Analytical Performance Research Articles

Electrochemical immunosensing of walnut and hazelnut allergenic proteins in processed foods

Nuts are a well-known cause of food allergy and, once this has been diagnosed, due to the likelihood of cross-sensitization to multiple tree nut allergens, their strict avoidance from the diet is advisable. In this context, we present electrochemical bioplatforms to detect traces of hazelnut and walnut in processed foods through the determination of their respective allergenic proteins Cor a 9 and Jug r 1 in a fast and sensitive assay. First, the evaluation of the single determination of both proteins was performed by building sandwich immunoconjugates on the surface of magnetic microbeads relying on specific antibodies unmodified or conjugated to horseradish peroxidase. Amperometric transduction was made upon trapping the magnetic bioconjugates on the surface of disposable carbon electrodes, using the hydroquinone/hydrogen peroxide system. The great analytical performance achieved with the individual platforms (detection limits of 0.12 and 0.56 ng mL−1 for Jug r 1 and Cor a 9, respectively), led us to the individual and dual quantification of both proteins in raw dough and baked cookies incurred with ground nuts. The developed method allowed detecting baked cookies incurred with 0.0025% ground walnut and 0.00002% ground hazelnut with results comparable to those provided by ELISA techniques. The feasibility of performing the dual determination of both allergens in a single run was demonstrated.

A new generation of fully-printed electrochemical sensors based on biochar/ethylcellulose-modified carbon electrodes: Fabrication, characterization and practical applications

Biochar is a material prepared by biomass pyrolysis, representing a more sustainable and efficient alternative to commonly used conventional carbon materials in electroanalysis. The aim of this paper is to point out that it can also show significant potential in the mass screen-printing production of miniaturized, low-cost, disposable and sensitive electrochemical sensors. Herein, a new generation of fully screen-printed electrochemical sensors is introduced, based on biochar/ethylcellulose-modified carbon working electrodes. The optimization in the sensor fabrication, involving the variability in the concentration of a binder and rheology modifier (ethylcellulose) and its impact on biochar inks from the viewpoint of viscoelasticity, printability and thermal stability, was performed to obtain the carbon-based electrochemical sensors with favourable robustness. The viability of these electrochemical sensors was demonstrated by the development and full validation of a new and sensitive differential pulse voltammetric method for the fast and reliable determination of paracetamol in pharmaceutical formulations. Within the method development, all necessary aspects, such as a study of the effect of ethylcellulose concentration, pH study of supporting electrolyte, selection of pulse parameters and analytical performance, were investigated. The obtained results allow us to predict the production and subsequent use of new, printable, cheap and environmentally friendly sensor platforms, which will exhibit convenient analytical performance with the possibility of commercialization.

Analytical Performance Evaluation of a Digital Real-Time PCR for Quantifying Major BCR::ABL1 Transcripts.

Accurate quantification of the BCR::ABL1 transcripts is essential for measurable residual disease (MRD) monitoring in chronic myeloid leukemia (CML) after tyrosine kinase inhibitor (TKI) treatment. This study evaluated the newly developed digital real-time PCR method, Dr. PCR, as an alternative reverse transcription-PCR (qRT-PCR) for MRD detection. The performance of Dr. PCR was assessed using reference and clinical materials. Precision, linearity, and correlation with qRT-PCR were evaluated. MRD levels detected by Dr. PCR were compared with qRT-PCR, and practical advantages were investigated. Dr. PCR detected MRD up to 0.0032%IS (MR4.5) with excellent precision and linearity and showed a strong correlation with qRT-PCR results. Notably, Dr. PCR identified higher levels of MRD in 12.7% (29/229) of patients than qRT-PCR, including six cases of MR4, which is a critical level for TKI discontinuation. Dr. PCR also allowed for sufficient ABL1 copies in all cases, while qRT-PCR necessitated multiple repeat tests in 3.5% (8/229) of cases. Our study provides a body of evidence supporting the clinical application of Dr. PCR as a rapid and efficient method for assessing MRD in patients with CML under the current treatment regimen.

