Sample Size Research Articles

Standardization of seed testing procedure techniques in Sunnhemp (Crotalaria juncea) var ADT 1

This abstract presents a comprehensive overview of seed testing procedures techniques specifically designed for sunnhemp (Crotalaria juncea) var ADT 1, an important leguminous plant exploited for its versatile uses in agriculture and various industries. The seed testing procedure comprises a systematic approach to evaluate the quality, viability, and germination potential of sunnhemp seeds, crucial for ensuring successful crop establishment and yield optimization. Seed testing procedure viz., test weight determination, sample size estimation, purity assessment, standardization of germination media, temperature requirement for germination and determination of first count, final count was highlighted. The experiment results revealed that submitted sample size could be 700g, while the working sample size was be 70g and minimum standards for the pure seed and the inert matter percentage were found to be 98 and 1.5 per cent respectively. In seed germination test, paper medium with roll towel registered maximum germination percentage (96%) and vigour index (2146). Similarly, 30oC temperature was registered maximum germination percentage. Based on this result the first count and final count was fixed as 3rd and 10th day in sunnhemp var ADT 1. Thus, seed testing procedures contributes to advancement in the evaluation of sunnhemp seed quality, thereby promoting sustainable agriculture and economic prosperity.

Abstract 637: Single-cell analysis of systemic immune response to sequential radiation and immune checkpoint blockade in metastatic colorectal cancers

Abstract Immune checkpoint blockade (ICB) has shown significant clinical efficacy in mismatch repair deficient colorectal cancers (CRCs). However, an effective means to use these therapies for mismatch repair proficient (pMMR) CRC has yet to be developed. To enhance the efficacy of ICB for patients with oligometastatic pMMR CRC, we performed a clinical trial evaluating the sequential use of stereotactic body radiotherapy (SBRT), pembrolizumab, surgical resection, and then adjuvant pembrolizumab (NCT02837263). The primary endpoint of 1-year recurrence-free survival (1 yr RFS) was met in 60% of trial participants compared to a historical control of 50%. From this trial, 13 subjects could have blood samples collected for peripheral blood mononuclear cell isolation pretreatment and after operative management. We hypothesize that the systemic immune response changes upon combined treatment and is distinct between responders and non-responders. We performed scRNA-Seq on these samples to compare the circulating immune cell populations with clinical outcomes. Despite a small sample size, integrated bioinformatics analysis identified (i) pre-existing CD8+ T cells were observed with treatment response (p = 0.031) (ii) combined RT and ICB induces changes in myeloid cell phenotypes, including reduced pro-inflammatory monocytes (p = 0.038) and conventional cDC2 (p = 0.030) in subjects without recurrence and increasing pDCs (p = 0.024) in most patients. CD8+ T cells from those recurrence-free subjects showed terminally differentiated effector phenotypes, expressing CX3CR1, GZMB, and KLRG1 before treatment. cDC2s expressed interferon activity markers, including STAT1, IFI44, and IRF7, that presented a more activated state. CD8+ T cell abundance remained stable, with no significant changes before and after treatment. In contrast, myeloid cells showed greater variability, reflecting unique polarization states through differences in cytokine (CCL3, CXCL8), interferon (ISG15, IFI44), and complement (C1QA, C1QB) associated genes. Future work will increase sample size in independent patient cohorts to elucidate the extent to which circulating phenotypes are also identified in tumors. Overall, this study demonstrates pre-existing T cell abundance and changes in myeloid cell phenotypes may be associated with clinical outcomes from combined immunotherapy, which have the potential to serve as predictive biomarkers for therapeutic response. Citation Format: Joshua Brand, Sean G. Kraus, Michael Bassetti, Dustin A. Deming, Huy Q. Dinh. Single-cell analysis of systemic immune response to sequential radiation and immune checkpoint blockade in metastatic colorectal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 637.

Convergence Analysis on A Data-Driven Inexact Proximal-Indefinite Stochastic ADMM

In this paper, we propose an Inexact Proximal-indefinite Stochastic ADMM (abbreviated as IPS-ADMM) to solve a class of separable convex optimization problems whose objective functions consist of two parts: one is an average of many smooth convex functions and the other is a convex but potentially nonsmooth function. The involved smooth subproblem is tackled by an inexact accelerated stochastic gradient method based on an adaptive expansion step to avoid the scenario that the sample size can be extremely huge so that computing the objective function value or its gradient is much more expensive. The involved nonsmooth subproblem is solved inexactly under a relative error criterion to avoid the case that the proximal operator is potentially unavailable. In contrast to most deterministic and stochastic ADMM algorithms, our dual variable updates twice and allows a more flexible and larger stepsize region. By a variational analysis, we characterize the generated iterates as a variational inequality and finally establish the sublinear convergence rate of this IPS-ADMM in terms of the objective function gap and constraint violation. Experiments on solving the 3D CT reconstruction problem in medical imaging and the graph-guided fused lasso problem in machine learning show that our IPS-ADMM is very promising.

