Augmenting control arms with real-world data for cancer trials: Hybrid control arm methods and considerations

Background

Hybrid controlled trials with real-world data (RWD), where the control arm is composed of both trial and real-world patients, could facilitate research when the feasibility of randomized controlled trials (RCTs) is challenging and single-arm trials would provide insufficient information.

Methods

We propose a frequentist two-step borrowing method to construct hybrid control arms. We use parameters informed by a completed randomized trial in metastatic triple-negative breast cancer to simulate the operating characteristics of dynamic and static borrowing methods, highlighting key trade-offs and analytic decisions in the design of hybrid studies.

Results

Simulated data were generated under varying residual-bias assumptions (no bias: HR_RWD = 1) and experimental treatment effects (target trial scenario: HR_Exp = 0.78). Under the target scenario with no residual bias, all borrowing methods achieved the desired 88% power, an improvement over the reference model (74% power) that does not borrow information externally. The effective number of external events tended to decrease with higher bias between RWD and RCT (i.e. HR_RWD away from 1), and with weaker experimental treatment effects (i.e. HR_Exp closer to 1). All dynamic borrowing methods illustrated (but not the static power prior) cap the maximum Type 1 error over the residual-bias range considered. Our two-step model achieved comparable results for power, type 1 error, and effective number of external events borrowed compared to other borrowing methodologies.

Conclusion

By pairing high-quality external data with rigorous simulations, researchers have the potential to design hybrid controlled trials that better meet the needs of patients and drug development.

Real-world racial disparities in EGFR testing and third-generation EGFR TKI use among U.S. patients with stage IV NSCLC

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Background: Biomarker testing for EGFR mutations (EGFRm) is recommended for all newly diagnosed patients with metastatic NSCLC. Third-generation EGFR TKIs are the recommended standard-of-care therapy for patients with EGFRm+ NSCLC regardless of race, although EGFRm occur more frequently in Asian patients (Table). We investigated the association between race, EGFR testing and receipt of subsequent first-line (1L) treatment with the third-generation EGFR TKI, osimertinib. Methods: This retrospective, observational study used the nationwide Flatiron Health EHR-derived de-identified database. Adults with an initial diagnosis of stage IV NSCLC who initiated systemic 1L therapy between Apr 2018 (osimertinib approval) and Feb 2022 (data cutoff date) were eligible. Two cohorts were defined: those eligible for EGFR testing, and those EGFRm+ patients eligible for 1L osimertinib. Multivariable logistic regression was used to investigate odds of 1) EGFR testing, and 2) 1L osimertinib use, by race. Random-effects logistic regression was used as a sensitivity analysis to evaluate the impact of inter-practice variation on each outcome. Confidence intervals (CI) were calculated at 95%. Results: 9,505 patients were eligible for EGFR testing. After adjustment, Asian patients were nearly twice as likely to be tested (adjusted odds ratio [aOR]: 1.93, CI: 1.33 – 2.89, p = 0.0001), while Black patients were 25% less likely to receive testing (aOR: 0.75, CI: 0.62 – 0.90, p = 0.002), both relative to White patients. Including a random factor of practice attenuated the effect of race for Asian patients (aOR: 1.74, CI: 1.15 – 2.64, p = 0.0009) as well as Black patients (aOR: 0.8, CI: 0.65-0.97, p = 0.021). Of these patients, 1,247 were confirmed EGFRm+ and were thus eligible for 1L osimertinib. Asian patients were marginally more likely to receive 1L osimertinib, even after adjustment ( aOR: 1.51, CI: 0.958 – 2.43, p =.082). The inclusion of a random factor of practice diminished the marginal effect of race ( aOR: 1.46, CI: 0.90 – 2.36, p = 0.1). Conclusions: Retrospective analyses using real-world data revealed differences across races in EGFR testing among patients with stage IV NSCLC, suggesting disparities in quality of care. Racial disparities were also observed in 1L osimertinib use among patients with EGFRm+. Sensitivity analyses suggest that these disparities may partially be attributed to differences in care between practices. Future studies are warranted to further characterize this unexpected race-based difference in biomarker testing and treatment initiation. This work highlights the need for investigations of racial disparities in access to both biomarker testing and effective treatment options across precision oncology.[Table: see text]

