Aims The aim of this study was to analyse a series of borderline and malignant phyllodes tumours (PTs) of the breast by whole-genome profiling to identify genomic markers that could help to recognise potentially malignant tumours within borderline tumours.
Methods We evaluated the genetic imbalances of a series of 53 PTs (30 borderline, 23 malignant) using the Human CNV370 BeadChip microarray (Illumina), containing 370 000 SNP markers and correlate this alterations with clinicopathological features.
Results Forty-five PTs (85%) showed chromosome copy number variations (CNVs). Twenty PTs (37%) showed five or more chromosomal imbalances (8/30 borderline (27%) and 12/23 malignant (52%)). The large-scale genetic changes associated with malignant were+7p (9/23), +1q (8/23), −10p (8/23), −13q14 (7/23), +8q (6/23) and +10q (6/23) and borderline were+1q (13/30), −13q14 (9/30), −6q (8/30) and −10p (8/30). Losses in 9p21.3, encompassing CDKN2A/B gene, were present in three tumours (malignant), whereas deletions of 13q, with a minimal region in 13q14.2 encompassing the RB1 gene, were found in 9/30 borderline and 7/28 malignant tumours. High-level amplifications were seen in eight tumours (seven malignant and one borderline): in 7p in three tumours (including EGFR in two), 7q31.2 (including TFEC and MET), 8q24.21 (including MYC) and 8q23.3 (including CSMD3) in one tumour each.
Conclusions Whole-genome profiling by SNP arrays in PTs leads to identify a high number of CNV, gains of 7p and 8q, losses of 13q and 10, losses in 9p21.3 (CDKN2A/B) and the presence of amplifications, especially involving EGFR, as markers of potentially malignant tumours.
- BREAST PATHOLOGY
- MOLECULAR PATHOLOGY
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This work has been presented at the 2015 American and Canadian Academy of Pathology (abstract, Laboratory Investigation (2015) 95, 30–75).
Handling editor Runjan Chetty
Contributors All contributors participated in the study and approved manuscript.
Competing interests None declared.
Patient consent Obtained.
Ethics approval Breast Cancer Study Group of Institut Curie.
Provenance and peer review Not commissioned; externally peer reviewed.