1145P Reliable detection of BRCA1 and BRCA2 large genomic rearrangements in FFPE tissue: A new diagnostic benchmark for somatic BRCA testing

Abstract

Methods: XmaI-RRBS dataset for 34 TNBC biopsies taken prior to NAC was used. Virtual amplicons were designed under the following criteria: at least two MSRE (BstHHI and/or HpaII) recognition sites within the amplicon, the amplicon length no more than 100 bp to provide high MSRE-qPCR efficiency, the average difference in the methylation level between adjacent CpG pairs no more than 10%. To select amplicons, MSRE sites were hierarchically clusterized with the distance metric of physical distance over the genome and the difference in their methylation level, followed by complete-linkage agglomeration to prevent lengthening of amplicons via chaining phenomenon. Diagnostic potential was assessed with cross-validated AUC. Markers with AUC 75% were selected to form panels.Results: Genes APCDD1L, RUSC1-AS1, MYO15B, EXOC2, THBS2, MXRA5, ANKRD64 were selected to form possible combinations of markers. Eventually, 120 combinations of amplicons panels that discriminate NAC response were obtained and top-10 are shown in the table.