Using real-world cohorts to assess the generalizability and relevance of randomized clinical trials (RCTs)

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Background: RCTs are the gold standard for understanding the efficacy of new treatments, however, patients (pts) in RCTs often differ from those treated in the real-world. Further, selecting a standard of care (SOC) arm is challenging as treatment options may evolve during the course of a RCT. Our objective was to assess the generalizability and relevance of RCTs supporting recent FDA approvals of anticancer therapies. Methods: RCTs were identified that supported FDA approvals of anticancer therapies (1/1/2016 - 4/30/2018). Relevant pts were selected from the Flatiron Health longitudinal, EHR-derived database, where available. Two metrics were calculated: 1) a trial’s pt generalizability score (% of real-world pts receiving treatment consistent with the control arm therapy for the relevant indication who actually met the trial's eligibility criteria) and 2) a trial’s SOC relevance score (% of real-world pts with the relevant indication and meeting the trial's eligibility criteria who actually received treatment consistent with the control arm therapy). All analyses excluded real-world pts treated after the relevant trial’s enrollment ended. Results: 14 RCTs across 5 cancer types (metastatic breast, advanced non-small cell lung cancer, metastatic renal cell carcinoma, multiple myeloma, and advanced urothelial) were included. There was wide variation in the SOC relevance and pt generalizability scores. The median pt generalizability score was 63% (range 35% - 88%), indicating that most real-world pts would have met the RCT eligibility criteria. The median SOC relevance score was 37% (range 15% - 74%), indicating that most RCT control arms did not reflect the way trial-eligible real-world pts in the US were actually treated. Conclusions: There is great variability across recent RCTs in terms of pt generalizability and relevance of SOC arms. Real-world data can be used to inform selection of control arms, predict impact of inclusion/exclusion criteria, and also assess the generalizability of the results of completed trials. Incorporating real-world data in planning and interpretation of prospective clinical trials could improve accrual and enhance relevance of RCT outcomes.

Real-World Outcomes of Patients with Metastatic Non-Small Cell Lung Cancer Treated with Programmed Cell Death Protein 1 Inhibitors in the Year Following U.S. Regulatory Approval

BACKGROUND

Evidence from cancer clinical trials has strong internal validity but can be difficult to generalize to real-world patient populations. Here we analyzed real-world outcomes of patients with metastatic non-small cell lung cancer (mNSCLC) treated with programmed cell death protein 1 (PD-1) inhibitors in the first year following U.S. regulatory approval.

MATERIALS AND METHODS

This retrospective study leveraged electronic health record (EHR) data collected during routine patient care in community cancer care clinics. The cohort included patients with mNSCLC who had received nivolumab or pembrolizumab for metastatic disease (n = 1,344) with >1 EHR-documented visit from January 1, 2011, to March 31, 2016. Patients with a > 90-day gap between advanced disease diagnosis and first EHR structured data entry were excluded.

RESULTS

Estimated median overall survival (OS) was 8.0 months (95% confidence interval 7.4-9.0 months). Estimated median OS was 4.7 months (3.4-6.6) for patients with anaplastic lymphoma kinase rearrangement- and epidermal growth factor receptor mutation-positive tumors, and 8.6 months (7.7-10.6) for patients without such mutations. Age at PD-1 inhibitor initiation or line of therapy did not impact OS.

CONCLUSION

This analysis suggests OS in real-world patients may be shorter than in conventional clinical trial patient cohorts, potentially due to narrow trial eligibility criteria. The lack of difference in OS by line of therapy or age at immunotherapy initiation suggests sustained benefit of PD-1 inhibitors in multitreated patients with mNSCLC and that age is not a predictor of outcome. Further studies are underway in patients with comorbidities, organ dysfunction, and multiple prior therapies.

IMPLICATIONS FOR PRACTICE

This study evaluated data derived from electronic health records of patients with metastatic non-small cell lung cancer treated with programmed cell death protein 1 (PD-1) inhibitors in the year following regulatory approval. This real-world cohort had shorter overall survival (OS) indexed to PD-1 inhibitor initiation than reported in clinical trials. Late-line treatment did not influence OS, and patients aged >75 at immunotherapy initiation did not have worse outcomes than younger patients. As new therapies enter clinical practice, real-world data can complement clinical trial evidence providing information on generalizability and helping inform clinical treatment decisions.

