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The paradigm of precision medicine suggests that cancer therapies to be personalized to individual patients based on the genomic characteristics of their tumors (1). Increasing evidence suggest that the approach of genomic-guided treatments may lead to improvements in patient outcomes (2, 3). With more targeted therapies approved in the past 10 years which work best in subsets of patients with specific alterations, comprehensive genomic profiling utilizing next-generation sequencing (NGS) technologies may significantly expand treatment options for patients with advanced cancers (4, 5).

HRD/gLOH new biomarkers: Pan-cancer analysis of homologous recombination repair-associated alterations and genome-wide loss of heterozygosity

Homologous recombination is one of the major mechanisms of repair of damaged DNA and functional deficiency of homologous recombination, known as HRD has emerged as a bona fide therapeutic target. Tumours with genomic alterations in certain homologous recombination repair (HR) genes BRCA 1 and BRCA 2 are associated with response to platinum-based chemotherapy and PARP inhibitors (6-8). However, the genomic effects of alterations in less common HR genes are not well documented. At the ESMO congress 2020, Benedikt Westphale et al presented a comprehensive assessment of the distribution of genomic alterations in a broad panel of HR genes in a large pan-cancer dataset, which could potentially guide clinical management and trial design.

In this study, comprehensive genomic profiling of 465 genes including many HR genes, including core and peripheral HR genes BRCA1, BRCA2, PALB2, ATR, ATRX, ATM, BAP1, RAD51B, RAD51C, RAD51D, BRIP1, NBN, CHEK1, CHEK2, FANCA, FANCC and MRE11 was performed in a pan-cancer cohort of 160,790 tumour samples (Foundation Medicine, Inc). Zygosity predictions, genome-wide loss of heterozygosity (gLOH) and biallelic status were calculated. HR alterations were found to be commonly present across all tumour types with average prevalence of 18.5%. In BRCA-associated (BA) cancers (ovarian, breast, pancreas, prostate), most HRR alterations were predicted biallelic (75.0%), with a lower rate in non-BA (NBA) cancers (45.7%).

Of note, some tumors with wild type BRCA1 or BRCA2 exhibit similar patterns of genomic scars and show increased sensitivity to platinum-based drugs . Hence genomic scars may present as potential biomarkers for HRD to select patients for specific therapies (9-12). In this study, the association of HR alterations and genomic scar signature gLOH was examined. Biallelic HR alterations had elevated gLOH relative to HR wildtype in both BA and NBA tumours. (BA: median gLOH 19.2 v 9.7, p <1e-100; NBA: median gLOH 11.0 v 7.1, p <1e-100). Monoallelic alterations were not associated with elevated gLOH (p = 1.0). The strength of association between biallelic HRR alterations and gLOH was strongest in BRCA1, RAD51D, PALB2, RAD51C and BRCA2 (median gLOH 25.5, 21.6, 19.8, 19.3, 19.0 v 7.8 in HR-WT, all p <1e-25). Other genes exhibited weak or no association with gLOH (all median gLOH <15).

These data reveal that comprehensive genomic profiling enables the identification of both genomic alterations in a panel of HR genes and genomic scar signature gLOH as a result of these alterations. These molecular characteristics could represent important therapeutically relevant biomarkers across malignancies. In addition, biallelic alterations in 5 genes were strongly associated with high gLOH and found no associations for heterozygous alterations. These results highlight the need to incorporate both gene and biallelic status when assessing HRD and this may have potential utility in personalised treatment and enrollment into clinical trials.

Next generation sequencing of metastatic prostate cancer - targetable alterations in DNA damage repair genes and beyond

Metastatic prostate cancer (mPC) is the second most common cancer in men globally (13). Identifying actionable genetic alterations is of increasing importance when looking for sensitivity to PARP inhibitors, targeted therapies and immune checkpoint inhibitors (14). Furthermore, certain alterations may predict sensitivity to standard chemotherapy and hormonal agents and can aid treatment planning (15, 16). In this study, authors prospectively collated data on mPC patients (Irish population) with somatic DNA profiling NGS analysis for 395 cancer-related genes (Foundation Medicine). Genetic variants were categorised as actionable, potentially actionable and not actionable using OncoKB precision oncology knowledge base for available compounds (, PubMed and for investigational agents in early phase clinical studies and for specific gene-drug interactions.

