bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A069: Effect of different voided urine sample storage time and temperature, and preservatives, on analysis with the multiplex bead-based Oncuria® bladder cancer immunoassay
Authors: Tanaka Sunao , Murakami Kaoru , Sakatani Toru , Lee Riko , Hogrefe Wayne , Siguencia Fernando , Smith Steven M , Rosser Charles J , Furuya Hideki 
Published: November 2024

Abstract
Urinalysis accuracy requires reliable sample stability that is dependent on the chosen collection and storage conditions. If urine sample storage at room temperature (20°C) does not affect sample quality, this may reduce laboratory handling time and expense. This study evaluated whether different voided urine sample collection and storage parameters affected subsequent biomarker analysis by the multiplex Oncuria® bladder cancer immunoassay. The Oncuria® immunoassay simultaneously quantifies 10 protein analytes in urine to generate a bladder cancer diagnostic signature. Samples were stored at varied temperatures (20°C, 4°C, -80°C) for up to 1 month. The effects of adding two commercial urine sample stabilizers and antibiotics (trimethoprim) were also assessed. Subsequently, multiple potential biospecimen stabilizers were added to urine samples and evaluated with Oncuria® in hopes of allowing the urine sample to remain at room temperature for extended periods of time. First, it was demonstrated that voided urine samples stored at room temperate without such stabilizers had different levels of the 10 analytes associated with the Oncuria® test compared to voided urine samples stored at 4°C. Next, we evaluated the effects of commercially available biospecimen stabilizers. Despite the addition of these stabilizers, the levels of the 10 analytes were altered when the samples were stored at room temperature for prolonged periods of time. Therefore, we could not identify a suitable biospecimen stabilizer that would not require sample refrigeration. In conclusion, to minimize sample degradation/alteration after collection, voided urine samples should be refrigerated until analyzed with Oncuria® as the refrigeration is advantageous for the storage and the transport of these urine samples.
Citation Format: Sunao Tanaka, Kaoru Murakami, Toru Sakatani, Riko Lee, Wayne Hogrefe, Fernando Siguencia, Steven M Smith, Charles J Rosser, Hideki Furuya. Effect of different voided urine sample storage time and temperature, and preservatives, on analysis with the multiplex bead-based Oncuria® bladder cancer immunoassay [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A069.
Abstract A073: The potential of multi-cancer early detection screening for reducing cancer mortality
Authors: Chhatwal Jagpreet , Xiao Jade , ElHabr Andrew , Tyson Christopher , Cao Xiting , Raoof Sana , Fendrick A. Mark , Ozbay A. Burak , Limburg Paul , Beer Tomasz M. , Deshmukh Ashish , Briggs Andrew 
Published: November 2024

Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR006) of the Conference Program/Proceedings.
Citation Format: Jagpreet Chhatwal, Jade Xiao, Andrew ElHabr, Christopher Tyson, Xiting Cao, Sana Raoof, A. Mark Fendrick, A. Burak Ozbay, Paul Limburg, Tomasz M. Beer, Ashish Deshmukh, Andrew Briggs. The potential of multi-cancer early detection screening for reducing cancer mortality [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A073.
Abstract B001: ctDNA release kinetics and fragmentation to monitor treatment response and resistance in esophageal adenocarcinoma
Authors: Bartolomucci Alexandra , Kienzle Laura , Ferrier Sarah Tadhg , Edward Lisa-Monique , Bruce Jeffrey , Joung Kwang-Bo , Prokopec Stephenie , Zeng Wotan , Sharma Abirami , Dickinson Kyle , Bertos Nicholas , Cools-Lartigue Jonathan , Ferri Lorenzo , Pugh Trevor J. , Burnier Julia V. 
Published: November 2024

Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR003) of the Conference Program/Proceedings.
Citation Format: Alexandra Bartolomucci, Laura Kienzle, Sarah Tadhg Ferrier, Lisa-Monique Edward, Jeffrey Bruce, Kwang-Bo Joung, Stephenie Prokopec, Wotan Zeng, Abirami Sharma, Kyle Dickinson, Nicholas Bertos, Jonathan Cools-Lartigue, Lorenzo Ferri, Trevor J. Pugh, Julia V. Burnier. ctDNA release kinetics and fragmentation to monitor treatment response and resistance in esophageal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B001.
Abstract B004: Biological insights into tissue-agnostic plasma cfDNA methylation signature for surveillance of head and neck tumor recurrence
Authors: Newton Yulia , Burgener Justin , Gruca Margaret , Melton Collin , Min Jun , Licon Abel , Bratman Scott , Williams Alan , De Carvalho Daniel D 
Published: November 2024

Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR004) of the Conference Program/Proceedings.
Citation Format: Yulia Newton, Justin Burgener, Margaret Gruca, Collin Melton, Jun Min, Abel Licon, Scott Bratman, Alan Williams, Daniel D De Carvalho. Biological insights into tissue-agnostic plasma cfDNA methylation signature for surveillance of head and neck tumor recurrence [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B004.
Abstract B006: Qualitative research study on the use of minimal residual disease as an intermediate endpoint in multiple myeloma clinical trials in Saudi Arabia
Authors: Alnasser Albandari A , Alqurayshah Tariq H 
Published: November 2024

Abstract
Introduction: The U.S. Food and Drug Administration has recently considered minimal residual disease (MRD) as an acceptable accelerated approval endpoint in multiple myeloma (MM). Meta-analysis studies have shown the clinical benefit of MRD negativity in certain hematological cancers such as MM. Objectives: This qualitative research study, with a unique focus on the Saudi context, aims to assess the opinions and experiences of hematology and oncology specialists and consultants in Saudi Arabia. The study is particularly interested in their views on the use of MRD as an intermediate endpoint in early-phase clinical trials for fast-track drug approval by the Saudi Food and Drug Authority in the context of multiple myeloma. This includes assessing the use of MRD in both newly diagnosed and relapsed/refractory MM. The secondary objective is to gather information about the feasibility and availability of sensitive MRD detection methods in real-world medical practice and clinical trials in Saudi Arabia. Study Design: The study will involve interviewing 30 registered male or female physicians specialized in hematology and oncology in Saudi Arabia. The physicians will be included in the study using purposive sampling methods. The study will collect the physicians’ opinions and experiences about MRD. The interviews will be conducted through a single focus group and several face-to- face interviews or performed online, using ZOOM. Participants should have more than one year of experience post-residency or post-fellowship training. The predetermined set of semi- structured questions will cover topics such as the definition of MRD, its clinical and research significance, MRD detection thresholds, duration of MRD negativity, and its correlation with other clinical endpoints, such as progression-free survival and overall survival. The interviews will be conducted by scientific oncology and hematology evaluation experts at the Saudi Food and Drug Authority, who play a crucial role in this study. The study will consist of 5–10 semi- structured one-to-one interviews and focused group discussions of as few as four participants. Before starting any interview, participants will complete consent forms, including the study’s goals and who will conduct the study. Qualitative data will be prepared and analyzed by an expert in data analysis, ensuring the highest research standards. The results will be presented using descriptive and interpretive methods.
Citation Format: Albandari A Alnasser, Tariq H Alqurayshah. Qualitative research study on the use of minimal residual disease as an intermediate endpoint in multiple myeloma clinical trials in Saudi Arabia [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B006.
Abstract B009: Individualized-tumor-informed panel approach enables ultra-sensitive ctDNA-based minimal residue disease monitoring for high-risk pediatric cancers
Authors: Salomon Rob , Chen Wenhan , Shale Charles , Toumari Mojgan , Lowe Aileen , Li Wenyan , Chen Jingwei , Razavi-Bazaz Sajad , Barahona Paulette , Cui Louise , Mayoh Chelsea , El-Kamand Sam , Tyrrell Vanessa , Wong-Erasmus Marie , Lau Loretta , Fuentes-Bolanos Noemi , Cuppen Edwin , Khoung-Quang Dong-Anh , Staunton Jordan , Mateos Marion K , Trahair Toby , Haber Michelle , Ziegler David S , Ekert Paul , Priestley Peter , Cowley Mark 
Published: November 2024