Development and Validation of a High-Quality Composite Real-World Mortality Endpoint

OBJECTIVE

To create a high-quality electronic health record (EHR)-derived mortality dataset for retrospective and prospective real-world evidence generation.

DATA SOURCES/STUDY SETTING

Oncology EHR data, supplemented with external commercial and US Social Security Death Index data, benchmarked to the National Death Index (NDI).

STUDY DESIGN

We developed a recent, linkable, high-quality mortality variable amalgamated from multiple data sources to supplement EHR data, benchmarked against the highest completeness U.S. mortality data, the NDI. Data quality of the mortality variable version 2.0 is reported here.

PRINCIPAL FINDINGS

For advanced non-small-cell lung cancer, sensitivity of mortality information improved from 66 percent in EHR structured data to 91 percent in the composite dataset, with high date agreement compared to the NDI. For advanced melanoma, metastatic colorectal cancer, and metastatic breast cancer, sensitivity of the final variable was 85 to 88 percent. Kaplan-Meier survival analyses showed that improving mortality data completeness minimized overestimation of survival relative to NDI-based estimates.

CONCLUSIONS

For EHR-derived data to yield reliable real-world evidence, it needs to be of known and sufficiently high quality. Considering the impact of mortality data completeness on survival endpoints, we highlight the importance of data quality assessment and advocate benchmarking to the NDI.

Characteristics of Real-World Metastatic Non-Small Cell Lung Cancer Patients Treated with Nivolumab and Pembrolizumab During the Year Following Approval

BACKGROUND

Evidence from cancer clinical trials can be difficult to generalize to real-world patient populations, but can be complemented by real-world evidence to optimize personalization of care. Further, real-world usage patterns of programmed cell death protein 1 (PD-1) inhibitors following approval can inform future studies of subpopulations underrepresented in clinical trials.

MATERIALS AND METHODS

We performed a multicenter analysis using electronic health record data collected during routine care of patients treated in community cancer care clinics in the Flatiron Health network. Real-world metastatic non-small cell lung cancer (NSCLC) patients who received nivolumab or pembrolizumab in the metastatic setting (n = 1,344) were selected from a starting random sample of 55,969 NSCLC patients with two or more documented visits from January 1, 2011, through March 31, 2016. The primary study outcome measurement was demographic and treatment characteristics of the cohort.

RESULTS

Median age at PD-1 inhibitor initiation was 69 years (interquartile range 61-75). Patients were 56% male, 88% smokers, 65% nonsquamous histology, and 64% diagnosed at stage IV. Of 1,344 patients, 112 (8%) were tested for programmed death-ligand 1 expression. Overall, 50% received nivolumab or pembrolizumab in the second line, with a substantial proportion of third and later line use that began to decline in Q4 2015.

CONCLUSION

During the year following U.S. regulatory approval of PD-1 inhibitors for treatment of NSCLC, real-world patients receiving nivolumab or pembrolizumab were older at treatment initiation and more had smoking history relative to clinical trial cohorts. Studies of outcomes in underrepresented subgroups are needed to inform real-world treatment decisions.

IMPLICATIONS FOR PRACTICE

Evidence gathered in conventional clinical trials used to assess safety and efficacy of new therapies is not necessarily generalizable to real-world patients receiving these drugs following regulatory approval. Real-world evidence derived from electronic health record data can yield complementary evidence to enable optimal clinical decisions. Examined here is a cohort of programmed cell death protein 1 inhibitor-treated metastatic non-small cell lung cancer patients in the first year following regulatory approval of these therapies in this indication. The analysis revealed how the real-world cohort differed from the clinical trial cohorts, which will inform which patients are underrepresented and warrant additional studies.

Opportunities and challenges in leveraging electronic health record data in oncology

The widespread adoption of electronic health records (EHRs) and the growing wealth of digitized information sources about patients is ushering in an era of 'Big Data' that may revolutionize clinical research in oncology. Research will likely be more efficient and potentially more accurate than the current gold standard of manual chart review studies. However, EHRs as they exist today have significant limitations: important data elements are missing or are only captured in free text or PDF documents. Using two case studies, we illustrate the challenges of leveraging the data that are routinely collected by the healthcare system in EHRs (e.g., real-world data), specific challenges encountered in the cancer domain and opportunities that can be achieved when these are overcome.

