Patterns of genomic instability in > 2000 patients with ovarian cancer across six clinical trials evaluating olaparib
Authors: Barnicle Alan , Ray-Coquard Isabelle , Rouleau Etienne , Cadoo Karen , Simpkins Fiona , Aghajanian Carol , Leary Alexandra , Poveda Andrés , Lheureux Stephanie , Pujade-Lauraine Eric , You Benoit , Ledermann Jonathan , Matulonis Ursula , Gourley Charlie , Timms Kirsten M. , Lai Zhongwu , Hodgson Darren R. , Elks Cathy E. , Dearden Simon , Egile Coumaran , Lao-Sirieix Pierre , Harrington Elizabeth A. , Brown Jessica S. 
Published: December 2024

Abstract

Background
The introduction of poly(ADP-ribose) polymerase (PARP) inhibitors represented a paradigm shift in the treatment of ovarian cancer. Genomic data from patients with high-grade ovarian cancer in six phase II/III trials involving the PARP inhibitor olaparib were analyzed to better understand patterns and potential causes of genomic instability.

Patients and methods
Homologous recombination deficiency (HRD) was assessed in 2147 tumor samples from SOLO1, PAOLA-1, Study 19, SOLO2, OPINION, and LIGHT using next-generation sequencing technology. Genomic instability scores (GIS) were assessed in BRCA1 and/or BRCA2 (BRCA)-mutated (BRCAm), non-BRCA homologous recombination repair-mutated (non-BRCA HRRm), and non-HRRm tumors.

Results
BRCAm was identified in 1021/2147 (47.6%) tumors. BRCAm tumors had significantly higher GIS than non-BRCAm tumors (P < 0.001) and high biallelic loss (815/838; 97.3%) regardless of germline (658/672; 97.9%) or somatic (101/108; 93.5%) BRCAm status. In non-BRCA HRRm tumors (n = 121) a similar proportion were HRD-positive (GIS ≥ 42: 55/121; 45.5%) relative to HRD-negative (GIS < 42: 52/121; 43.0%). GIS was highly variable in non-BRCA HRRm (median 42 [interquartile range (IQR) 29–58]) and non-HRRm (n = 1005; median 32 [IQR 20–55]) tumors. Gene mutations with high GIS included HRR genes BRIP1 (median 46 [IQR 41–58]), RAD51C (median 58 [IQR 48–66]), RAD51D (median 62 [IQR 54–69]), and PALB2 (median 64 [IQR 58–74]), and non-HRR genes NF1 (median 49 [IQR 25–60]) and RB1 (median 55 [IQR 30–71]). CCNE1-amplified and PIK3CA-mutated tumors had low GIS (CCNE1-amplified: median 24 [IQR 18–29]; PIK3CA-mutated: median 32 [IQR 14–52]) and were predominantly non-BRCAm.

Conclusions
These analyses provide valuable insight into patterns of genomic instability and potential drivers of HRD, besides BRCAm, in ovarian cancer and will help guide future research into the potential clinical effectiveness of anti-cancer treatments in ovarian cancer, including PARP inhibitors as well as other precision oncology agents.

Trial registration
The SOLO1 trial was registered at ClinicalTrials.gov (NCT01844986) on April 30, 2013; the PAOLA-1 trial was registered at ClinicalTrials.gov (NCT02477644) on June 18, 2015 (retrospectively registered); Study 19 was registered at ClinicalTrials.gov (NCT00753545) on September 12, 2008 (retrospectively registered); the SOLO2 trial was registered at ClinicalTrials.gov (NCT01874353) on June 7, 2013; the OPINION trial was registered at ClinicalTrials.gov (NCT03402841) on January 3, 2018; the LIGHT trial was registered at ClinicalTrials.gov (NCT02983799) on November 4, 2016.