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JP-2026514517-A - Methods for diagnosing homologous recombination deficiencies in human tumors

JP2026514517AJP 2026514517 AJP2026514517 AJP 2026514517AJP-2026514517-A

Abstract

This invention relates to an improved method for diagnosing homologous recombination deficiencies (HRDs) in tumors. The method according to this invention particularly includes the steps of: evaluating the number of large genomic alterations (LGAs) in a tumor sample by obtaining a copy number alteration (CNA) profile using shallow coverage whole-genome sequencing (sWGS); and determining an LGA score corresponding to the number of LGAs adjusted for the complexity of the tumor genome and the presence of one or two markers selected from a group of markers consisting of (1) phenotypes associated with mutations in cyclin-dependent kinase 12 (CDK12) with multiple intermediate gains in the CNA profile; (2) amplification of cyclin E1 (CCNE1); (3) amplification of human epidermal growth factor receptor-2 (HER2); and (4) phenotypes of amplification at multiple sites.

Inventors

  • マルク－アンリ・スターン
  • タチアナ・ポポヴァ
  • セリーヌ・カラン
  • アレクサンドル・エエックウット

Assignees

  • アンスティテュ・クリー
  • アンスティチュート、ナシオナル、ドゥ、ラ、サンテ、エ、ドゥ、ラ、ルシェルシュ、メディカル

Dates

Publication Date
20260511
Application Date
20240428
Priority Date
20230428

Claims (8)

  1. A method for diagnosing homologous recombination deficiency (HRD) in tumors, - A process to evaluate the number of large genomic alterations (LGA) in tumor samples by obtaining copy number variation (CNA) profiles using shallow coverage whole-genome sequencing (sWGS). A method comprising the step of determining an LGA score that corresponds to the complexity of the tumor genome and the presence of a marker selected from a group of markers consisting of (1) a phenotype associated with mutations in cyclin-dependent kinase 12 (CDK12) with multiple intermediate gains in the CNA profile, (2) amplification of cyclin E1 (CCNE1), (3) amplification of human epidermal growth factor receptor-2 (HER2), and (4) a phenotype of amplification at multiple sites.
  2. The method according to claim 1, wherein the sample is selected from fresh tumor samples and preserved tumor samples, such as frozen tumor samples and formalin-fixed paraffin-embedded (FFPE) tumor samples.
  3. The method according to claim 2, wherein the tumor sample is a formalin-fixed paraffin-embedded (FFPE) sample of the tumor, and the sWGS CNA profile is corrected by eliminating the FFPE noise profile.
  4. A high LGA score is associated with HRD, a low LGA score is associated with HR pathway functionality (HRP), and there are borderline cases. - Complexity of the tumor genome, - LGA_max, which is the upper limit of the number of LGAs seen in the segmented copy number profile. The method according to any one of claims 1 to 3, wherein the presence of a marker selected from a group of markers consisting of (1) a phenotype associated with a mutation in cyclin-dependent kinase 12 (CDK12) accompanied by multiple intermediate gains in the CNA profile, (2) amplification of cyclin E1 (CCNE1), (3) amplification of human epidermal growth factor receptor-2 (HER2), and (4) a phenotype of amplification at multiple sites is determined by considering the presence of such a marker.
  5. The method according to any one of claims 1 to 4, wherein the tumor is a breast tumor.
  6. The method according to any one of claims 1 to 4, wherein the tumor is an ovarian tumor.
  7. A method for predicting the effectiveness of a treatment in a patient with cancer, wherein the treatment comprises PARPi and/or an alkylating agent, and the method comprises diagnosing HRD in a tumor sample according to the method of any one of claims 1 to 6.
  8. A PARPi and/or alkylating agent for use in a method for treating cancer in a patient diagnosed with a tumor exhibiting HRD according to the method described in any one of claims 1 to 6.

