Poster Presentation NSW State Cancer Conference 2023

Towards routine homologous recombination DNA repair deficiency testing for ovarian cancer patients (#215)

Nikilyn Nevins 1 2 3 , Cristina Mapagu 1 2 4 , Swetansu Pattnaik 5 , Marina Pavanello 2 , Yoke-Eng Chiew 1 2 3 , Jessica Boros 2 3 , Natalie Bouantoun 2 , Catherine Kennedy 1 2 3 , Carina Lauter 2 3 , Eunice Lee 2 , Pamela Provan 1 2 , Sivatharsny Srirangan 2 , Ramanand Athavale 6 , Sally Baron-Hay 7 8 9 , Michael Burling 3 , Alexander Dobrovic 10 11 , Rhonda Farrell 12 13 , Bo Gao 1 14 15 , Sue Gerty 16 , Amaan Hamad 7 , Michelle Harrison 12 , Unine Herbst 3 , Russell Hogg 1 7 17 , Sadaf Kalam 12 , Yeh Chen Lee 12 , Jayne Maidens 7 , Christie Norris 16 , Abiramy Ragunathan 15 , Greg Robertson 6 18 , Josie Rutovitz 17 , Spinder Samra 19 , Jenny Shannon 20 , Raghwa Sharma 1 19 , Nina Singh 17 , Amanda Stevanovic 20 , Rebecca Stevenson 17 , Sue Valmadre 7 8 9 , King Man Wan 6 , Fang Zhang 10 11 , Lyndal Anderson 21 , Phillip Beale 1 12 , Alison Brand 1 3 22 , David Bowtell 5 23 , Michael Friedlander 16 18 , Paul Harnett 1 15 , Deborah Marsh 1 24 , Goli Samimi 5 25 , Rosemary Balleine 1 2 , Anna DeFazio 1 2 3
  1. University of Sydney, Sydney, NSW, Australia
  2. Center for Cancer Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
  3. Department of Gynaecologic Oncology, Westmead Hospital, Westmead, NSW, Australia
  4. Illawara and Shoalhaven Cancer Care Centres, Nowra, NSW, Australia
  5. Garvan Institute, Sydney, NSW, Australia
  6. Royal Hospital for Women, Sydney, NSW, Australia
  7. Royal North Shore Hospital, Sydney, NSW, Australia
  8. North Shore Private Hospital, Sydney, NSW, Australia
  9. Mater Hospital, Sydney, NSW, Australia
  10. University of Melbourne, Melbourne, VIC, Australia
  11. Department of Surgery, Austin Hospital, Melbourne, VIC, Australia
  12. Chris O'Brien Lifehouse, Sydney, NSW, Australia
  13. Prince of Wales Private Hospital, Sydney, NSW, Australia
  14. Blacktown Hospital, Blacktown, NSW, Australia
  15. Crown Princess Mary Cancer Center, Westmead Hospital, Westmead, NSW, Australia
  16. Prince of Wales Hospital, Sydney, NSW, Australia
  17. Sydney Adventist Hospital, Sydney, NSW, Australia
  18. University of New South Wales, Sydney, NSW, Australia
  19. Pathology West, NSW Health Pathology, Westmead, NSW, Australia
  20. Nepean Cancer Care, Nepean Hospital, Kingswood, NSW, Australia
  21. Royal Prince Alfred Hospital, NSW Health Pathology, Camperdown, NSW, Australia
  22. Westmead Private Hospital, Westmead, NSW, Australia
  23. Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
  24. University of Technology Sydney, Sydney, NSW, Australia
  25. National Cancer Institute, National Institutes of Health, Rockville, MD, USA

Background

Homologous recombination DNA repair deficiency (HRD) is found in approximately 50% of high-grade serous ovarian carcinomas and associated with sensitivity to platinum and poly (ADP-ribose) polymerase (PARP) inhibitors. HRD status is becoming an important clinical indicator, with the potential to change treatment. HRD is assessed by several methods including whole-genome copy-number alterations determined by single nucleotide polymorphism (SNP) arrays or next generation sequencing (NGS). A limitation of applying these methods into routine practice is tumour sample content and quality. We investigated HRD testing in routine clinical samples that are formalin-fixed and often collected after neoadjuvant chemotherapy, which can limit the quality of testable DNA.

Methods

Cases were selected from INOVATe1, a molecular profiling program that recruited ovarian cancer patients between 2016-2020, with testing including NGS, methylation and copy number profiling for HRD status. Of 506 eligible patients, 204 with frozen tumour tissue were selected for assessment of HRD, and of these, HRD was compared in 160 cases with both frozen and formalin-fixed paraffin-embedded (FFPE) tissue available.

Results

In cases with frozen tissue, a high confidence HRD result was obtained in 185/204 (90.6%), 92% of which were concordant with NGS and methylation results. 

Cases with both frozen and FFPE tissue for testing (n=160) were examined to determine DNA quality and compare HRD status in matched samples. Mean block age was 22 months (range, 1-130 months), and 76% (n=121) of samples were chemotherapy-naïve. The average DNA integrity number (DIN) of fixed samples was 3.68 (range 1.5-6.6).

After SNP array testing, results from 101 (63%) FFPE samples passed bioinformatic processing or quality metrics, of which sensitivity for detection of HRD was 90% and accuracy was 88%. The strongest predictor of a successful HRD determination from FFPE was DNA quality, although this was not an absolute predictor of test success. Increasing block age and prior chemotherapy exposure were associated with test failure (p-value <0.05).

Conclusions

In conclusion, HRD testing on frozen samples was successful, although limited by the availability of the frozen material in routine settings. Testing on FFPE samples using whole-genome SNP arrays is possible, although there is a significant rate of sample failure. These failures are apparent by bioinformatic analysis, and test performance is excellent on samples which pass all quality metrics.  HRD status can be determined in FFPE tissues to complement sequencing, although adequate tumour sampling prior to chemotherapy is needed to increase the likelihood of an interpretable result.