Of the 36 patients with sequencing results, 26 (72%) had actionable or potentially actionable alterations and the remainder had alterations in genes with no known therapeutic approach (28%). The most commonly observed actionable alterations included PTEN (25%), ATM (17%), BRCA2 (14%), BRCA1 (6%), CHEK2 (3%) and MSH2 (3%) as shown in Figure 1. The most commonly observed potentially actionable alteration are TMPRSS2 (42%), TP53 (36%), MLL3 (14%), CDK12 (14%), AR (11%), RB1 (8%), MYC (8%), NF1 (6%), SPTA1 (6%), ATR (3%) (Table 2).

In this cohort, 33% of patients had actionable genes targetable by PARP inhibitors (ATM, BRCA1, BRCA2, CHECK2), 25% were targetable by signal transduction blockers (PTEN) and 3% were targetable by immunotherapeutic agents (MSH2). In addition 13% of patients had potentially actionable alterations targetable by PARP inhibitors and 45% by signal transduction blockers (Figure 2).

Prostate cancer harbours a wide array of both actionable and potentially actionable alterations that might offer alternative treatment strategies for patients. Recent and evolving clinical trials show deep and durable responses to these novel agents in some patients with mPC. Identifying pathogenic variants by comprehensive genomic profiling could potentially have led to further treatment options in 72% of mPC patients in this study. The next step is for prospective studies to evaluate if CGP in mPC will enable patients to receive genomic directed therapy and whether this might improve outcomes.

Association of TMB with efficacy of first-line pembrolizumab in advanced gastric cancer

Tumor mutational burden (TMB) has been shown to predict response to pembrolizumab across multiple tumor types (17-19). Currently, TMB genomic signature can only be measured by whole exome sequencing and more recently by broad panel genomic profiling. An exploratory analysis from the phase 3 KEYNOTE-062 trial investigated the association between TMB and the clinical outcomes in patients with advanced gastric or gastroesophageal junction (G/GEJ) cancers treated with pembrolizumab, pembrolizumab + chemotherapy, or chemotherapy alone as first-line therapy. TMB was assessed in formalin-fixed, paraffin-embedded tumor tissues by FoundationOne® CDx (Foundation Medicine). Forty percent of patients (306/763) had evaluable TMB data (pembrolizumab, 107; pembrolizumab + chemotherapy, 100; chemotherapy, 99). The overall prevalence of TMB ≥10 mut/Mb was 16%.

In this study, tissue TMB cutoff score of ≥10 mut/Mb showed potential clinical utility as a predictive biomarker of benefit with pembrolizumab versus chemotherapy. Objective response rate (ORR) was 55.6 % vs 41.2 % in TMB ≥10 mut/Mb subgroup and 6.7% vs 47.6% in TMB <10 mut/Mb subgroup. Median PFS of 11.1 vs 7.0 months in TMB ≥10 mut/Mb subgroup (HR, 0.52) and 2.6 vs 7.1 months in TMB <10 mut/Mb subgroup (HR, 1.73) was observed. Similarly, overall survival was 31.6 vs 13.4 months in TMB ≥10 mut/Mb subgroup (HR, 0.34) and 7.5 vs 12.6 in TMB <10 mut/Mb subgroup (HR, 1.41). Similar trends were reported for pembrolizumab + chemotherapy versus chemotherapy with respect to ORR, mPFS and OS results when tissue TMB cutoff score of ≥10 mut/Mb was applied.

The authors concluded that tissue TMB was positively associated with clinical outcomes with first-line pembrolizumab monotherapy and pembrolizumab + chemotherapy, but not with chemotherapy alone, in patients with advanced G/GEJ cancer. Pembrolizumab monotherapy and pembrolizumab + chemotherapy demonstrated a potential OS benefit versus chemotherapy in TMB-H ≥10 mut/Mb subgroup of patients.

