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Rare protein-truncating variants (PTVs) in  PALB2  confer increased risk to breast cancer, but relatively few studies have reported the characteristics of tumours with  PALB2  PTVs. In this study, we describe molecular characteristics of tumours with either germline or somatic alterations in  PALB2 . DNA from fresh frozen tumour tissues and matched peripheral blood lymphocytes for 560 breast cancer patients was subjected for whole-exome sequencing (WES), and RNA from tumour tissues was subjected to RNA sequencing (RNA-seq). We found six cases with germline and three with somatic protein-truncating variants in  PALB2 . The characteristics of tumours in patients with  PALB2  PTVs were similar to those with  BRCA1  and  BRCA2  PTVs, having significantly more somatic alterations, and a high proportion of the mutational signature and genomic scar scores characteristic of deficiencies in homologous recombination (HR), compared to tumours arising in non-carriers. Unlike tumours arising in patients with  BRCA1  and  BRCA2  PTVs,  PALB2  tumours did not have high prevalence of  TP53  somatic alterations or an enriched immune microenvironment. In summary,  PALB2  tumours show the homologous recombination deficiencies characteristic of  BRCA1  and  BRCA2  tumours, and highlight the potential clinical relevance of  PALB2  mutational status in guiding therapeutic choices.

Characterisation of PALB2 tumours through whole-exome and whole-transcriptomic analyses