Abstract 842: Early clinical outcomes of pembrolizumab plus neoadjuvant chemotherapy in early stage triple negative breast cancer in a Hispanic majority community

Abstract Background: Triple-negative breast cancer (TNBC) accounts for 15% of breast cancers, and it has a poor prognosis with a five-year survival of 8 to 16% lower than that of hormone receptor-positive disease. There is a high prevalence of TNBC among Hispanics. In KEYNOTE-522 (KN522), a phase 3 trial, pembrolizumab plus neoadjuvant chemotherapy had been shown to be an effective option for pathological complete response (pCR) in early-stage TNBC as compared to neoadjuvant chemotherapy alone at the time of definitive surgery. While this treatment protocol showed promising data, immune checkpoint inhibitors such as pembrolizumab have been known to cause immune-related adverse effects (iRAEs) such as thyroiditis. There are limited studies on the efficacy of this treatment protocol and its adverse effects in Hispanic communities. Our study aims to present the relationship between pCR and immune-mediated thyroiditis in pembrolizumab plus neoadjuvant therapy for early-stage TNBC in a Hispanic-majority population in South Texas. Methods: This is a retrospective analysis of patients with stage II or III TNBC at Mays Cancer Center in San Antonio, Texas between January 2020 to November 2024. This KN522 treatment protocol included neoadjuvant therapy with four cycles of pembrolizumab every 3 weeks plus paclitaxel and carboplatin. Patients then received four additional cycles of pembrolizumab and doxorubicin-cyclophosphamide or epirubicin-cyclophosphamide. At the 24-week mark, patients were assessed to see if they had successfully completed the KN522 protocol as planned. Patients were assessed for pCR at the time of definitive surgery. Outcomes include assessing for the development of immune-mediated thyroiditis. Statistical analysis to compare outcomes between Hispanics and non-Hispanics was performed using R v4.2. Results: 66 patients were originally identified on review. 3 patients were excluded based on incomplete data. 63 patients were identified (68.3% Hispanic, 31.6% Non-Hispanic). At the time of definitive surgery, 55.6 % of patients had pCR (62.9% Hispanic, 37.1% Non-Hispanic) vs 44.4% with no pCR (75.0% Hispanic, 25.0% Non-Hispanic) with a p-value = 0.3. Comparing pCR and the development of immune-mediated thyroiditis, 14 patients with pCR (40%) vs 9 patients with no pCR (32.1%) developed immune-mediated thyroiditis with a p-value = 0.5. Conclusion: There was no difference in pCR with pembrolizumab plus neoadjuvant chemotherapy between Hispanic and non-Hispanic populations. Furthermore, there was no difference in pCR between patients who developed immune-mediated thyroiditis or not. Our results were notable for occurring in a Hispanic majority population, but our study was limited by a small sample size. More studies are needed with a larger sample size to ascertain if there is a difference in outcomes between Hispanic vs non-Hispanic patients. Citation Format: Aymen Baig, Erin C. Kaser, Nico-al Paolo Gotera, Jay Parekh, Ranjit S. Banwait, Marcela Mazo Canola. Early clinical outcomes of pembrolizumab plus neoadjuvant chemotherapy in early stage triple negative breast cancer in a Hispanic majority community [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 842.

White core thickness effect on 3D-printed color reproduction

Abstract 3D printing is an ever-expanding set of techniques with different materials and applications. Of these applications, color 3D printing has proven to be essential in various fields. Some color 3D printing techniques use colored inks, and the characteristics of these inks, especially translucency and scattering, are vital in color reproduction using 3D printing. 3D-printed color models usually contain two parts: a colored exterior and a hidden white core. Ink translucency is known to affect the output color, but the influence of translucency and scattering from the white core is yet to be studied. Studying the effect of the white core will allow for more accurate color reproduction using translucent ink. In this paper, we investigate the effect of white core thickness on reproduced colors using translucent-colored inks. We quantify and illustrate the change in color via color measurements using a hand-held spectrophotometer and a hyper-spectral camera. CIEDE2000 color difference between the samples varying in white core thickness is calculated, and the visual color change is studied via color gamut comparison. It is observed that, up until a certain thickness, reproduced color, when using translucent inks, varies with the thickness of the white core, even when the colored layers of the samples are intact. This, in turn, means that for optimal color reproduction using translucent ink, the sample size, i.e., the white core thickness, is a variable that should be accounted for in the design process, especially for models with a thickness less than 2 mm.

Demystifying the Attitudes of Small and Medium Enterprises Employers towards Gender Diversity in Namibia

This study explored for the attitudes of small and medium enterprises employers towards gender diversity. The study was conducted through qualitative methods, with data collected from a purposively selected sample drawn from the population of 1238 SMEs operating within the capital city, Windhoek. The sample size was 65 and data were gathered through focus group discussions. Data were analyzed through content analysis conducted manually in order to allow in- depth interaction with data. The study found that many SME employers adopt an indecisive stance toward the implementation of gender diversity. While some SMEs recognize the importance of gender diversity, there is limited indication of formal policy supporting it. Findings also pointed to the absence of understanding and poor training on the value of gender diversity as causes of failure by SMEs to adopt gender diversity. Low leadership commitment to creating diversity and inclusion in the workplace is also a challenge. The findings further show that management's perceptions of gender diversity are not necessarily congruent with the expectations of employees. It has also been found that most SMEs fall behind in embracing realistic approaches to a diverse workplace, primarily because of constrained resources or strategic plans. Further, the research highlights organizational culture as an important predictor of gender diversity attitudes. Employee recruitment and promotion in most SMEs are dictated by social norms and traditional gender roles. To enhance gender diversity in Namibian SMEs, these businesses should have a proper gender diversity policies, offering definite guidelines on recruitment, promotion, and inclusion. The study also recommended diversity audits every year to track progress, inclusion of mandatory gender sensitivity and bias training for employees and management. Training could be performed quarterly using inexpensive workshops or web-based courses, with the impact assessed within a year. SMEs should also set specific objectives for gender diversity, such as having more women in leadership positions. This would allow continuous measurement of progress.