Analytical performance characteristics of Micro-structured surfaces for laser-induced breakdown spectroscopic analysis of liquids

We have previously shown the design and fabrication studies of 3-D micro-structured surfaces, to be used as a sample loading substrate for liquids analysis via dried-droplet LIBS methodology. Among the three designs, the substrate structured with 20-μm diameter cylinders, CYL-20, has shown the highest signal enhancement for the elements, Cu, Cr, and Pb, compared to 5-μm diameter cylinders, CYL-5, and 5-μm side-length triangular prisms, TAP-5, surfaces. Here, in this study, the analytical performance characteristics (LOD, accuracy, and precision) of these micro-structured Si-wafer surfaces are presented in comparison with unstructured surfaces. The dried-droplet residue of aqueous heavy metal solutions of Pb, Cr, and Cu were analyzed at their respective emission wavelengths under optimized experimental conditions. The results obtained from CYL-20 structured surfaces in comparison to 300 nm thin-film coated surfaces indicate up to 17, 11, and 7-fold increases in LIBS signal strength for Cu, Cr, and Pb, respectively. The experiments were performed using single and multi-element standards, and certified reference water samples. Sub-picogram absolute detection limits, 0.8 pg Pb, 0.5 pg Cu, and 0.45 pg Cr were obtained from the analysis of 500 nanoliters standard solutions, via dried-droplet methodology. Results with 70–75% accuracy and 95% precision were obtained from the repeated measurements. Though the results are promising, more extensive fabrication and application studies are required to find optimum structures of different sizes and shapes.

Tetrad metal ion mediated molecular switch aptamer sensor for fluorescence assay of plasma IP-10 in clinical tuberculosis

Interferon-γ-inducible protein 10 (IP-10) has demonstrated enormous potential as a novel biomarker for tuberculosis (TB), particularly in the monitoring of patient progression for active or latent tuberculosis infection (LTBI). Herein, we established a tetrad metal ion-mediated molecular switch aptamer sensor for the convenient detection of IP-10 in plasma and the diagnosis of TB. The simple sensor relied on the partially complementary IP-10 aptamer and four DNA hairpin strands rich in cytosine (C), which can form a relatively stable tetrad C-Ag+-C structure when combined with Ag+ without additional modification. Based on the specific recognition of IP-10 and aptamer, a large amount of Ag+ could be released in a short time. Combining with cadmium telluride quantum dots (CdTe QDs) as the signal reporter, we achieved superior analytical performance, with the limits of detection (LOD) reaching 3 fg/mL for IP-10 analysis in 1 h. Clinical practicality was confirmed by evaluating 38 clinical samples (19 TB-positive patients, 14 non-TB patients, and 5 latent TB infection patients). The results showed that the detected IP-10 levels were significantly different between the non-TB and TB/LTBI groups, and the results aligned with clinical computed tomography (CT) results, indicating that the method could represent a reliable diagnostic technique for TB.

Abstract 5036: Analytical and clinical validity of Northstar Select, a quantitatively enhanced liquid biopsy assay for comprehensive genomic profiling of solid tumors

Abstract Background: Liquid biopsy assays have emerged as vital tools in precision oncology. Among these assays, Comprehensive Genomic Profiling (CGP) tests in particular have improved treatment selection for late-stage solid tumor cancer patients by allowing for the detection via circulating tumor DNA (ctDNA) of somatic mutations in the tumor, many of which have corresponding targeted therapies. However, technical restrictions in the performance of such tests have limited their utility when ctDNA signal is low. BillionToOne’s Northstar Select assay is a new CGP test that achieves increased performance by addressing these limitations. Innovation: By using Quantitative Counting Template (QCT) technology, Northstar Select is able to track the yield of multiple processing steps, contributing to the higher sensitivity of the assay by maximizing the number of decoded molecules after sequencing. In addition, it employs chemistry and panel design optimizations, as well as novel algorithms for SNV, indel, CNV, fusion, and MSI calling to increase sensitivity and specificity. Analytical Performance: The performance of Northstar Select surpasses that of other commercially available tests for multiple mutation types, detecting more pathogenic and actionable mutations at low tumor DNA fraction while maintaining similarly high specificity. In analytical validation (N=103), limit of detection was determined to be 0.13-0.16% variant allele fraction (VAF) for SNVs and indels, 2.11 copies for copy number amplifications, 1.8 copies for copy number losses, 0.35% VAF for fusions, and 0.07% tumor fraction for MSI. Clinical Performance: Northstar Select was determined to have high clinical utility as well, with a study of clinical samples (N=481) from a variety of tumor types yielding <2% of reports with 0 mutations detected. A head-to-head comparison with other commercial liquid biopsy assays on a subset of the clinical samples (N=192) showed that the assay detected 115 additional pathogenic mutations in total, leading to a higher proportion of patients with at least one pathogenic mutation detected (90%) compared to comparators (79%). Conclusion: These results demonstrate that the Northstar Select assay is an innovative and high-performing diagnostic for treatment selection in oncology, leveraging quantitative approaches in process design, chemistry, and bioinformatics to offer superior analytical and clinical performance compared to the current landscape of liquid biopsy CGP tests. Citation Format: Xavier Bower, Jan Wignall, Joyce Zhu, Naomi Searle, Matthew Varga, Emilio Rosas-Linhard, Jason Luong, Esther Lin, Marie Simon, John ten Bosch, Wen Zhou. Analytical and clinical validity of Northstar Select, a quantitatively enhanced liquid biopsy assay for comprehensive genomic profiling of solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5036.