Abstract
While the use of ctDNA-based minimal residual disease (MRD) monitoring is gaining popularity in adult cancers, this approach is not yet widely adopted in pediatric cancers (PCs). We developed a robust and sensitive assay to monitor ctDNA in PCs, which overcomes PC-specific challenges including low tumor mutational burden, paucity of hotspot mutations and low blood volume. To address these challenges, our innovations include personalized panel design that targets primary tumor mutations from each patient, a fixed panel targeting hotspot mutations, error suppression from duplex deep sequencing and customized pipeline for tumor burden estimation. We retrospectively analyzed 661 blood or cerebrospinal fluid (CSF) samples from 168 patients. We achieved an average detection limit of 0.005% ctDNA purity leading to MRD detected ranging from 0.001% to 100% with brain tumor consistently showing a low MRD. At disease diagnosis, progression and relapse, our assay identified ctDNA in over 93% of extra- cranial solid tumors, 90% of leukemia, 89% of sarcoma, and 90% of neuroblastoma. For brain tumors, we detected MRD in ∼90% of CSF samples, and in ∼60% of blood samples, a major advance over previous approaches. Importantly, we detected MRD in ∼ 20% of cases with a clinically complete response, predicting relapse up to 6 months before clinical confirmation. Overall, these results demonstrate that our monitoring assay for PCs is an important addition to standard of care for precision-guided treatment.
Citation Format: Rob Salomon, Wenhan Chen, Charles Shale, Mojgan Toumari, Aileen Lowe, Wenyan Li, Jingwei Chen, Sajad Razavi-Bazaz, Paulette Barahona, Louise Cui, Chelsea Mayoh, Sam El-Kamand, Vanessa Tyrrell, Marie Wong-Erasmus, Loretta MS Lau, Noemi Fuentes-Bolanos, Edwin Cuppen, Dong-Anh Khoung-Quang, Jordan Staunton, Marion K Mateos, Toby Trahair, Michelle Haber, David S Ziegler, Paul Ekert, Peter Priestley, Mark Cowley. Individualized-tumor-informed panel approach enables ultra-sensitive ctDNA-based minimal residue disease monitoring for high-risk pediatric cancers [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B009.
Abstract B010: Prognostic value of circulating tumor cells in stage III and IV melanoma: A systematic review and meta-analysis
Authors: Chen Jennifer H. , Hwang Hyunsoo , Dong Bamboo , Sarli Vanessa N. , Upshaw Joshua R. , Meas Salyna , Lucci Anthony 
Published: November 2024