Abstract 4560: Use of ctDNA fragmentomics as a predictive biomarker in locally advanced non-small cell lung cancer

Abstract Introduction: Locally advanced non-small cell lung cancer (NSCLC) is a serious condition with a poor 5-year survival rate of approximately 30%. Standard treatment involves chemoradiotherapy (CRT) followed by immunotherapy (IO). However, predicting benefit prior to CRT and monitoring response post treatment are areas of unmet need. Cancers, like many tissues, release fragments of DNA into the bloodstream, which can be detected using whole genome sequencing (WGS). Research has shown that cancer cells tend to release shorter DNA fragments, typically between 90-150 base pairs, at higher rates than normal tissues. This study aims to analyze cell-free DNA fragment sizes (fragmentomics) as a predictive tool for assessing treatment response in patients with LA NSCLC. This tumor-uninformed approach is cost-effective and can be implemented using routine blood samples. Methods: Low-pass WGS at 0.1x coverage was performed on 40 pre-treatment plasma samples from patients LA NSCLC obtained from the UCL biobank. The median follow-up for the cohort was 33 months. To investigate the cancer origin of short DNA fragments (90-150 bp), mutation calling was conducted using Mutect2. Mutation density was defined as the number of mutations per million bases (MPM). Tumor volumes were obtained using CT imaging, and the percentage quantity of short DNA fragments was plotted against tumor volume. Enrichment of short fragments (SFE) <20% was assessed and correlated with clinical outcomes, including relapse and overall survival. Results: Short DNA fragments (90-150 bp) had a significantly higher mutation density (973.8 MPM) compared to unselected fragments (381.7 MPM; p<0.0001). This elevated mutational burden supports the hypothesis that shorter fragments are of cancer origin. Linear regression analysis showed no significant relationship between tumor volume and the percentage of short DNA fragments for the entire cohort (R2 = 0.035, p = 0.35). However, in lung squamous cell carcinoma (LUSC), a strong positive correlation was observed (R2 = 0.6787, p = 0.003). Suggesting a potential quantitative link between tumor burden and ctDNA quantity in this subtype. SFE was observed in 31 of 40 patients (78%) prior to treatment. SFE was found in similar proportions in LUSC (78%; 15/19) and lung adenocarcinoma (75%; 15/20). Mortality occurred in 45% (14/31) of patients with SFE, compared to 11.1% (1/9) of those without enrichment. Among patients for whom consolidation IO was indicated, relapse rates were higher in those with SFE (44%; 7/16) than in those without enrichment (25%; 1/4). Findings of the research were limited by sample size; however further centers have been recruited to address this issue. These findings suggest that fragmentomic patterns represent a cost-effective, non-invasive prognostic biomarker for LA NSCLC, with particular potential in LUSC. Ongoing research is exploring patterns following treatment. Citation Format: Kishen R. Patel, Anisha Mistry, Robert Monfries, Florent Mouliere, John R. Conibear, James Wilson, Karim Keshwani, Wing K. Liu, Crispin Hiley. Use of ctDNA fragmentomics as a predictive biomarker in locally advanced non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4560.

EVALUATING THE LEVEL OF CONTENTMENT AMONG NURSING STUDENTS AT NURSING INSTITUTES, KARACHI, PAKISTAN

Background: Life contentment denotes the measure to which an individual finds joy in their life, encompassing introspective reflections and constituting an element of overall happiness and self-well-being. Objective: To evaluate the level of contentment among generic BSN students. Methodology: The cross-sectional research study was conducted at two nursing institutes of Karachi, Pakistan from November 2024 to January 2025. The sample size was calculated by using Open Epi version 3.0 by taking the mean of 19.03 with a standard deviation 4.94 from a previous study. A convenient sample technique was used to collect the data from 103 respondents by using a validated questionnaire, CLASS after approval from the designated nursing institutes. All the 18 years above generic BSN students were included, while all the nursing interns and Post- RN BSN students were excluded. Results: As contentment has a significant impact on their path to become future nurses, encouraging happiness is an essential part of nursing students' education and growth. Results of this study showed that (13.6 %) of the participants had a low degree of contentment, (40.77%) had average level of contentment while (45.63%) reported a high degree of contentment. Conclusion: Majority of the study participants reported high degree of contentment. The findings provided valuable insights into the well-being and contentment of nursing students.

Abstract 5810: Distinct mechanisms of CD28 and 4-1BB costimulation in glofitamab combination therapies for relapsed/refractory non-Hodgkin lymphoma (R/R NHL)

