Significance of scores generated by a cancer therapy matching engine for patient outcomes.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15099-e15099
Author(s):  
Eden Romm ◽  
Emiliya Davtyan ◽  
Kevin Bush ◽  
Ramsay Sutton ◽  
Itamar Patek ◽  
...  

e15099 Background: Oncologists need effective precision medicine tools to navigate the myriad of therapeutic options to best address each patient’s unique tumor profile. Described here is a digital solution, which analyzes tumor data (NGS, other), scores and ranks known and novel matching combinations of cancer drugs with molecular-level precision for decision support. Methods: All data was acquired through the published supplement of the I-PREDICT study (NCT 02534675). Patients with available progression-free survival (PFS) and sequencing data who received <3 matched non-experimental cancer drugs in combination were evaluated (n=77). To determine each patient’s score (represented as %), the system used expert-curated content integrated within an artificial intelligence (AI) reasoning framework that computed how well the therapy each patient received matched their tumor’s genomic profile. The dataset was binarized at 36 possible thresholds, which split the data into higher vs. lower score bins. Relationship with PFS and the degree of separation between bins were evaluated with Kaplan-Meier plots and assessed in terms of p-value, hazard ratios and related confidence intervals (Table). To prevent sampling bias at high and low thresholding extremes of this dataset, a limit was imposed of >25 patients per bin. Results: Significant separation between high and low scoring bins was observed in >73% of evaluable thresholds. The mean p-value was 0.044 (range, 0.011-0.13). The hazard ratio was consistently ̃2 (mean, 1.81, range, 1.50-2.08). A similar level of statistical significance was observed for all thresholds up to and including bracketing of 60% (Table). Despite the small size of this dataset and the disparity between sample counts per bin seen at the end of the range, significant p-values of <0.05 were achieved. Ex., a 68-year-old female with an ampullary adenocarcinoma harboring ERBB2, CDK6 and other alterations, received a combination of pertuzumab and trastuzumab scoring 56%. The PFS was 745+ days. However, had palbociclib, ribociclib, or abemaciclib been added to this combination, the resulting 3-drug options would have scored even higher due to also targeting CDK6. Conclusions: Our study indicates that therapies with higher scores were predictive of better PFS, while lower scores were predictive of worse PFS. The results will be validated on larger datasets but are already demonstrative of the utility of this system in providing digital guidance to oncologists in selecting the most suitable treatment. [Table: see text]

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 11076-11076 ◽  
Author(s):  
W. A. Franklin ◽  
D. R. Gandara ◽  
E. S. Kim ◽  
R. S. Herbst ◽  
J. Moon ◽  
...  

11076 Background: High EGFR gene copy number is associated with efficacy in NSCLC patients (pts) receiving combined chemotherapy and cetuximab (S0342). EGFR protein is typically overexpressed in tumors with high copy number but no consistent association has yet been demonstrated between EGFR protein expression and outcome in pts treated with chemotherapy plus cetuximab. EMT is associated with aggressive biological behavior and resistance to anti-EGFR TKI therapy in NSCLC. Our objective was to identify any association between EGFR protein and EMT and to correlate findings with pt outcomes from cetuximab/chemotherapy in SWOG trials S0342 (paclitaxel [P]-carboplatin [CB] plus sequential or concurrent cetuximab [CX]) and S0536 (P-CB-CX + bevacizumab). Methods: Paraffin sections were stained by immunoperoxidase methods using monoclonal antibodies against EGFR and the EMT markers vimentin, E-cadherin and Zeb1. Sections were scored on continuous scale ranging from 0–300 based on the H score (sum of % positive at each intensity from 0–3). Results were compared to outcome by Kaplan-Meier plot. Results: 79 samples from S0342 were evaluated for EGFR and EMT markers. 67 samples from S0536 were assessed for EGFR only. Mean EGFR H score was 153 and 137 for S0342 and S0536 respectively. At all cut points tested (scores 0, <100, <300) no association between EGFR H score and response or progression-free survival (PFS) was detected in either trial. There was a trend for overall survival and EGFR level at each cutpoint in S0536 but the results did not achieve statistical significance (15 vs 11 mos, p=0.14; 15 vs 11 mos, p=0.20 and 14 mos vs not reached, p=0.10, respectively). Vimentin (6 positive pts) was associated with a shorter PFS, HR=2.60 (1.10–6.14), p=0.03. ECAD and Vimentin were significantly inversely correlated with one another (Spearman p-value<0.01) Conclusions: EGFR protein level by IHC does not significantly correlate with efficacy parameters in chemotherapy/cetuximab-treated NSCLC pts. Patients with vimentin producing tumors (and possible other EMT markers) had shorter PFS, suggesting possible relative resistance to EGFR blockade from cetuximab. [Table: see text]