Abstract
Introduction: Previous studies have demonstrated a role for assessing circulating tumor cells (CTC) in melanoma, but significant heterogeneity among studies has limited application in the clinical setting. We sought to evaluate the prognostic value of CTCs in advanced stage melanoma using a standardized CTC enumeration platform. Methods: A PubMed literature search was conducted up to March 2024. All studies evaluating CTC enumeration using CellSearchTM with outcomes data were included. Student's t-test was used to compare differences between groups. Hazard ratios (HR) were pooled using random effects model to assess the association of CTCs with overall survival (OS). I 2 statistic and Cochran’s Q test, sensitivity analyses, and Egger’s test of asymmetry were used to assess study heterogeneity, differential impact of individual studies, and publication bias, respectively. Results: Of the 12 studies identified, nine met inclusion criteria. A total of 678 patients were included, of which 337 (49.6%) were stage III and 342 (50.4%) were stage IV. The majority of studies reported CTC rates using a cut-off of ≥ 1 (6 studies, 66.7%), while three studies used ≥ 2 and five studies used both. Median follow-up time was available for six studies and ranged from 5.9-48 months (median 13.4). Average CTC detection rate (≥ 1 or 2) was 41% (SD 14.0) and was significantly higher using a cut-off of ≥ 1 (45.4%, SD 12.6) compared to ≥ 2 (26.1%, SD 2.7, p = 0.02). Pooled analysis of two studies demonstrated significantly worse OS with CTC ≥ 1 (HR 1.6, 95% CI: 1.0-2.6, p = 0.04). Similarly, pooled analysis of five studies with available HRs demonstrated significantly worse OS with CTC ≥ 2 (HR 2.1, 95% CI: 1.4-3.1, p = 0.0003). Among these five studies, moderate heterogeneity was observed (I2 = 43.4%), although this was not statistically significant (Q statistic p = 0.13). Sensitivity analyses confirmed the prognostic value of CTC ≥ 2, with pooled HRs ranging from 1.9-2.4 after consecutive omission of each study from the overall analysis. Conclusion: Regardless of the CTC cutoff used (≥ 1 or 2), presence of any CTCs was a strong prognostic marker in patients with advanced stage melanoma. Incorporation of CTC assessments in clinical practice may help risk stratify patients and guide treatment decisions. Further studies are needed to determine the optimal cut-off point for CTC status in assessing prognosis.
Citation Format: Jennifer H. Chen, Hyunsoo Hwang, Bamboo Dong, Vanessa N. Sarli, Joshua R. Upshaw, Salyna Meas, Anthony Lucci. Prognostic value of circulating tumor cells in stage III and IV melanoma: A systematic review and meta-analysis [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B010.
Abstract B029: Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction
Authors: Li Xinxing , Liu Tao , Bacchiocchi Antonella , Li Mengxing , Cheng Wen , Wittkop Tobias , Mendez Fernando , Wang Yingyu , Tang Paul , Yeung George , Yao Qianqian , Bosenberg Marcus , Sznol Mario , Yan Qin , Faham Malek , Weng Li , Halaban Ruth , Jin Hai , Hu Zhiqian 
Published: November 2024

Abstract
While whole genome sequencing (WGS) of cell-free DNA (cfDNA) holds enormous promise for detection of molecularresidual disease (MRD), its performance is limited by WGS error rate. Here we introduce AccuScan, an efficient cfDNA WGS technology that enables genome-wide error correction at single read level, achieving an error rate of 4.2 × 10-7, which is about two orders of magnitude lower than a read-centric de-noising method. Application of AccuScan to MRD demonstrated analytical sensitivity down to 10-6 circulating tumor allele fraction at 99% sample level specificity. AccuScan showed 90% landmark sensitivity (within 6 weeks after surgery) and 100% specificity for predicting relapse in colorectal cancer. It also showed 67% sensitivity and 100% specificity with esophageal cancer using samples collected within one week after surgery. When AccuScan was applied to monitor immunotherapy in melanoma patients, the circulating tumor DNA (ctDNA) levels and dynamic profiles were consistent with clinical outcomes. Overall, AccuScan provides a highly accurate WGS solution for MRD detection, empowering ctDNA detection at parts per million rangewithout requiring high sample input or personalized reagents.
Citation Format: Xinxing Li, Tao Liu, Antonella Bacchiocchi, Mengxing Li, Wen Cheng, Tobias Wittkop, Fernando Mendez, Yingyu Wang, Paul Tang, George Yeung, Qianqian Yao, Marcus Bosenberg, Mario Sznol, Qin Yan, Malek Faham, Li Weng, Ruth Halaban, Hai Jin, Zhiqian Hu. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B029.
Abstract B033: Towards magnetic resonance microscopy for liquid biopsy in cancer therapy monitoring
Authors: Briegel Karl D. , Allert Robin D. , Bucher Dominik B. , Draeger Julia D. , Grafenstein Nick R v. , Nie Linyan 
Published: November 2024