Abstract Background: Two recent Phase I studies (NCT04077723, NCT05219513) investigated CD19-targeted 4-1BB or CD28 costimulatory bispecifics combined with glofitamab in patients with R/R NHL, showing added efficacy benefit but with distinct response dynamics (Hutchings et al; Dickinson et al, ASH 2024). While both costimulators are designed to enhance the anti-tumor effects of T-cell engagers, we present, for the first time, key differences in the mechanisms and response profiles of CD28 and 4-1BB costimulation in these combinations. Methods: Exploratory biomarker analyses included 28 indolent and aggressive NHL patients treated with RO7443904 (CD19-CD28) and 99 with englumafusp alfa (CD19-4-1BBL) on Cycle 2 (C2) Day 8, after completion of glofitamab step-up dosing, followed by administration on the same day as glofitamab from C3 onwards (Q3W) for a fixed duration of 12 cycles. Peripheral immune profiling was done by flow cytometry, and gene expression and mutational profile of the tumors were characterized by mRNA- and targeted DNA-sequencing. On-treatment pharmacodynamic changes were compared to historical glofitamab data from NCT03075696 (n=140). The cross-trial comparisons were adjusted for differences in baseline characteristics and sample size. Results: Compared to glofitamab monotherapy, both costimulators boosted and sustained peripheral T-cell activation and proliferation, with 4-1BB primarily expanding HLA-DR+ CD8 cells (1.5-fold), indicating prolonged activation, and CD28 boosting CD4/CD8 proliferation (2-fold). Additionally, 4-1BB further increased both effector and central memory CD8 cells (1.5-fold), while CD28 selectively expanded effector memory CD8 cells (1.5-fold) relative to glofitamab alone. Both costimulators limited PD1+ T-cell expansion in a dose-dependent manner, with 4-1BB mainly affecting Temra cells and CD28 targeting effector memory cells. Complete responses occurred independently of recurrent mutations (e.g. TP53, CREBBP, B2M) or cell-of-origin. However, tumor-infiltrating conventional dendritic cells (cDCs) were linked to response to 4-1BB and immunosuppressive macrophages were linked to lack of response to CD28, as determined by gene expression profiling of pre-treatment biopsies. Conclusion: Our findings reveal distinct mechanisms of CD28 and 4-1BB costimulation with glofitamab, which may explain their different response dynamics. Specifically, 4-1BB promotes a sustained and prolonged immune response, while CD28 triggers rapid T-cell activation and proliferation. Moreover, 4-1BB appears to bypass macrophage suppression, and benefits from cDC-mediated antigen presentation and CD8 T-cell priming. These effects mirror those observed in second-generation CAR T-cell therapies and provide insight into how these off-the-shelf costimulators may be utilized based on tumor biology. Citation Format: Koorosh Korfi, Zhiwen Jiang, Sabine Wilson, Ailsa Christiansen, Wilfred Leung, Katharina Lechner, Natalie Dimier, Philip Knuckles, Kat Reyskens, Iva Lelios, Annika Blank, Alexandra Epp, Sylvia Herter, Johannes Sam, Paolo Caimi, Lorenzo Falchi, Roch Houot, Fritz Offner, Harriet Walter, Herve Ghesquieres, Guillaume Cartron, William Townsend, Giuseppe Gritti, Francesc Bosch, Michael Dickinson, Carmelo Carlo-Stella, Martin Hutchings, Franck Morschhauser. Distinct mechanisms of CD28 and 4-1BB costimulation in glofitamab combination therapies for relapsed/refractory non-Hodgkin lymphoma (R/R NHL) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5810.

Joint modeling of longitudinal endpoints and its applications to trial planning, monitoring and analysis

ABSTRACT In the context of clinical trial practices, the study power and sample size are typically determined based on the expected treatment effects on the primary endpoint collected over time. The utilization of longitudinal modeling for the primary endpoint offers a flexible approach that has the potential to reduce the sample size and duration of the trial, thereby improving operational efficiency and costs. Joint modeling of multiple endpoints presents a unique opportunity to understand how the primary endpoint evolves over time with other clinically important endpoints, and has the potential to increase precision of estimates and therefore increase study power when designing a study at planning stage and enhance understanding and interpretation of the data at a multi-dimensional level at the analysis stage. This approach enables a comprehensive evaluation of clinical evidence from various perspectives, rather than relying solely on isolated pieces of information. Joint modeling of multiple longitudinal endpoints would also help trial monitoring process as the trial accumulates clinical evidence of efficacy data, and there is a high demand in developing tools for statistical learning the treatment benefits on the go especially when the endpoint(s) is not well-established yet in some therapeutic indications. In this article, we will illustrate the use of joint modeling of longitudinal endpoints and its applications to study design, analysis, and trial monitoring practices. Simulation studies suggest that the potential efficiency gain would be achieved via leveraging information within endpoint over time and/or between endpoints. We developed an R shiny application to aid in and support identifying promising efficacy signals from endpoints under investigation during the trial monitoring. The implementation of the joint models and the added values will be discussed through case studies and/or simulation studies.

Therapeutic drug monitoring in anti-tuberculosis treatment: a systematic review.

The treatment of tuberculosis (TB) depends on anti-TB drugs to eradicate the infection and prevent its transmission. Variability in drug metabolism, interactions, and adherence can affect treatment efficacy. Therapeutic drug monitoring (TDM) is essential for optimizing treatment by adjusting dosages. This systematic review aimed to assess the effectiveness of TDM for anti-TB drugs using different biological matrices and to reveal the techniques employed in TDM. A systematic review included studies reporting anti-TB drug monitoring with relevant analytical methods. Reports were screened to include the type of study, population, countries, sample size, anti-TB drugs, biological matrices, sampling time, and analytical methods. This systematic review includes 35 articles that focus on methods for quantifying anti-TB drugs in clinical settings through observational studies. The research covers 21 countries, including China, USA, India, Italy, Indonesia, the Republic of Korea, and Germany, and involves diverse populations such as adults, children, and patients with MDR- and XDR-TB, as well as those with HIV co-infection. The studies examine a range of anti-TB drugs, from first-line treatments like isoniazid and rifampicin to second-line options such as bedaquiline and linezolid. Various sampling methods were employed, including human plasma, dried blood spots, urine, hair, and peripheral blood mononuclear cells, with analytical techniques such as LC-MS/MS, HPLC, and UPLC utilized to ensure precise measurement of drug levels. The assessment of diverse biological matrices and analytical techniques demonstrates that TDM improves treatment efficacy and safety by individualizing drug dosages. Further research is essential to standardize TDM protocols and investigate novel methodologies to enhance TB treatment outcomes.