Synthesis and characterization of regiorandom and regioregular poly(3-octylfuran)

Poly(3-octylfuran) has been synthesized with three regioregularities: P3OF-95, P3OF-75, and P3OF-50, where the number signifies the percentage HT content. The 95% HT material is highly crystalline with a structure similar to that of HT-poly(3-octylthiophene), P3OT. The lamellar spacing is 22.1 A and the pi-stacking distance is 3.81 A. UV-vis spectroscopy reveals that P3OF-95 is aggregated in CHCl(3) solution, and solid films of P3OF-95, but not P3OF-75 or -50, show Davydov and exciton band splitting due to the interactions of the pi-systems in the stacked morphology. An estimate of the Davydov splitting is 0.15 eV (1200 cm(-1)). P3OF is reversibly oxidized at 0.32 V vs ferrocene/ferrocenium, but increasing the potential to 1.15 V leads to irreversible oxidation. Films of P3OF may be p-doped with iodine vapor. Doped P3OF-95 and -75 films have electrical conductivities of 10(-2) and 10(-7) S/cm, respectively. The UV-vis-NIR spectra of the iodine-doped films are interpreted in terms of molecular-like transitions involving the LUMO, HOMO, HOMO-1, and transitions across a Peierls distortion-induced gap in the intermolecular conduction band that is formed by the overlap of the pi-systems of the stacked partially oxidized chains. The conduction band gap estimated for P3OF-95 is 0.34 eV, and that for P3OF-75 is 0.9 eV. The P3OF samples are thermally stable in N(2) atmosphere to between 275 degrees C (P3OF-50) and 380 degrees C (P3OF-95), but suffer thermal oxidation above 150 degrees C or light-induced oxidation at room temperature.

Asymmetric syntheses of fused bicyclic compounds by conjugate additions of allylic organolithium species to activated olefins and subsequent cyclizations

[reaction: see text]. Addition of the configurationally stable organolithium species produced by enantioselective deprotonation of N-Boc-N-(p-methoxyphenyl) allylamines to alpha,beta-unsaturated carbonyl compounds affords 1,4-addition products in good yields with high diastereomeric and enantiomeric ratios. Further transformations of these compounds provide [3.3.0]-, [4.3.0]-, [5.3.0]-, and [5.4.0]-carbocycles and heterocycles with high stereoselectivities.

Dynamic thermodynamic resolution: control of enantioselectivity through diastereomeric equilibration

A theoretical foundation, tools for recognition and control, and recent examples of a class of asymmetric transformation termed dynamic thermodynamic resolution are presented. Enantioselective reaction pathways that involve an induced diastereomeric equilibration to intermediates, which are configurationally stable on the time scale of a subsequent reaction, are illustrated. Dynamic thermodynamic resolution differs from the classic, well-documented pathways of kinetic resolution and dynamic kinetic resolution in that equilibration and resolution can be operative on one system in separate controllable steps. This approach offers a high level of flexibility and provides multiple opportunities for optimization of enantioselectivity.

The promoter of the plant defensin gene PDF1.2 from Arabidopsis is systemically activated by fungal pathogens and responds to methyl jasmonate but not to salicylic acid

The plant defensin PDF1.2 has previously been shown to accumulate systemically via a salicylic acid-independent pathway in leaves of Arabidopsis upon challenge by fungal pathogens. To further investigate the signalling and transcriptional processes underlying plant defensin induction, a DNA fragment containing 1184 bp and 1232 bp upstream of the transcriptional and translational start sites, respectively, was cloned by inverse PCR. To test for promoter activity this DNA fragment was linked to the beta-glucuronidase (GUS)-encoding region of the UidA gene as a translational fusion and introduced into Arabidopsis ecotype C-24. Challenge of the transgenic plants with the fungal pathogens Alternaria brassicicola and Botrytis cinerea resulted in both local and systemic induction of the reporter gene. Wounding of the transgenic plants had no effect on GUS activity. Treatment of the transgenic plants with either jasmonates or the active oxygen generating compound paraquat strongly induced the reporter gene. In contrast, neither salicylate nor its functional analogues 2,6-dichloroisonicotinic acid and 1,2,3-benzothiodiazole-7-carbothioic acid S-methyl ester resulted in reporter gene induction. These results are consistent with the existence of a salicylic acid-independent signalling pathway, possibly involving jasmonates as regulators, that is triggered by pathogen challenge but not by wounding. The transgenic plants containing the PDF1.2-based promoter-reporter construct will provide useful tools for future genetic dissection of this novel systemic signalling pathway.

