Accurate tumor purity determination is critical for the analysis of homologous recombination deficiency (HRD)

Michael Menzel; Volker Endris; Constantin Schwab; Klaus Kluck; Olaf Neumann; Susanne Beck; Markus Ball; Christian Schaaf; Stefan Fröhling; Peter Lichtner; Peter Schirmacher; Daniel Kazdal; Albrecht Stenzinger; Jan Budczies

doi:10.1016/j.tranon.2023.101706

Accurate tumor purity determination is critical for the analysis of homologous recombination deficiency (HRD)

Transl Oncol. 2023 Sep:35:101706. doi: 10.1016/j.tranon.2023.101706. Epub 2023 Jun 14.

Authors

Affiliations

¹ Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany; Center for Personalized Medicine (ZPM) Heidelberg, Heidelberg 69120, Germany.
² Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
³ Center for Personalized Medicine (ZPM) Heidelberg, Heidelberg 69120, Germany; Institute of Human Genetics, Heidelberg University Hospital, Heidelberg 69120, Germany.
⁴ Center for Personalized Medicine (ZPM) Heidelberg, Heidelberg 69120, Germany; German Cancer Consortium (DKTK), Heidelberg 69120, Germany; Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg 69120, Germany; NCT Molecular Diagnostics Program, NCT Heidelberg and DKFZ, Heidelberg 69120, Germany.
⁵ Core Facility Genomics, Helmholtz Zentrum München, Neuherberg 85764, Germany.
⁶ Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany; Center for Personalized Medicine (ZPM) Heidelberg, Heidelberg 69120, Germany; German Cancer Consortium (DKTK), Heidelberg 69120, Germany.
⁷ Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany; German Center for Lung Research (DZL), Heidelberg site, Heidelberg 69120, Germany.
⁸ Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany; Center for Personalized Medicine (ZPM) Heidelberg, Heidelberg 69120, Germany; German Cancer Consortium (DKTK), Heidelberg 69120, Germany; German Center for Lung Research (DZL), Heidelberg site, Heidelberg 69120, Germany. Electronic address: [email protected].
⁹ Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany; Center for Personalized Medicine (ZPM) Heidelberg, Heidelberg 69120, Germany; German Cancer Consortium (DKTK), Heidelberg 69120, Germany; German Center for Lung Research (DZL), Heidelberg site, Heidelberg 69120, Germany. Electronic address: [email protected].

Abstract

Homologous recombination deficiency (HRD) is a predictive marker for response to poly (ADP-ribose) polymerase inhibitors (PARPi) in ovarian carcinoma. HRD scores have entered routine diagnostics, but the influence of algorithms, parameters and confounders has not been analyzed comprehensively. A series of 100 poorly differentiated ovarian carcinoma samples was analyzed using whole exome sequencing (WES) and genotyping. Tumor purity was determined using conventional pathology, digital pathology, and two bioinformatic methods. HRD scores were calculated from copy number profiles determined by Sequenza and by Sclust either with or without fixed tumor purity. Tumor purity determination by digital pathology combined with a tumory purity informed variant of Sequenza served as reference method for HRD scoring. Seven tumors had deleterious mutations in BRCA1/2, 12 tumors had deleterious mutations in other homologous recombination repair (HRR) genes, 18 tumors had variants of unknown significance (VUS) in BRCA1/2 or other HRR genes, while the remaining 63 tumors had no relevant alterations. Using the reference method for HRD scoring, 68 tumors were HRD-positive. HRDsum determined by WES correlated strongly with HRDsum determined by single nucleotide polymorphism (SNP) arrays (R = 0.85). Conventional pathology systematically overestimated tumor purity by 8% compared to digital pathology. All investigated methods agreed on classifying the deleterious BRCA1/2-mutated tumors as HRD-positive, but discrepancies were observed for some of the remaining tumors. Discordant HRD classification of 11% of the tumors was observed comparing the tumor purity uninformed default of Sequenza and the reference method. In conclusion, tumor purity is a critical factor for the determination of HRD scores. Assistance by digital pathology helps to improve accuracy and imprecision of its estimation.

Keywords: HRD; Homologous recombination deficiency; Tumor cell content; Tumor purity; WES; Whole exome sequencing.