Telemedicine apps and their influence on the tourism industry: a qualitative study

Purpose In spite of increasing interest in telemedicine, its impact on tourism remains underexplored. This study aims to analyse how telemedicine apps improve health-care access for tourists, emphasizing usability, benefits, challenges and safety perceptions while identifying integration barriers and opportunities. Design/methodology/approach This study uses a qualitative approach using grounded theory to develop a structured understanding of telemedicine’s role in tourism. Data collection involved semi-structured in-depth interviews, participant observation and document review with 10 experts from medicine, tourism, app development, consumer advocacy and academia recruited through theoretical sampling. The analysis used ATLAS.ti software with open, axial and selective coding to generate themes and construct a theoretical framework. Findings Telemedicine apps, primarily designed for medical management, also enhance tourist safety. However, usability challenges for older users and poor integration with tourism services hinder their adoption. Experts emphasized the importance of accessibility and user-friendly design, while concerns about medical data security were minimal. Research limitations/implications The findings are based on a small sample size of experts. Future studies could broaden the participant sample and include actual tourists to gain deeper insights. Practical implications Tourism providers should partner with telemedicine developers to enhance tourist safety. Training older users will improve adoption rates. Social implications Integrating telemedicine into tourism can improve access to health care, reduce travel-related health risks and promote proactive health management among tourists, benefiting public health. However, the widespread adoption of telemedicine in tourism requires alignment with existing data protection regulations such as the GDPR in Europe and the HIPAA in the USA. Originality/value This research provides novel insights into the connection of telemedicine and tourism, highlighting how telemedicine apps can enhance tourist safety and convenience. By integrating expert perspectives, the study offers practical recommendations for tourism stakeholders and app developers to foster innovation and adoption in both sectors.

Abstract 4927: Tumor tissue microbiome in the high-grade serous ovarian cancer: a pilot investigation within the African American Cancer Epidemiology Study

Abstract Background: High-grade serous ovarian cancer (HGSOC) is the most common histological subtype of ovarian cancer. Notably, Black and African American (AA) women face a ∼40% higher mortality risk from this disease compared to White women. Recent studies have suggested that intratumor microbes may play a key role in shaping the tumor microenvironment and influencing the prognosis of ovarian cancer. However, to date, no studies have investigated the tumor microbiome in Black/AA women diagnosed with HGSOC using formalin-fixed paraffin-embedded (FFPE) samples and a whole metagenome sequencing approach. Methods: We analyzed tumor FFPE samples from 20 HGSOC cases who self-identified as Black/AA and participated in the African American Cancer Epidemiology Study (AACES). Tumor DNA was extracted using a standardized protocol, and microbial profiling was performed using 2bRAD sequencing for microbiome (2bRAD-M), a high-precision, reduced-metagenome sequencing technique that enables species-level resolution. To assess tumor microbial differences by cancer stage and age at diagnosis, we compared tumor tissue microbial diversity, taxonomic composition, and functional pathways. Conventional statistical analyses (two-sample t-test and analysis of variance) were employed to evaluate significant differences across groups. Results: 2bRAD-M sequencing successfully detected tumor microbial DNA in all 20 participants of this pilot study. A total of 285 microbial species were identified, including 160 genera and 11 phyla, from results that passed quality control assessments. The mean alpha diversity, as measured by the Shannon index, was 2.41, and the Chao1 index was 15. Compared to women with localized (stage 1 and 2, n=8) HGSOC, those with stage 3 HGSOC (n=12) exhibited higher Shannon (mean 2.45 vs. 1.57, p=0.12) and Chao1 indices (mean 21 vs. 13, p < 0.001). Stage 3 tumors also showed a higher relative abundance of microbial species from the phyla Pseudomonadota, Bacteroidetes, and Bacillota, compared to localized stage tumors (p < 0.001). Pathway analysis identified secondary bile acid biosynthesis as the most significantly enriched pathway in stage 3 tumors, with over 1.5-fold higher abundance of this pathway (p < 0.0001) than stage 1 and 2 tumors. Age at diagnosis was also associated with microbiome composition; women diagnosed at a younger age (<50) had higher Shannon and Chao1 indices compared to older women. Additionally, women with younger age at diagnosis vs. ≥50) were more likely to have a lower relative abundance of Bacteroidetes and a higher abundance of the prolactin signaling pathway. Conclusion: Our pilot findings suggest that HGSOC tumor microbiome features measured among Black/AA women differ by stage and age at diagnosis, and thereby may influence the progression of HGSOC. Further studies with larger sample size are warranted as the next step. Citation Format: Tengteng Wang, Lauren C. Peres, Jeffrey R. Marks, Courtney E. Johnson, Elisa V. Bandera, Joellen M. Schildkrau. Tumor tissue microbiome in the high-grade serous ovarian cancer: a pilot investigation within the African American Cancer Epidemiology Study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4927.