2022 ◽  
Author(s):  
Daniel Serie ◽  
Amanda A Myers ◽  
Daniela A Haehn ◽  
Alexander Parker ◽  
Essa Bajalia ◽  
...  

Introduction: Limited data exists on utilization of protein post-translational modifications as biomarkers for clear cell renal cell carcinoma (ccRCC). We employed high-throughput glycoproteomics to evaluate differential expression of glycoprotein-isoforms as novel markers for ccRCC progression-free survival (PFS). Methods: Plasma samples were obtained from 77 patients treated surgically for ccRCC. Glycoproteomic analyses were carried out after liquid chromatography tandem mass spectrometry. Age-adjusted Cox proportional hazard models were constructed to evaluate PFS. Optimized Harrells c-index was employed to dichotomize the collective for the construction of Kaplan-Meier curves. Results: The average length of follow-up was 3.4 (range: 0.04-9.83) years. Glycoproteomic analysis identified 39 glycopeptides and 14 non-glycosylated peptides that showed statistically significant (false discovery rate p ≤0.05) differential expression associated with PFS. Five of the glycosylated peptides conferred continuous hazard ratio of > 6 (range 6.3-11.6). These included prothrombin A2G2S glycan motif (HR=6.47, P=9.53E-05), immunoglobulin J chain FA2G2S2 motif (HR=10.69, P=0.001), clusterin A2G2 motif (HR=7.38, P=0.002), complement component C8A A2G2S2 motif (HR=11.59, P=0.002), and apolipoprotein M glycopeptide with non-fucosylated and non-sialylated hybrid-type glycan (HR=6.30, P=0.003). Kaplan-Meier curves based on dichotomous expression of these five glycopeptides resulted in hazard ratios of 3.9-10.7, all with p-value < 0.03. Kaplan-Meyer plot using the multivariable model comprising 3 of the markers yielded HR of 11.96 (p <0.0001). Conclusion: Differential glyco-isoform abundance of plasma proteins may be a useful source of biomarkers for the clinical course and prognosis of ccRCC.


2018 ◽  
Vol 36 (18) ◽  
pp. 1805-1812 ◽  
Author(s):  
Thomas J. Hwang ◽  
Jessica M. Franklin ◽  
Christopher T. Chen ◽  
Julie C. Lauffenburger ◽  
Bishal Gyawali ◽  
...  