The value of detecting resistance through liquid biopsy

Liquid biopsy has been established as an important diagnostic step in identifying EGFR T790M resistance mutation to 1st and 2nd generation EGFR TKIs (20). This has led to significant interest in exploring the value of liquid biopsy in patients with other oncogene-addicted cancers and acquired resistance to targeted therapy. This study is being conducted at 6 Canadian centres using a validated circulating cell-free DNA genomic profiling assay that identifies variants in 74 cancer-associated genes, including fusions and copy number gain (Guardant 360TM). The results on Cohort 2 of the study are reported. Non-small cell lung cancer patients with known oncogenic drivers (e.g. EGFR, ALK, ROS1, BRAF) that have progressed on tyrosine kinase inhibitors were included in this cohort. Fifty-three patients (88%) had characterized genomic alterations detected 7 (12%) had no alterations or only a variant of unknown significance detected. Table 2 shows the summary of actionable and potentially actionable alterations detected beyond the existing known driver mutations. The results showed that 15% patients had actionable targets while 25% patients has potentially actionable targets (table 2). Interesting concurrent aberrations were identified in 15% of patients consisting of

1) ALK G1202R + ALK C1156Y + EGFR amplification

2) MET amplification + EGFR T790M + EGFR amplification + FGFR1 amplification 

3) RET fusion + EGFR amplification

4) MET amplification + EGFR amplification + EGFR C797S

5) BRAF V600E + BRAF amplification + EGFR amplification

6) EGFR G724S + EGFR amplification

7) BRAF amplification + EGFR amplification

8) CDK4 amplification + EGFR C724S + EGFR amplification

9) CCND2 amplification + EGFR amplification

The authors conclude that liquid biopsy provides a minimally invasive initial approach to the molecular characterization of resistance in patients with driver mutations in lung cancer failing targeted therapy, yielding actionable or potentially actionable results in nearly 30% of patients beyond EGFR T790M. In addition, the detection of concurrent alterations through such genomic profiling can potentially provide insights to combination therapy.

Clinical utility of liquid biopsy assay as an aid to select patients for entrectinib treatment

FoundationOne liquid CDx (F1L CDx, Foundation Medicine) is a new FDA-approved comprehensive genomic profiling platform for detecting genetic alterations in circulating cell-free DNA. In this study, Dziadziuszko et al presented concordance data between gene rearrangements (NTRK and ROS1 fusion and non-fusion rearrangements) determined by F1L CDx and clinical trial assays (CTAs). The clinical efficacy of the TRK/ROS1 kinase inhibitor, entrectinib in patients with NTRK rearrangement-positive (rp) or ROS1-rp tumours identified by F1L CDx was evaluated as well. Plasma samples were collected from patients with NTRK-rp solid tumours and ROS1-rp non-small cell lung cancer (NSCLC) enrolled in phase 2 STARTRK-2 trial (NCT02568267) and NTRK/ROS1 rearrangement-negative non-NSCLC tumours from external vendor. A total of 98 samples were evaluable by F1L CDx. CTAs consisted of assay technologies such as FISH and multiple tissue DNA/RNA-based platforms.

Clinical efficacy in F1L CDx+ cohorts was calculated by clinical bridging and compared with efficacy in CTA+ cohorts from the integrated analyses of entrectinib clinical trials (ALKA-372-001, STARTRK-1 and STARTRK-2) (Table 2). Clinical bridging from CTAs to F1L CDx estimated the objective response rate (ORR) as 72.2% (95% CI 50.0–88.9) in both the F1L CDx NTRK-rp and ROS1-rp cohorts. This is greater than the CTA+ NTRK-rp subset of 57.4% (95% CI 43.2–70.8) and similar to the CTA+ ROS1-rp subset.

The sensitivity of the F1L CDx assay has been evaluated in the study. Estimated positive percent agreement (PPA) between F1L CDx assay and CTAs was 47.4% (95% CI: 31.0–64.2) for NTRK-rp and 64.5% (95% CI: 45.4–80.8) for ROS1-rp samples (Table 3). The observed PPA likely reflects the comparison of plasma versus multiple tissue DNA/RNA-based CTAs and is in line with other plasma versus tissue PPA estimates of FDA-approved plasma CDx assays (21, 22). Positive and negative predictive values (PPV; NPV) were computed after adjustment for fusion prevalence (NTRK, 0.32%; ROS1, 1%). PPV for the F1L CDx assay was 100% for both NTRK-rp and ROS1-rp samples (Table 3), indicating a high confidence in both the ROS1 and NTRK rearrangements reported by this assay.

This clinical bridging study has demonstrated the clinical validity of the F1L CDx assay as a complementary aid to tissue-based testing for the identification of patients with NTRK-rp tumours and ROS1-rp NSCLC who may benefit from entrectinib treatment. The current levels of agreement described above between liquid and tissue testing for rearrangements should be noted.


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