Abstract 5024: Analytical performance of a genome-wide methylome enrichment platform to detect minimal residual disease from plasma-derived cell-free DNA

Abstract Introduction: Plasma-derived cell-free DNA (cfDNA) can be used to identify cancer signals, including minimal residual disease (MRD), in patients who have undergone curative cancer treatments. The cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) methodology is combined with custom algorithms that leverage differentially methylated regions (DMRs) found in cfDNA to distinguish between cancer and non-cancer signals. This novel non-degradative, tissue-agnostic approach was developed to bypass the limitations of bisulfite-sequencing and tissue-informed methods used in other liquid biopsy technologies. Here we present preliminary analytical performance metrics of an algorithm in development for detecting MRD. Methods: In the genome-wide methylome enrichment platform, plasma-derived cfDNA is subjected to standard library preparation, combined with DNA filler, denatured, and immunoprecipitated using an anti-5-mC antibody. Captured DNA is amplified and sequenced. For this study, a candidate algorithm comprised of differentially methylated regions (DMRs) and 12 cancer types was used to quantify cancer-specific methylation. Control samples from 12 non-cancer donors were used to establish a selected 95% true negative rate threshold. This threshold was used to determine assay sensitivity, which was evaluated using contrived cancer samples intended to mimic low-level circulating tumor DNA (ctDNA) representative of MRD. Samples were contrived by titrating fragmented DNA from three immortalized tumor-derived cell-lines into plasma-derived cfDNA in a titration series targeting <1% ctDNA levels. Cell-lines were of non-small cell lung cancer and head and neck squamous cell carcinoma origin; titration series were replicated for a total of 65 tests. Results: All non-cancer and contrived cancer samples met in-process quality control metrics. This included ≥98.5% methylation specificity and ≥80 million unique molecules. Limit of detection calculations at 95% sensitivity (LoD95) were <0.1%. Conclusions: Tissue-agnostic approaches for detecting cancer signals from plasma have significant benefit, especially in settings where tissue is not accessible for evaluation. However, these tests must have highly sensitive methods of cancer signal detection for clinical applications. Our preliminary analytical data demonstrates the use of a blood-based, tissue- agnostic genome-wide methylome enrichment platform utilizing non-degradative methodology combined with specific algorithms and DMRs for MRD quantification and prognostic prediction, using treatment-naïve plasma samples. Future studies in post-treatment and longitudinal samples are ongoing to evaluate the utility of this genome-wide methylome enrichment platform for cancer management. Citation Format: Shu Yi Shen, Iulia Cirlan, Felicia Vincelli, Ben Brown, Jun Min, Justin Burgener, Junjun Zhang, Yulia Newton, Margaret Gruca, Abel Licon, Jing Zhang, Anne-Renee Hartman, Alan Williams, Hestia Mellert, Daniel D. De Carvalho. Analytical performance of a genome-wide methylome enrichment platform to detect minimal residual disease from plasma-derived cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5024.

Abstract 3754: High staining reproducibility and scoring precision demonstrated in endometrial cancer stained with PD-L1 IHC 22C3 pharmDx used in conjunction with combined positive score