Purpose The breakthrough therapy program was established in 2012 to expedite the development and review of new medicines. We evaluated the times to approval, efficacy, and safety of breakthrough-designated versus non–breakthrough-designated cancer drugs approved by the US Food and Drug Administration (FDA). Methods We studied all new cancer drugs approved by the FDA between January 2012 and December 2017. Regulatory and therapeutic characteristics (time to FDA approval, pivotal trial efficacy end point, novelty of mechanism of action) were compared between breakthrough-designated and non–breakthrough-designated cancer drugs. Random-effects meta-regression was used to assess the association between breakthrough therapy designation and hazard ratios for progression-free survival (PFS), response rates (RRs) for solid tumors, serious adverse events, and deaths not attributed to disease progression. Results Between 2012 and 2017, the FDA approved 58 new cancer drugs, 25 (43%) of which received breakthrough therapy designation. The median time to first FDA approval was 5.2 years for breakthrough-designated drugs versus 7.1 years for non–breakthrough-designated drugs (difference, 1.9 years; P = .01). There were no statistically significant differences between breakthrough-designated and non–breakthrough-designated drugs in median PFS gains (8.6 v 4.0 months; P = .11), hazard ratios for PFS (0.43 v 0.51; P = .28), or RRs for solid tumors (37% v 39%; P = .74). Breakthrough therapy–designated drugs were not more likely to act via a novel mechanism of action (36% v 39%; P = 1.00). Rates of deaths (6% v 4%; P = .99) and serious adverse events (38% v 36%; P = 0.93) were also similar in breakthrough-designated and non–breakthrough-designated drugs. Conclusion Breakthrough-designated cancer drugs were associated with faster times to approval, but there was no evidence that these drugs provide improvements in safety or novelty; nor was there a statistically significant efficacy advantage when compared with non–breakthrough-designated drugs.


2018 ◽  
Vol 10 (04) ◽  
pp. 363-369 ◽  
Author(s):  
Serife Solmaz ◽  
Ozcan Uzun ◽  
Celal Acar ◽  
Omur Gokmen Sevindik ◽  
Ozden Piskin ◽  
...  

ABSTRACT BACKGROUND: Recent reports showed neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and monocyte-to-lymphocyte ratio (MLR), as a predictor of progression-free survival (PFS) and overall survival (OS) in various malignancies. MATERIALS AND METHODS: We retrospectively examined the PLR, NLR, and MLR in a cohort of 186 newly diagnosed multiple myeloma (MM) patients. This study investigated the prognostic relevance of NLR, PLR, and MLR in MM patients. NLR, PLR, and MLR were calculated from whole blood counts before therapy. The Kaplan–Meier curves and multivariate Cox models were used for the evaluation of survival. RESULTS: Applying cutoff of 1.9 (NLR), 120.00 (PLR), and 0.27 (MLR), decreased PLR showed a negative impact on the outcome. Decreased PLR is an independent predictor for PFS and OS. There were no significant differences in median survival between the high and low NLR (P = 0.80) and MLR (P = 0.87) groups. CONCLUSIONS: In this study, thrombocytopenia and low PLR are associated with poor survival in MM patients does this P value apply to thrombocytopenia or low PLR and may serve as the cost-effective prognostic biomarker.


2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
M N U M Meah ◽  
T J Joseph ◽  
W Y D Ding ◽  
M S Shaw ◽  
J H Hasleton ◽  
...  

