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This recurrent alteration event has been validated using fluorescence in situ hybridization in an independent set of OPLs.
A new finding was frequent chromosomal losses in RNO5q32 (in 20/28 of tumors, 71%), which represented the second most recurrent alteration observed in the present work.
On the contrary, the mutation c.5763dupT, the only recurrent alteration of the BRCA2 gene identified in our study, was not found in Moravia.
As shown in Table 4, deletion in the locus encompassing SEC11L3 (18q21.32) was observed to be the most recurrent alteration (13 out of 19 samples; 68%).
The novel c.5763dupT mutation, which appeared in two unrelated families, was the only recurrent alteration of the BRCA2 gene identified in this study.
A recurrent alteration was considered when two samples with CHD harbored the same aberration (hyper- or hypo-methylation) at the same CpG.
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To focus on minimally recurrent alterations, we also only included genes that were altered in two or more of the final 84 cases.
This approach revealed that the metastatic transition is accompanied by massive and recurrent alterations in enhancer activity.
The boundaries of amplicons/deletions did not correspond to known germline CNVs (reported in the Database of Genomic Variants), and, for the subset of recurrent alterations, finding distinct boundaries in different cell lines was more consistent with somatic alteration.
While some potential driver genes could be rapidly identified from this data due to their location on focal alterations, the majority of recurrent alterations are large and encompass numerous genes.
The results obtained from pathway-based analysis of the same data set produce a striking improvement and suggest that pathways may represent a better way to evaluate recurrent alterations.
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