Abstract Background: PD-L1 IHC 22C3 pharmDx (SK006) is a qualitative immunohistochemical (IHC) assay using anti-PD-L1 clone 22C3 to detect PD-L1 in formalin-fixed, paraffin-embedded (FFPE) human endometrial cancer (ENDO) tissues. PD-L1 expression is determined using the Combined Positive Score (CPS) algorithm, which is the number of PD-L1 staining cells (tumor cells, lymphocytes, macrophages) divided by the total number of viable tumor cells, multiplied by 100. Validation testing evaluated the sensitivity and analytical performance of SK006 PD-L1 expression in FFPE ENDO specimens based on two PD-L1 expression cutoffs for all applicable studies: CPS ≥ 1 and CPS ≥ 10. Analytical performance studies included precision (combined precision, intra-run and intra-inter observer) and robustness (time, temperature, pH and re-use) testing. Methods: FFPE ENDO specimens were stained with SK006 and scored using CPS. Negative percent agreement (NPA), positive percent agreement (PPA), and overall agreement (OA) with two-sided 95% bootstrap confidence intervals (CIs) were used for data analysis, based on PD-L1 binary status (positive/negative) at the evaluated cutoffs. Acceptance Criteria (AC): the lower bound of the two-sided 95% CI computed on percent agreement (NPA, PPA, and OA) must meet or exceed 85%. Sensitivity determined if SK006 could detect a range of CPS expression levels in ENDO specimens. Combined precision measured inter-instrument, -operator, and -day variation nested within the same study. Intra-run measured repeatability within the same run and Inter/Intra-Observer measured scoring reproducibility by 3 pathologists over 3 non-consecutive days. Robustness evaluated the staining performance of SK006 under varying Target Retrieval Solution (TRS) laboratory conditions: time (18-22min), temperature (95-99°C), pH (5.9-6.3) and re-use (up to 3 uses). Results: The sensitivity data showed that SK006 could detect a range of CPS expression levels in ENDO specimens. Analyses for each analytical validation study, subject to AC, showed NPA, PPA, OA point estimates (PE) of ≥ 95.5% and CI lower bounds (CILB) of ≥ 87.1%. Conclusion: PD-L1 IHC 22C3 pharmDx (SK006) used in conjunction with CPS provides high staining reproducibility and scoring precision for ENDO specimens at the CPS ≥ 1 and CPS ≥ 10 cutoffs, under standard day-to-day laboratory testing and scoring conditions. Citation Format: Julia Hand, Amber Morones, Deanna Moquin, Kelly Martyniuk, Megan Kalpakoff, Siena Tabuena-Frolli, Jay Milo, Stephanie Hund. High staining reproducibility and scoring precision demonstrated in endometrial cancer stained with PD-L1 IHC 22C3 pharmDx used in conjunction with combined positive score [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3754.

Abstract 2337: Accelerated optical genome mapping analysis with Stratys Compute and Guided Assembly

Abstract Background Optical genome maps (OGM) from Bionano enable the detection of genomic structural and copy number variants that cannot be detected by next-generation sequencing (NGS) technologies and are often missed by conventional cytogenetic techniques. Bionano has developed bioinformatics pipelines for calling structural and copy number variants including the Bionano Solve de novo assembly pipeline for constitutional analysis and the Rare Variant Analysis (RVA) pipeline for low-allele-fraction cancer applications. Both pipelines are computationally intensive and currently take 5-10 hours on the latest generation of the Bionano Saphyr® Compute which is deployed as a four-node compute cluster and requires significant IT resources. Methods To increase throughput and simplify the deployment of the compute resources needed to support the Stratys™ optical genome mapping instrument, Bionano has developed Stratys™ Compute. Stratys Compute improves both compute and analytical performance by adapting compute-intensive stages in the Solve pipeline to run on GPUs and by developing the Guided Assembly pipeline. Stratys Compute is powered by state-of-the-art NVIDIA RTX 6000 Ada generation cards and CUDA-optimized refinement, alignment, and structural variation detection kernels to accelerate OGM analysis. Stratys Compute is a standalone workstation placed adjacent to Stratys instrument. This will minimize the IT footprint and bypass the integration with the customer site’s data center. We have incorporated these optimizations into the new Guided Assembly pipeline, which aims to combine the low-allele fraction detection capability of the RVA pipeline with the whole genome coverage and ability to detect smaller structural variants enabled by the de novo assembly pipeline. The Guided Assembly pipeline uses the reference genome as an initial seed followed by extension, refinement, and structural variant calling. This new analysis method has been evaluated through comparison to previous results from both existing pipelines and standard benchmarking datasets used to estimate structural variant calling performance and is deployed on Stratys Compute for both constitutional and low allele-fraction applications. Results Guided Assembly has been adapted to run on GPU hardware in a simplified compute tower that can be deployed to a lab along with the Stratys instrument without the need for a dedicated server room. We found concordance between the guided assembly results and our previous de novo and RVA pipeline results. We also found increased sensitivity at low allele fractions for detecting insertion variants smaller than 5 kb and larger than 200 kb while finding equivalent performance for other variant types with the updated methods. The accelerated Guided Assembly for constitutional and low-allele-fraction applications will be available to early access customers in Q4 2023 with full commercial release in Q2 2024. Citation Format: Damla Senol Cali, Thomas Anantharaman, Martin Muggli, Samer Al-Saffar, Charles Schoonover, Neil Miller. Accelerated optical genome mapping analysis with Stratys Compute and Guided Assembly [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2337.