Abstract Introduction Current guidelines recommend immediate revascularisation in patients with ST elevation myocardial infarction (STEMI). However it remains unclear whether PPCI reduces mortality in nonagenarians. We aimed to compare mortality in nonagenarians, presenting via the PPCI pathway, who were managed medically (MM) versus those who underwent PCI. Methods Electronic records of every nonagenarian who presented as a PPCI activation between 2013–2018 were reviewed. Patients were divided into those who had PCI and those MM. Standard univariate and Kaplan Meier survival analyses were performed. We compared outcomes to an age and sex matched cohort using life tables from the Office for National Statistics (ONS). Results There were 157 nonagenarians presenting via the PPCI pathway, of which 111 were “true” myocardial infarction. Table 1 summarises baseline variables and comorbidities. The cohorts were generally well matched. Both groups had similar BCIS PCI 30-day mortality risk scores. The commonest reason to treat medically was presentation 12 hours after symptom onset. There was a trend towards increased 30-day mortality in the MM group. Kaplan Meier analysis (Figure 1) show the survival curves diverge immediately and reach statistical significance at 3 years. Compared to a matched population from ONS life tables, outcomes are worse in MM. Table 1.S Admission variables & results PCI Group (n=42) Medically Managed Group (n=69) P-value Age 92 (91, 94) 93 (91, 95) 0.22 Female 21 (50.0%) 45 (65.2%) 0.11 Left ventricular failure (EF <45%) 27 (64.3%) 46 (66.6%) >0.99 Cardiogenic shock (Systolic BP <90mmHg) 4 (9.5%) 6 (8.7%) >0.99 Hx of hypertension 24 (57.1%) 45 (65.2%) 0.39 Hx of diabetes 5 (11.9%) 18 (26.1%) 0.07 Hx of chronic kidney disease 12 (28.6%) 25 (36.2%) 0.41 Hx of previous stroke 8 (19.1%) 15 (21.7%) 0.73 Hx of atrial fibrillation 1 (2.4%) 16 (23.2%) 0.003 Presented as non-STEMI 1 (2.4%) 12 (17.4%) 0.017 Presented as completed STEMI 2 (4.8%) 30 (43.5%) <0.001 BCIS PCI 30-day mortality risk 15.7 (14.3, 23.6) 17.5 (15.3, 22.3) 0.17 30-day mortality 10 (23.8%) 28 (40.6%) 0.07 Figure 1. Kaplan Meier Chart Conclusions Long term survival even in nonagenarians is significantly improved by timely PPCI when compared with medical management.


2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e15532-e15532
Author(s):  
Ramon Andrade De Mello ◽  
Dania Sofia Marques ◽  
Joana Savva-Bordalo ◽  
Monica Gomes ◽  
Joana Assis ◽  
...  

e15532 Background: Interleukine (IL) 10 –592C/A and IL8 –251T/A polymorphisms previous showed an important role in cell proliferation, cell migration and angiogenesis. Therefore, we conduct a study in order to assess the role of those genetic polymorphisms as prognostic biomarkers in epithelial ovary cancer (EOC). Methods: Design: Retrospective study from 1996 to 2010. Setting: Histological confirmed EOC patients treated at our institution. Laboratory: Genotyping of IL10–592 C/A and IL8 -251T/A were performed by PCR-RFLP. DNA samples were obtained from patients’ peripheral blood. Statistical analysis: Logistic regression were used to calculate odds ratio (OR) and 95% confidential interval (95% CI). Overall survival (OS) and progression-free-survival (PFS) were performed using Kaplan-Meier analysis. Statistical significance was considered for p < 0.05. Results: It was recruited 156 participants. Median age was 53 (16 – 80) years-old. Genotype frequency distribution for IL8-251 were T/T (50%), T/A (50%) and for IL10–592, C/C (53.8%), C/A (39.7%), A/A (6.4%). These follow genotypes were associated with lymph node, pelvic and peritoneal relapse: IL10–592C/A (OR 0.229, 95% CI: 0.055 – 0.943, p = 0.041) and IL8–251T/A (OR 6.667, 95% CI: 1.359 – 32.701, p = 0.019). In overall, IL8–251T/A genotype had higher OS than IL8-251T/T genotype: 115 versus 95 months, p = 0.010. In clear cell tumors (CCT), IL8–251T/A genotype had less OS than IL8-251T/T genotype: 92 versus 107 months, p = 0.004. To IL10–592 genotypes, OS were 104 (A/A), 107 (C/A), 103 (C/C) months, p = 0.637, and PFS were 9 (A/A), 14 (C/A), 20 (C/C) months, p = 0.057. However, in CCT, PFS for IL10–592 genotypes were 4 (A/A), 56.73 (C/A), 20 (C/C) months, p = 0.023. Conclusions: Our results suggest that IL8–251T/A polymorphism could represent a prognostic biomarker in overall EOC. IL10–592C/A polymorphisms are associated with relapse and PFS mainly in CCT. Nevertheless, furthers prospective studies are warranted in order to assess its role in pharmacogenomics framework.