Abstract 4644: Real-world outcomes in dual checkpoint inhibitor therapy: A single community center perspective

Abstract Introduction: Immunotherapy using dual checkpoint inhibitors is used to induce an antitumor response towards cancer. The varied response in treatment outcomes for those who receive dual checkpoint may be influenced by many factors. We attempted to interrogate factors impacting response to dual checkpoint inhibitor therapies in a single-center retrospective analysis, with the primary objective of examining how these factors may influence cancer progression. Methods: This single-center retrospective analysis examines patients with documented treatment histories of dual immunotherapy between 2015 and 2023. Additional data collected included: demographics, disease characteristics, additional treatment history, imaging, and next generation sequencing results. The primary endpoint of this study was progression free survival, with the secondary endpoint of overall survival. Patients were excluded from the study if they passed within one month of starting dual immunotherapy, were being treated for more than one form of cancer or had insufficient documentation. Results: In this study, the median age at the start of dual immunotherapy was 65 years old (range 30 to 84). Of the 144 patients examined, 20% were diagnosed with stage II or stage III cancer, 76% were diagnosed with stage IV cancer, and 3.5% had an undetermined stage at the start of dual immunotherapy. The most common diagnoses were melanoma (42%), kidney cancer (29%), and lung cancer (9%). 47% of the patients received 4 doses of dual immunotherapy and the next most common group received 2 doses (22%). 51 of the patients had their tumor mutation burden (TMB) assessed with 31% of the patients in this subgroup determined to have a high TMB. 33 patients had PD-L1 assessed, with 69% having a positive PDL-1 status. 46% of patients had not received prior lines of immunotherapy or chemotherapy while 22% received a single line. There was no significant change in survival found for PDL1 status (p=0.49), TMB (p=0.48), or age (p=0.68). The relationship between doses of dual checkpoint immunotherapy to survival was found to be significant (p < 0.001) when assessed over 8000 days but showed insignificant (p=0.18) when assessed over 2500 days. The number of prior lines to survival also was found to be significant (p=0.0014) when assessed over 2500 days. Conclusions: An increase in cancer survivorship was found to be higher in patients that received more doses of dual checkpoint immunotherapy which may suggest that doses of dual immunotherapy received may increase the lifespan of some individuals with cancer. The small sample size of this study is a limitation to this analysis as well as the limited results for PD-L1 and NGS testing results, including TMB. Citation Format: Victoria Moe, Rachel Elsey, Tobias Meissner, Bing Xu, Yuliang Sun, Crystal Hattum, Casey Williams. Real-world outcomes in dual checkpoint inhibitor therapy: A single community center perspective [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4644.

Abstract 4938: Socioeconomic position and survival after lung cancer diagnosis: Comparisons in 4 continents

Background: The incidence of lung cancer is lower among higher socioeconomic position (SEP) groups in most settings. It is important to assess whether this translates to disparities in survival by SEP after lung cancer diagnosis. We sought to describe the relationship between SEP and survival after lung cancer diagnosis across different countries. Methods: We analyzed data from the Lung Cancer Cohort Consortium (LC3) and included 18 prospective cohorts from 14 countries in North America, Europe, Asia, and Australia. The total sample size included 48,482 lung cancer cases with pre-diagnostic risk factor information, amongst whom 37,559 died during the follow-up (median, IQR= 10.8, 6.5-15.0 years). Information on education was harmonized using the International Standard Classification of Education and then modeled as an ordinal variable in 4 categories. We evaluated the relationship between educational level and survival after lung cancer diagnosis using Cox proportional hazards models. Models were adjusted for age at diagnosis, sex, and (where applicable) cohort, smoking duration, cigarettes per day, and time since cessation. Results: We observed a clear trend toward better survival in participants with higher educational level in lung cancer cases diagnosed in North America, Europe and Asia, but not in Australia. After accounting for detailed smoking history, the hazard ratios were partly attenuated (North America: hazard radio per 1-unit increase in educational level [HR]=0.94, 95%CI=0.93-0.96; Europe: HR=0.94, 95%CI: 0.92-0.95; Asia: HR=0.81, 95%CI=0.77-0.85), but not in Australia. When additionally adjusting for stage at diagnosis, the inverse relationship between educational level and survival was further attenuated in Asian lung cancer cases, but not in European or North American study participants. We estimated that differences in tobacco exposure mediated approximately 20% of the relationship between education and lung cancer survival, and that disease stage mediated an additional 14% of this relationship in Asian lung cancer cases. Conclusion: Higher educational attainment is consistently associated with better lung cancer survival in North America, Europe, and Asia. Differences in tobacco exposure may partly, but not entirely mediate this relationship, and differences in stage at diagnosis may be additionally important in mediating the survival differences seen in Asian lung cancer cases. This study highlights the importance of socioeconomic position in the continuum of lung cancer disparities. Citation Format: Justina Ucheojor Onwuka, Karine Alcala, Hilary A. Robbins, Mattias Johansson, The Lung Cancer Cohort Consortium. Socioeconomic position and survival after lung cancer diagnosis: Comparisons in 4 continents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4938.

Abstract 7418: HPV and EBV coinfection in Puerto Rican people with HIV: insights into oropharyngeal cancer risk