Abstract
The advancement of liquid biopsy techniques promises to revolutionize cancer diagnostics and therapy monitoring, by offering a minimally invasive approach to track tumor progression and treatment efficacy. One central issue preventing advancements are innovations in sensor technology, necessary to enable the detection of molecular and cellular biomarkers with sufficient precision. Over the past decade, atomic-scale quantum sensors have emerged as powerful detectors, offering the ability to perform precise measurements of temperature, pressure, and magnetic fields on the single cell scale. These sensors, based on the interaction of spin qubits with their environment, have the unique capability to amplify and exploit environmental interactions for highly accurate detection, making them ideal for complex biological applications. In this context, we present an advanced quantum sensing platform specifically tailored for liquid biopsy applications in cancer therapy monitoring. This platform integrates the capabilities of optical microscopy with magnetic resonance imaging (MRI) techniques, utilizing nitrogen-vacancy (NV) centers in diamond as quantum sensors by converting magnetic resonance signals into optical signals, which are subsequently captured by a high-speed camera. Our platform offers a novel approach, promising quantitative analysis of single cancer cells from liquid samples with unprecedented accuracy. Unlike traditional MRI, our method captures signals over a wide field of view directly in real space. Each camera pixel records a magnetic resonance spectrum, providing detailed multicomponent information about the sample, such as molecular concentration, diffusion, and relaxation behavior, which are critical for understanding the tumor’s microenvironment. Our quantum sensing technology holds significant potential for enhancing the sensitivity of liquid biopsies. By capturing detailed molecular information from blood or other body fluids, it will enable in-depth analysis of Circulating Tumor Cells (CTCs), circulating tumor DNA (ctDNA), exosomes, and other biomarkers.
Citation Format: Karl D. Briegel, Robin D. Allert, Dominik B. Bucher, Julia D. Draeger, Nick R v. Grafenstein, Linyan Nie. Towards magnetic resonance microscopy for liquid biopsy in cancer therapy monitoring [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B033.
Abstract B046: Methylation based circulating tumor DNA serial monitoring correlates with immunotherapy response in non-small cell lung cancer
Authors: Hsiao Angela , Woodward Brian , Ye Patrick , Varga Matthew , Lu Kevin , Altaie Ghaith , Searle Naomi , Veins Robb , Langpap Sydne , Li Zeqian , Palmer Gary , Husain Hatim 
Published: November 2024

Abstract
Purpose: Circulating tumor DNA (ctDNA) can reflect the genetic and epigenetic composition of malignancies and can serve as a non-invasive biomarker for cancer diagnostics and monitoring. This study aimed to evaluate the utility of a methylation based ctDNA assay as a predictive tool in non-small cell lung cancer (NSCLC) anti-PD1 based immunotherapy monitoring. Methods: We evaluated a cohort of patients with NSCLC treated with anti-PD1 based immunotherapy, from which 108 blood specimens were collected at baseline and during treatment follow-up. Tumor Methylation Scores (TMS) were measured with an amplicon-based, multiplexed cfDNA assay that utilizes quantitative counting templates (QCTs) in conjunction with next-generation sequencing to count the number of methylated molecules at more than 500 genomic locations that are hypermethylated in cancer tissue. The association between TMS and real-world progression-free survival (rwPFS) on therapy was conducted using Cox proportional hazards model and plotted using the Kaplan-Meier method. Results: The change in TMS measured 4-10 weeks post-treatment initiation strongly correlated with immunotherapy response, as measured by rwPFS (p&lt;0.0001), compared to a weaker correlation of imaging RECIST v1.1 measurements with rwPFS (p=0.55). Furthermore, TMS tracked with tumor burden on therapy in real-world cases. Conclusions: In this real-world dataset of NSCLC patients treated with anti- PD1 immunotherapy regimens, TMS scores measured within a 4-10 week window after treatment initiation can be predictive of response to therapy. Beyond this window, the TMS score can be associated with rwPFS and tumor dynamics. Early evidence suggests that changes in the methylation profile may be informative for monitoring occurrence of new somatic mutations. The cases presented demonstrate the applicability of using TMS for serial therapeutic response monitoring.
Citation Format: Angela Hsiao, Brian Woodward, Patrick Ye, Matthew Varga, Kevin Lu, Ghaith Altaie, Naomi Searle, Robb Veins, Sydne Langpap, Zeqian Li, Gary Palmer, Hatim Husain. Methylation based circulating tumor DNA serial monitoring correlates with immunotherapy response in non-small cell lung cancer [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B046.