A peroxidase gene promoter induced by phytopathogens and methyl jasmonate in transgenic plants

The expression of two closely related peroxidase isogenes, Shpx6a and Shpx6b, of the legume Stylosanthes humilis was studied using isogene-specific reverse transcriptase PCR techniques. Results indicated that transcripts of both genes were rapidly induced following inoculation with the fungal pathogen Colletotrichum gloeosporioides, wounding and treatment with the defense regulator methyl jasmonate (MeJA). In contrast treatment of leaves of S. humilis with abscisic acid (ABA) and salicylic acid (SA) did not induce transcripts of either isogene. A genomic clone containing the Shpx6b gene was isolated and 594 bp of 5' sequence upstream of the translation start was fused in frame to the coding region of the uidA reporter gene and introduced into tobacco. Expression from the Shpx6b promoter in transgenic plants was determined by histochemical staining and quantitative assays of beta-glucuronidase (GUS). In transgenic tobacco, GUS expression was detected in cotyledons, vascular cells of young leaves, anthers, pollen, and the stigma and style. Wounding of the tobacco plants produced very localized GUS staining. Much more extensive staining for GUS was observed following inoculation of tobacco leaves with conidia of the fungal pathogen Cercospora nicotianae and the inoculation of wound sites with mycelium of the Oomycete pathogen Phytophthora parasitica var. nicotianae. Treatment of mature leaves with methyl jasmonate induced GUS activity while treatment with ABA, SA, and H2O2 had no effect. A similar strong induction of GUS activity was measured in young transgenic seedlings germinated on MeJA while some, but much weaker, induction of GUS activity was observed in seedlings treated with SA. The sequence of the promoter contained motifs homologous to putative cis elements in other plant genes responsive to MeJA. The Shpx6b gene is the first plant peroxidase gene shown to be induced by both microbial pathogens and MeJA and its promoter will be useful for investigations of signaling processes during fungal infection and for the expression of foreign gene products at infection sites.

Gypsy-class retrotransposon sequences in organisms related to the leaf mould fungus, Cladosporium fulvum

Gypsy retrotransposons are a major branch of retroid elements and have been found in a wide diversity of eukaryotic organisms including CfT-1 in the tomato leaf mould pathogen, the fungus Cladosporium fulvum (syn. Fulvia fulva). We have examined organisms that are either ecologically or phylogenetically related to C. fulvum, for elements related to CfT-1. Using PCR and Southern hybridisation, similar sequences were found only in the co-genic fungus Cladosporium cladosporioides. This finding confirms the apparent ubiquity of retroelements, suggests that the phylogeny of retrotransposons is consistent with the phylogeny of their hosts and argues against frequent horizontal gene transfer.

Differential expression of peroxidase isogenes during the early stages of infection of the tropical forage legume Stylosanthes humilis by Colletotrichum gloeosporioides

Infection of Stylosanthes humilis by the fungal phytopathogen Colletotrichum gloeosporioides is associated with an increase in peroxidase enzyme activity within 24 h postinoculation. Peroxidase gene expression was investigated as a first step towards understanding the regulation and functional importance of this host response to fungal attack. Four distinct cDNAs Shpx 2, 5, 6, and 12, isolated from a cDNA library of S. humilis contained deduced amino acid (aa) sequence motifs characteristic of peroxidases. Three of these (Shpx 2, 5, and 6) were full-length and their deduced proteins each fell into a different homology group based on comparisons with other plant peroxidases. Each cDNA appeared to hybridize to only one or two genes in S. humilis. mRNAs corresponding to Shpx2, Shpx6, and Shpx12 were expressed relatively abundantly in young leaves, with lesser expression of Shpx2 and Shpx6 and no expression of Shpx12 detected in roots. No expression of these genes was detected in stems or old leaves. The mRNA of Shpx5 was relatively abundant in stems and to a lesser extent in young leaves. However, infection of young leaves with C. gloeosporioides greatly increased expression of the mRNAs of Shpx2 and Shpx6 but not Shpx5 nor Shpx12 compared to mock-inoculated controls. The mRNA of Shpx6 was strongly induced by the pathogen 4 h postinoculation, a time which precedes fungal penetration, while Shpx2 was induced to higher levels than controls at 24 h after inoculation. The mRNAs of both Shpx2 and Shpx6 but not Shpx5 and Shpx12 were also induced by wounding.(ABSTRACT TRUNCATED AT 250 WORDS)