Description

This invention relates to a method for diagnosing homologous recombination defects in tumors. BRCA1/2 mutant tumor cells have a defect in the HR pathway (homologous recombination deficiency or HRD), and therefore rely on alternative DNA repair pathways such as non-homologous end joining (NHEJ), alternative end joining (AltEJ), single-strand annealing (SSA), or base excision repair (BER) to avoid cell death, all of which involve the PARP1 and PARP2 enzymes (Groelly et al., Nat Rev Cancer, 2022). As a result, inhibiting these PARP1/2 enzymes in BRCA1/2-deficient tumor cells leads to cell death (Bryant et al., Nature 434:pp. 913-917, 2005; Farmer et al., Nature 434:pp. 917-921, 2005). PARPi represents a significant advance in the treatment of BRCA1/2-deficient tumors. Several clinical trials have demonstrated that maintenance with or without bevacizumab-containing PARP inhibitors, followed by platinum-based therapy, improves progression-free survival in patients with advanced ovarian cancer (AOC) with BRCA1/2 deficiency or HRD (Moore et al., N Engl J Med, 2018; Ray-Coquard et al., N Engl J Med 381:2416–2428, 2019; Gonzalez-Martin et al., N Engl J Med 381:2391–2402, 2019; Coleman et al., Lancet 390:1949–1961, 2017). Following the Myriad MyChoice CDx Plus test (MG test), as in the PAOLA-1 trial, showed a significant PFS benefit in patients with HRD-positive tumors, including those without BRCA1/2 mutations (BRCAmut). The olaparib (ova) + bevacizumab (bev) maintenance regimen was thus approved in the USA/Europe/Japan for patients with BRCAmut or HRD-positive tumors. However, MG testing was largely inconsistent and remained inconsistent until very recently. Therefore, there is a need to develop novel, highly reliable, and feasible non-aggregated HRD tests. The European HRD ENGOT Initiative (EHEI) is a unique European academic research collaboration aimed at providing reliable HRD biomarkers for selecting AOC patients who are most likely to benefit from PARPi ± bevacizumab as first-line treatment (Pujade-Lauraine et al., International Journal of Gynecologic Cancer 31:A208–A208, 2021). Recently, a novel HRD test called Shallow HRD, based on shallow/low-coverage whole-genome sequencing (sWGS), has shown good performance in fresh, frozen samples (Eeckhoutte et al., Bioinformatics 36: pp. 3888-3889, 2020). sWGS is an easy and inexpensive technique and can be applied to clinical samples, including formalin-fixed paraffin-embedded (FFPE) samples. The bioinformatics pipeline for Shallow HRD is very simple and computationally easy. However, poor performance in noisy samples (frequent in clinical FFPE) and a high number of uninterpreted cases around the HRD cutoff have hindered the clinical application of this test. Groelly et al., Nat Rev Cancer, 2022Bryant et al., Nature 434: pp. 913-917, 2005.Farmer et al., Nature 434: pp. 917-921, 2005.Moore et al., N Engl J Med, 2018Ray-Coquard, I. et al., Olaparib plus Bevacizumab as First-Line Maintenance in Ovarian Cancer. N Engl J Med 381, pp. 2416-2428 (2019)Gonzalez-Martin et al., N Engl J Med 381:2391–2402, 2019.Coleman et al., Lancet 390: pp. 1949–1961, 2017.Pujade-Lauraine et al., International Journal of Gynecologic Cancer 31:A208-A208, 2021Eeckhoutte et al., Bioinformatics 36:3888–3889, 2020.Popova et al., Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation, CANCER RES. (2012) 72:5454-5462Boeva et al. (2012), Bioinformatics, 28, pp. 423-425.Popova et al., Cancer Res 2016, PMID 26787835Boeva, V. et al., Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28, pp. 423-425 (2012)Popova, T. et al., Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications. Cancer Res 76, pp. 1882-1891 (2016)Ray-Coquard, I. L. et al., Final overall survival (OS) results from the phase III PAOLA-1/ENGOT-ov25 trial evaluating maintenance olaparib (ola) plus bevacizumab (bev) in patients (pts) with newly diagnosed advanced ovarian cancer (AOC). Ann Oncol 33, pp. S808-S869 (2022)Callens, C. et al., Concordance Between Tumor and Germline BRCA Status in High-Grade Ovarian Carcinoma Patients in the Phase III PAOLA-1/ENGOT-ov25 Trial. J Natl Cancer Inst 113, pp. 917-923 (2021)Coussy, F. and Bidard, F. C., Expanding biomarkers for PARP inhibitors. Nat Cancer 3, pp. 1141-1143 (2022).Gruber, J. J. et al., A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes. Nat Cancer 3, pp. 1181-1191 (2022)Loverix, L. et al., Predictive value of the Leuven HRD test compared with Myriad myChoice PLUS on 468 ovarian cancer samples from the PAOLA-1/ENGOT-ov25 trial (LBA 6). Gynecologic Oncology 166, pp. S51-S52 (2022)Willing, E.-M. et al., 2022-RA-873-ESGO Validation study of the‘NOGGO-GIS ASSAY’ based on ovarian