2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e19022-e19022
Author(s):  
Liza Cosca Villaruz ◽  
Mark A. Socinski ◽  
Jyoti D. Patel ◽  
Larry Leon ◽  
Sebastien Hazard ◽  
...  

e19022 Background: Progression-free survival (PFS) is a key trial end point for clinical practice, as it relates to a change of treatment line. Grade 4 progression-free survival (G4PFS; defined as time from treatment start to the earlier of progressive disease [PD], onset of a G4 adverse event [AE], or death from any cause) is a composite end point incorporating a measure of tolerability to PFS. This post hoc analysis evaluates G4PFS and the effect of G4 AEs on PFS and overall survival (OS) in patients (pts) enrolled in PointBreak (PB) and AVAiL. Methods: Pts in PB were randomized to bevacizumab (BEV) 15 mg/kg q3w with carboplatin and paclitaxel (CP) or pemetrexed (CPem) for ≤4 cycles. Eligible pts received either BEV or BEV + Pem q3w until PD or unacceptable toxicity. Pts in AVAiL received cisplatin and gemcitabine for ≤6 cycles and either placebo or BEV (7.5 or 15 mg/kg) q3w until PD. AEs were graded via NCI-CTCAE v3.0. Kaplan-Meier and Cox model methods were used to estimate medians and hazard ratios (HRs) for PFS, G4PFS, and OS. PFS and OS were also compared in each arm for pts with occurrence of a G4 AE before week 12 of treatment vs those without. Results: Of those receiving BEV, ~30% of AVAiL pts and 38% of PB pts had a G4 AE. Uncomplicated neutropenia was the most common G4 AE in the CP + BEV arm of PB (26%) and in the BEV arms of AVAiL (11%). PFS, G4PFS, and outcomes by G4 AE occurrence are shown (Table). Conclusions: In both the PB and AVAiL trials, median G4PFS was numerically shorter than median PFS. G4 AE occurrence, however, did not affect subsequent PFS or OS in either trial. Clinical trial information: NCT00762034 and NCT00806923. [Table: see text]


2013 ◽  
Vol 31 (6_suppl) ◽  
pp. 426-426 ◽  
Author(s):  
Shukui Qin ◽  
Jie Jin ◽  
Jun Guo ◽  
Jin-Wan Wang ◽  
Fang-Jian Zhou ◽  
...  

426 Background: In an open-label, phase IV study of sunitinib as 1st-line treatment (Tx) in Chinese pts with mRCC, median progression-free survival (PFS) and overall survival (OS) were 61.7 and 133.4 wk, respectively; objective response rate (ORR) was 31.1% (Ann Oncol 2012;23:851P). We retrospectively investigated correlations between on-Tx hypertension (HTN), neutropenia (N), and thrombocytopenia (T) and efficacy endpoints in pts from this trial. Methods: HTN was defined by either maximum systolic blood pressure ≥140 mm Hg (S-HTN) or maximum diastolic blood pressure ≥90 mm Hg (D-HTN). Using CTCAE assessment, N grade ≥2 and T grade >1 were used as cut-points for the analyses. Median PFS and OS were estimated by Kaplan−Meier method. The log-rank test was used to compare PFS and OS between groups with and without HTN, N grade ≥2, or T grade >1. Fisher’s exact test was used for ORR. Results: 102 pts were included in the HTN analyses, 60% with S-HTN versus 40% without S-HTN. Pts with S-HTN had greater ORR and longer PFS and OS than pts without S-HTN (Table). (Results were similar with D-HTN; see Table.) 103 pts were included in the N and T analyses, 67% with N grade ≥2 versus 33% with N grade <2, and 56% with T grade >1 versus 44% with T grade ≤1. Pts with N grade ≥2 had significantly greater ORR and significantly longer PFS and OS than pts with N grade <2 (Table). Pts with T grade >1 had greater ORR and significantly longer PFS and OS than pts with T grade ≤1 (Table). Conclusions: The developments of N grade ≥2 and T grade >1 during Tx with sunitinib were significantly associated with better outcome. Median PFS was more than twice as long for pts with S-HTN as for those without S-HTN, but the association did not reach statistical significance. [Table: see text]


2014 ◽  
Vol 32 (4_suppl) ◽  
pp. 2-2 ◽  
Author(s):  
Charles G. Drake ◽  
Eugene D. Kwon ◽  
Karim Fizazi ◽  
Alberto Bossi ◽  
Alfons JM van den Eertwegh ◽  
...  