The phylogeny of the tomato leaf mould fungus Cladosporium fulvum syn. Fulvia fulva by analysis of rDNA sequences

The nucleotide sequence of part of the ribosomal DNA from races of the fungal tomato pathogen Cladosporium fulvum and other Cladosporium species have been determined. Comparisons of the internal transcribed spacer regions (ITS1 and ITS2) of several C. fulvum races showed complete sequence homology suggesting a recent evolutionary divergence. Comparisons of these nucleotide sequences in the ITS region with those of other Cladosporium species showed the close relationship within the Cladosporium genus. Using the nucleotide sequence of part of the 18s ribosomal subunit from these isolates and comparing them with sequences of some Ascomycetes, Basidiomycetes and Chytridiomycetes, obtained from GenBank, we infer the phylogeny of the Cladosporium species studied here. Our analysis shows that the Cladosporia form a monophyletic group which falls within the order Ascomycotina.

Investigation of the specificity of the interaction between colicin E9 and its immunity protein by site-directed mutagenesis

Comparison of the amino acid sequences of the C-terminal domain of three DNAase type E colicins has identified six candidate specificity determinants for the interaction of these E colicins with their homologous immunity proteins. We have changed these candidate specificity determinants of colicin E9, using site-directed mutagenesis, to the corresponding amino-acids of colicin E8. A 'mutant' colicin E9, in which four of the six candidate specificity determinants have been changed, demonstrated colicin activity against Escherichia coli indicator strains which carried either the E8imm or the E9imm genes, indicative of a 'novel' E. colicin. After changing all six of the candidate specificity determinants, the resulting colicin E9 'mutant' exhibited a phenotype very similar to that of colicin E8.

An evolutionary relationship between the ColE5-099 and the ColE9-J plasmids revealed by nucleotide sequencing

The nucleotide sequence of a 1124 bp fragment of the ColE5-099 plasmid which encodes colicin E5 immunity, a lys gene involved in colicin release from the host cell, and the 3' end of the colicin E5 structural gene has been determined. Open reading frames corresponding to the three genes have been located by analogy with similar sequences from other E colicin plasmids. The location of these open reading frames corresponds with the position of the genes as determined by subcloning and transposon mutagenesis. The amino acid sequence of the carboxy-terminal 107 amino acid residues of the colicin E5 gene shows no homology with any other E colicin, suggesting a different mode of action in killing sensitive cells. A comparison of the nucleotide sequence of this region of the ColE5-099 plasmid with that of the equivalent region of the ColE9-J plasmid suggests a close evolutionary relationship between these two plasmids.

Automated nursing documentation: a design perspective

The concept of an automated nursing documentation system has been subject to casual debate for a number of years. During this time, Hewlett-Packard developed a system that is both adequate and workable from many perspectives (i.e. the Staff Notes Subsystem of the Patient Data Management System-PDMS). This package has been used as the primary method to document patient care for six years in the Critical Care Units of Phoenix Baptist Hospital. With the aid of Baptist Hospitals and Health Systems (BHHS) Design Engineers, it continues to evolve predicated on a singular intent: To provide the type of documentation required by the medical staff. The objective of this paper is multifold. Foremost, generalized criteria are established to provide a vehicle for standardizing the design or evolution of a staff notes package. The generic structure of the PDMS notes subsystem is discussed in regard to its parity with these criteria. Finally, custom modifications and additions to this package will be presented, and recommendations for future enhancements will be outlined.