Abstract Background: People with HIV (PWH) are disproportionately affected by Human papillomavirus (HPV), a major risk factor for oropharyngeal cancers. Additionally, PWH are more susceptible to acquiring opportunistic infections, such as Epstein-Barr Virus (EBV). EBV may lead to the development and progression of Burkitt’s and Hodgkin’s lymphoma and other types of cancers. HPV-related malignancies coupled with EBV infection have been associated with an increased risk of cervical cancer, however the relationship between EBV and HPV in in the oral cavity, particularly in PWH has not been investigated. In this study, we evaluated the prevalence of EBV in PWH and assessed their relationship with oral HPV infection due to their potential impact in immune suppression and oropharyngeal cancer development. Methods: Saliva samples, sociodemographic, and clinical data from 91 sexually active subjects (68 PWH and 23 people without HIV [PWOH]) from a community clinic in San Juan, Puerto Rico. We analyzed for oral HPV infection (34 HPV+ and 57 HPV-) and genotyped HPV using the DNA ELISA kit HPV SPF10 and RHA kit HPV SPF10-LiPA25 that detects 40 HPV subtypes. We quantified EBV levels in saliva using qPCR. Statistical analyses of levels of EBV were assessed in relation to HPV status using R-statistical software. Results: PWH had a median CD4 count of 791 cells/µL. The prevalences of EBV in PWH was 88% (60/68) vs in PWOH was 74% (17/23). In addition, the prevalence of EBV was higher in males than females (90% vs 63%). PWH with HPV had a 62% (21/34) of high-risk HPV genotypes, with HPV-18 being the most prevalent subtype 38% (8/21). Furthermore, EBV detectability had a trend with HPV status (p=0.07), especially in males with HPV showed higher detectability of EBV (p=0.002). In a multivariate model, EBV detectability was associated with biological sex after adjusting for HIV status and HPV status (p=0.004). Conclusions: Higher prevalence of EBV were observed in males than females. The trend observed between EBV detectability and HPV status, suggest a potential association between these viral infections, which could have implications for immune regulation in PWH. The high prevalence of HPV in PWH, and the association with EBV, particularly in males may indicated a need to underline the importance of HPV vaccination and regular screening in this population. We aim to increase the sample size to further validate the association of EBV and HPV in Puerto Rican PWH and include sociodemographic and lifestyle variable to investigate how socio-cultural characteristics may influence this association. Citation Format: Jurelis Torres-Reyes, Oscar A. Loperena-González, Jeyra L. Pérez-Lozada, Juliana M. Serrano-Rodríguez, Gabriel Borges-Vélez, María M. Sánchez-Vázquez, Magaly Martínez-Ferrer, Josué Pérez-Santiago. HPV and EBV coinfection in Puerto Rican people with HIV: insights into oropharyngeal cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7418.

Biomarker-guided adaptive enrichment design with threshold detection for clinical trials with time-to-event outcome

ABSTRACT Biomarker-guided designs are increasingly used to evaluate personalized treatments based on patients’ biomarker status in Phase II and III clinical trials. With adaptive enrichment, these designs can improve the efficiency of evaluating the treatment effect in biomarker-positive patients by increasing their proportion in the randomized trial. While time-to-event outcomes are often used as the primary endpoint to measure treatment effects for a new therapy in severe diseases like cancer and cardiovascular diseases, there is limited research on biomarker-guided adaptive enrichment trials in this context. Such trials almost always adopt hazard ratio methods for statistical measurement of treatment effects. In contrast, restricted mean survival time (RMST) has gained popularity for analyzing time-to-event outcomes because it offers more straightforward interpretations of treatment effects and does not require the proportional hazard assumption. This paper proposes a two-stage biomarker-guided adaptive RMST design with threshold detection and patient enrichment. We develop sophisticated methods for identifying the optimal biomarker threshold and biomarker-positive subgroup, treatment effect estimators, and approaches for type I error rate, power analysis, and sample size calculation. We present a numerical example of re-designing an oncology trial. An extensive simulation study is conducted to evaluate the performance of the proposed design.

Abstract 4513: Impact of patient safety regulatory considerations on early oncology clinical investigations

Introduction: Model assisted approaches such as mTPI2 designs are widely applied in early phase oncology trials to guide dose escalation decisions. Recent health authority interactions have highlighted the importance of design parameters such as the target dose limiting toxicity (DLT) rate and the equivalence interval (EI), in situations where lower toxicity is desired. As the dose escalation strategy may vary with different parameter configurations, the shift of target DLT and EI motivated us to explore the optimal cohort size for a given design. Methods: We simulated thousands of escalation trials using the mTPI2 design with five dose levels under five common scenarios with monotonal dose toxicity relationship, maximum total N=36-48 and maximum cohort size of n=12 in each simulated trial. The target DLT was set at 25% with an EI of (20%, 33%). Using simulation, we compared the mTPI2 performance with cohort sizes of three, four, and five, evaluating: 1) Reliability: Probability of identifying the true MTD; 2) Safety: Proportion of patients experiencing DLT or overdosed (receiving MTD or higher doses); 3) Dose Escalation Efficiency (DEE): Reliability adjusted by number of patients treated; and 4) Incorrect Dosing Decisions: Proportion of decisions escalating above or de-escalating below the true MTD. Results: Preliminary results show that a cohort size of four increased the sample size by 1.4-4.9 but improved reliability by 4.6%-10.8% in absolute value compared to a cohort size of three, resulting in the highest DEE among all cohort sizes tested in all scenarios. A cohort size of five also increased reliability but marginally diminishing. A cohort size of four had the lowest likelihood of incorrect dosing decisions (an average ∼4% absolute reduction) compared to a cohort size of three in all scenarios, which indicated that cohort size four generates the shortest dose escalation/de-escalation pathway to estimating MTD that ensures the highest DEE among the three cohort sizes tested. The simulation also indicated that, generally, safety performance improved when cohort size increased. When cohort size increased from three to four, the proportion of patients experiencing DLT reduced by 1-2% and proportion of overdosed patients reduced by 2.9-5.0% both in absolute values. Conclusions: When using the mTPI2 dose escalation design in early clinical trials, we strongly recommend that trial statisticians conduct simulations to assess various configurations across all potential scenarios. This approach optimizes the dose escalation process, increasing the likelihood of identifying the true MTD and minimizing patient exposure to toxicity. Increasing cohort size can offer operational benefits, such as reducing the need to replace non-evaluable participants. Enhanced reliability may also mitigate risks in further development, at the cost of a small number of additional patients treated at early stages. Citation Format: Baisong Huang, Cindy Lu, Danny Lu, Daniel Slade, Hazel Kurz, Thomas Jahn, Sergio Vicente, Bruno Medeiros, Jayne Marshall. Impact of patient safety regulatory considerations on early oncology clinical investigations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4513.

