Germline mutations in ATM, CHEK2, and other known/potential breast cancer susceptibility genes among BRCA-negative Uruguayan patients with breast cancer.
Authors: Delgado Lucia Beatriz , Cayota Alfonso , Artagaveytia Nora , Silveyra Olivera Noelia , Ximenez Gulaute Sebastian Francisco , Manrique Gonzalo , Simoes Camila , Spangenberg Lucia , Naya Hugo , Sanguinetti Julia , Blanco Valentina , Camejo Natalia , Castillo Cecilia , Cataldi Sandra 
Published: June 2022

10596

Background: Breast cancer (BC) is the most frequent and the leading cause of death from cancer in Uruguayan women. In a previous study, we found BRCA1/2 germline mutations in less than 25% of the Uruguayan breast/ovarian cancer families studied. Due the impact and relevance of genetic testing in BC prevention and with the commitment to assure a wide accessibility, we developed genetic testing facilities at the University Hospital with the aim of analyzing and characterizing germline mutations in non BRCA known susceptibility and likely susceptibility genes. Methods: We studied 104 families who met the National Comprehensive Cancer Network (NCCN) criteria of hereditary BC. Analysis by next generation sequencing of BRCA1/2 genes revealed that 23 out of 104 cases studied (22%) carried pathogenic variants. Germline DNA from 42 cases BRCA negative was sequenced and analyzed for nine additional susceptibility genes (ATM, BARD1, CDH1, CHEK2, NBN, PALB2, PTEN, STK11 y TP53) included in a genetic panel. Also, in 24 cases negative for this panel we analyzed large deletions in BRCA1/2 by multiplex ligation-dependent probe amplification (MLPA) testing. In addition, to identify novel non-canonical causative genes, we extended our analysis to a complete exome sequencing of cases tested negative in genetic panels and MLPA analysis. Results: Among the 42 cases BRCA negative the sequencing of the extended genetic panel revealed 12 (28.8%) variants, 8 of uncertain significance (VUS) and 4 pathogenic, 2 novel (one in the ATM gene: NM_000051: c.614T > G and other in p53: NM_000546: c.245insT) and 2 previously reported (one in PALB2: NM_024675: c.2186insA and one in PALB2/1: NM_024675c.G7T genes). Regarding the VUS, it is worth highlighting the one found in exon 12 of CHEK2 (NM_007194: c.1333T > C) which was unusually frequent (16.7%) in our cohort when compared with public databases. Analysis of large deletions in BRCA1/2 in 24 cases without mutations in the genetic panel were negative for MLPA testing. Otherwise, complete exome sequencing of germline DNA from 22 cases negative for BRCA1/2 and for the genetic panel, revealed 18 variants, 16 that generate stop codons and 2 that generate loss of the termination codon (stoploss), suggesting a high potential for pathogenicity. Some striking examples are represented by the PSG2, CEP 135 y CEP 162, ZNF17 and ZNF260 genes. Conclusions: Of the 42 BRCA-negative cases, 4 (9.5%) carried a PV in a cancer susceptibility gene. The negative results obtained with MLPA in cases negative for BRCA and the extended genetic panel suggest that large deletions of BRCA are not a relevant cause of cancer susceptibility in this cohort. Otherwise, whole exome sequencing of 22 cases negatives for the previous genetic test showed pathogenic or probably PV in genes with no current evidence of association with breast and ovarian cancer.