2, CCND1, TP53, BRCA1, BRCA2, PTEN, PIK3CA, MAPK and other.
According to the authors, results from this pilot study show that conducting an international molecular screening programme for patients with metastatic breast cancer is feasible and can be carried out across Europe.
The investigators found that the mutation calls validation rate was acceptable. Overall, alteration detection rate was 96%. In general, Ion Torrent SNVs are reliable for clinically “actionable” mutations and manual curation is required for other mutations. CNA detection by TGS is challenging.
Based on these findings, BIG is proceeding with the AURORA initiative and is endeavouring to enroll 1300 patients with metastatic breast cancer from more than 80 centres throughout Europe.
92O The Breast International Group (BIG) AURORA pilot study for molecular screening in metastatic breast cancer (MBC) patients