Abstract 2406: LossFinder: a novel algorithm for detecting PTEN homozygous deletions in cancer

Abstract Introduction: The PTEN gene, located at 10q23.31, is a tumor suppressor that regulates the PI3K/AKT signaling pathway. PTEN deletions and/or loss of protein are common in cancers, with The Cancer Genome Atlas (TCGA) reporting a prevalence of 10-85%, about half of which are due to copy number loss. PTEN homozygous deletions, more significant than hemizygous deletions, are key markers in cancer treatment, especially with the approval of the AKT inhibitor capivasertib. Homozygous PTEN deletions occurs in 4.28% of cancers, 5.08% in breast cancer, and 17.42% in prostate cancer. Detecting exon-level deletions in the PTEN gene is particularly challenging, given the short coding regions, the influence of tumor heterogeneity, and the effects of sample quality on Next-Generation Sequencing (NGS) data. To overcome these challenges, we developed LossFinder, a novel algorithm for detecting homozygous PTEN deletions. Methods: LossFinder is designed to detect homozygous gene copy number deletions in tumor NGS sequencing. The algorithm: 1) employs multi-depth correction and noise reduction to enhance the signal-to-noise ratio, mitigating the effects of tumor heterogeneity and experimental noise; 2) uses the circular binary segmentation (CBS) algorithm for precise breakpoint localization, improving detection of small exon-level copy number alterations; 3) assesses tumor purity and ploidy through mutation frequency and copy number alterations, restoring absolute copy numbers to distinguish homozygous from hemizygous deletions. We evaluated limits of detection (LoD) and precision using mixed tumor cell lines from ATCC. Additionally, clinical tumor samples were analyzed for PTEN deletion prevalence, with IHC used as the gold standard for comparison. Results: In cell line simulations, the algorithm demonstrated 100% specificity and 96.21% sensitivity when tumor purity was ≥30%. The LoD was achieved with 30% tumor purity, and precision with 35% tumor purity was 100%. In a cohort of 5,944 clinical FFPE tissue samples from over 20 cancer types, the prevalence of PTEN homozygous deletions was 4.32% overall, 6.56% (12/183) in breast cancer, 6.52% (3/46) in prostate cancer, and 3.77% (116/3078) in lung cancer, matching TCGA data for breast cancer but with a lower prevalence in prostate cancer, likely due to sample size limitations. Whole PTEN gene homozygous deletions accounted for 40% of PTEN homozygous deletion-positive samples. IHC validation in 97 clinical samples showed 85.71% consistency with NGS. Conclusions: The LossFinder algorithm offers high sensitivity and specificity in detecting PTEN homozygous deletions. It accurately identifies both whole and partial homozygous deletions, showing a high level of consistency with IHC. Citation Format: Ting Kuang, Chenglin Liu, Zhihong Zhang, Zhou Zhang, Fujun Qiu, Yuzi Zhang. LossFinder: a novel algorithm for detecting PTEN homozygous deletions in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2406.

Abstract 3647: Validation of a computational reasoning model for precision oncology with large-scale patient-derived xenograft data

Abstract Comprehensive tumor molecular testing is key in precision oncology. However, interpretation of complex molecular profiles in clinical practice can be challenging and subjective. The Digital Drug Assignment (DDA) system is a computational reasoning model that scores treatment options based on full tumor genomic data. This approach was predictive of relative benefit of the agents as used in the SHIVA01 trial (DOI: 10.1038/s41698-021-00191-2). Here, we analyzed patient-derived xenograft (PDX) data from Gao et al. (DOI: 10.1038/nm.3954). Molecular profiles of 179 solid tumors were processed by DDA, the resulting personalized drug scores were evaluated with treatment outcome data in PDX models for 1151 molecularly targeted agent (MTA) monotherapies, using 23 MTAs, targeting key oncogenic signaling pathways. In the PDX avatar system, multiple treatments can be tested for the same tumor, and outcomes can be measured in clinical metrics, enabling direct evaluation of drug ranking. To this end, cohorts were formed based on DDA ranking positions for each MTA-tumor pair. DDA ranking position was predictive of relative treatment benefit (Table, upper panel). Because the difference between neighboring ranks is probably minor, and to increase group sample sizes, larger cohorts were formed by combining neighboring rank groups. Here, a clear pattern of gradual decrease of treatment benefit with ranking distance from the top cohort was demonstrated (Table, lower panel). In this study, utilizing the unique advantages of the PDX system, we could demonstrate the predictive power of DDA treatment ranking. Digital drug assignment can serve as a practical and economic in silico avatar system for treatment planning and can potentially address challenges with complex molecular profiles in routine clinical settings. Citation Format: Robert Doczi, Akos Takacs, Anna Dirner, Dora Lakatos, Maria Kocsis-Steinbach, Barbara Vodicska, Dora Tihanyi, Eniko Kispeter, Reka Szalkai-Denes, William T. Beck, Petak Istvan. Validation of a computational reasoning model for precision oncology with large-scale patient-derived xenograft data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3647.