The coding exons, including approx. 20 bp of the flanking intronic regions, of the following genes were analysed by NGS (WES Library Prep: Gen® Exome Research Panel v2.0 (IDT)); sequenced with NovaSeq 6000 and S1 Reagent Kit (300 cycles) (Illumina Inc.), analysed with NxClinical software; approximately 95% of the tested exons had coverage of 100%: 30 or more reads): ACD, AKT1, APC, ATM, AXIN2, BAP1, BLM, BMPR1A, BRCA1, BRCA2, BRIP1, CASR, CDC73, CDH1, CDK4, CDKN1B, CDKN2A, CHEK2, CYLD, CTRC, DDB2, DICER1, DKC1, EPCAM, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FH, GALNT12, GREM1, HRAS, KIF1B, KIT, MAX, MC1R, MEN1, MITF, MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NF1, NTHL1, PALB2, PDGFRA, PMS1, PMS2, POLD1, POLE, POT1, PRKAR1A, PRSS1, PTCH1, PTEN, RAD51C, RAD51D, RB1, RECQL4, RET, RNF43, RPS20, SDHA, SDHAF2, SDHB, SDHC, SDHD, SLX4, SMAD4, SPINK1, SPRED1, STK11, SUFU, TERF2IP, TERT, TMEM127, TP53, TRIM37, TSC1, TSC2, VHL, WRN, XPA, XPC, XRCC2.

The samples were analysed with the Oncoscan FFPE Assay Kit (cat. 902695; Thermo Fisher Scientific) following the manufacturer’s instructions. The arrays were stained at the GeneChip Fluidics Station (Thermo Fisher Scientific) and scanned via a Gene Chip scanner (Thermo Fisher Scientific, Waltham, Massachusetts, United States). CEL files (Affymetrix DNA microarray image analysis software output) generated from the scanned array image were converted to Oncoscan array data (OSCHP files) and analysed via Chromosome Analysis Suite (ChAS) software (version 4.0; Thermo Fisher) with reference files NetAffxGenomicAnnotations.Homo_sapiens, hg19; NA33.r1. The copy number variation segments were evaluated manually in ChAS. The HRD score (nLST) was computed in R with the OncoscanR package [29].