2 Background: The CA184-043 phase 3 study did not reach statistical significance for its primary endpoint of OS (HR=0.85, p=0.053). However, antitumor activity was observed in other efficacy endpoints, including progression-free survival. Prespecified subset analyses were performed to understand if any prognostic features may identify mCRPC patients (pts) more likely to benefit from Ipi treatment. Methods: 799 pts were randomized to receive a single dose of radiotherapy (RT) followed by either Ipi (N=399) or Pbo (N=400). Prespecified subset analyses based on Kaplan-Meier/Cox methodology were performed using known prognostic factors for OS in mCRPC. Results: Prespecified subset analyses suggested that Ipi may be more active in pts with favorable prognostic factors, including no visceral disease, alkaline phosphatase <1.5 ULN, and hemoglobin ≥11 g/dL (Table). The safety profile in this study was consistent with previous reports of Ipi. Conclusions: Based on these subset analyses, Ipi added to RT appears to have greater activity than RT alone in pts with a favorable prognostic profile. These results support continued investigation of Ipi in the ongoing CA184-095 study in chemotherapy-naive mCRPC pts. Clinical trial information: NCT00861614. [Table: see text]


2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 280-280
Author(s):  
Pashtoon Murtaza Kasi ◽  
Fergus Couch ◽  
William R Bamlet ◽  
Chunling Hu ◽  
Steven Hart ◽  
...  

280 Background: Patients with pancreatic adenocarcinoma (PDAC) can have mutations in breast cancer associated genes ( BRCA1/2) and other homologous recombination (HR) pathway genes. The therapeutic significance of these mutations for PDAC patients is not yet established. We performed a comprehensive survival analysis of 3,030 unselected PDAC patients comparing non-carriers and carriers of BRCA1/2, PALB2, and ATM mutations. Methods: We analyzed germline DNA samples and outcomes from confirmed PDAC patients recruited from 1999-2014 into the Mayo Clinic SPORE in Pancreatic Cancer registry. A total of 3,046 genomic DNA samples were analyzed by next generation sequencing. All pathogenic variants were validated by Sanger sequencing. Survival analysis of PDAC patients with and without BRCA1, BRCA2, PALB2, or ATM germline mutations was performed using the Kaplan-Meier method and log-rank tests. Hazard ratios (HR) were calculated using Cox proportional hazard modeling adjusted for co-variates including age, sex, and stage. A p-value < 0.05 was considered statistically significant. Pre- and post-FOLFIRINOX eras were defined as before and after June 1, 2011. Results: A total of 139 (4.6%) patients were noted to have deleterious mutations in BRCA1, BRCA2, PALB2, or ATM genes. After exclusion of patients with missing data, final analysis was restricted to 2,452 PDAC patients. Overall survival was slightly better (14.2 months versus 11.3 months) in patients with mutations as compared to those without mutations, although this finding was not statistically significant (p = 0.07). When stratified by FOLFIRINOX era, 40 patients with these mutations in the post-FOLFIRINOX era had better outcomes than 668 non-carriers (adjusted HR 0.62; 95% CI 0.43-0.89; p = 0.0062). Conclusions: Deleterious germline BRCA1/2, PALB2, and ATM mutations were seen in approximately 5% of patients with PDAC. Post-FOLFIRINOX era patients with these mutations had improved outcomes, possibly secondary to exposure to DNA-damaging chemotherapies. Germline screening of PDAC patients and development of trials incorporating this information (e.g., PARP inhibitors) has potential value for PDAC patients.


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