Abstract 340: Validation of TSO500 NGS panel for comprehensive genomic profiling from FFPE tumor samples

Abstract Comprehensive genomic profiling (CGP) of tumor sample using large targeted NGS panels (e.g. MSK-IMPACT) has been shown to allow the detection of biomarkers from hundreds of cancer relevant genes involved in targeted and immunotherapy. Illumina TruSight Oncology 500 (TSO500), a commercial CGP assay, allows concurrent analysis of DNA and RNA to simultaneously detect multiple types of variants across 523 genes. The assay is intended to detect single nucleotide variants (SNV), insertions and deletions (indel), and multinucleotide variants (MNV), copy number gain (CNV), tumor mutational burden (TMB) and microsatellite instability (MSI) in DNA, and fusions and splicing variants (exon skipping) in RNA. Here we aimed to validate TSO500 assay for its analytical performance on FFPE tumor samples. The validation samples include commercial controls, cell lines, clinical FFPE from NSCLC, CRC, Uterus and GIST (tumor content ≥20%). Library preparation was performed from minimum of 40 ng DNA and 40ng RNA. The data analysis is performed using TruSight Oncology 500 Local App software (LRM v2.2). A custom script (v1.0) was used to add SNP annotation for small variants and combine data output into cumulative format. For SNV and indel detection QC, 61 of 64 DNA libraries (95%) passed the QC for library size (median insert size ≥70bp) and coverage (median exon coverage ≥150). The percentage of DNA libraries passing QC for CNV and MSI are 95% and 88%, respectively. All 64 RNA libraries passed QC. The analytical performance of TSO500 was summarized in the Table below. In summary, the results showed that all the acceptance criteria were met and the TSO500 assay can be utilized for genomic profiling of FFPE tumor samples. The study also identified a few limitations of the Illumina LRM software e.g. potential false positive SNV within a indel background, potential false negative of complex indel, and the challenge of long indel detection. Summary of analytical performance of TSO500 Sensitivity and specificity Assay LoD Accuracy by concordance Inter-run reproducibility SNV/Small indel Sensitivity for SNV and indel detection are 99.24% and 99.36%. The LoD for SNV is 3-5%, for DEL is 5-10% and for INS is 3-5%. PPA for SNV detections is 96.64% (115/119; 95% CI: 91.68%, 98.69%) and for small indel is 92.86% (13/14; 95% CI: 68.53%, 98.73%) between TSO500 and comparator assays. The positive call rate across all SNV and small indel variants is 98.7% (42842/43419). Specificity for SNV and small indel detection are 99.9998% and 100.00%, respectively. MSI Sensitivity and Specificity for MSI detection are both 100%. NA MSI status for all samples were detected with 100% of concordance by three assays; MSI concordance for MSI-H is 100% (95% CI: 60.97%, 100.0%) and for MSS is 100% (87.13%, 100.0%). PPA is 100% (95% CI: 51.01%, 100%) and NPA is 100% (95% CI: 34.24%, 100%). TMB NA NA TSO500 reported TMB is well correlated and comparable to exome determined TMB. The CV values for samples are acceptable. CNV NA NA All positive CNVs detected by the comparator assay were detected by the TSO500 assay with similar fold changes; The overall reproducible call rate is 91.5% (43/47). PPA between TSO500 and OCAV3 assays is 100% (95% CI: 51.01%, 100%). Fusion Sensitivity and specificity for fusion detection is 91.94% and 100%, respectively. NA All TSO500 assay detected fusions were confirmed by other assays;PPA is 100% (95% CI: 60.97%, 100%) and NPA is 100% (95% CI: 75.75%, 100%) The reproducibility of fusion call is 92.59% (25/27; 95% CI: 76.63%, 97.94%). Splicing Sensitivity and Specificity for splicing variant detection are 91.67% and 100.00%, respectively. NA The splicing variant detections were confirmed by OCAV3, OFA and Archer assays; The overall reproducibility of positive call is 100% with 95% CI (43.85%, 100%) and negative call reproducibility is 100% with 95% CI (87.13%, 100%). PPA is 100% (95%% CI: 20.65%, 100%) and NPA is 100% (95% CI: 83.18%, 100%) Citation Format: Jin Li, Zhenyu Yan, Weihua Liu, Lin Shi, Cynthia Spittle, Chad Galderisi. Validation of TSO500 NGS panel for comprehensive genomic profiling from FFPE tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 340.

Abstract 2300: AI enabled whole exome& transcriptome liquid biopsy addressing MCED, MRD, and therapy selection on a single platform

Abstract Effective clinical management of cancer patients requires an accurate and early diagnosis, highly sensitive monitoring of minimal residual disease (MRD), and precise therapy selection. There are multiple tests available that attempt to address each of these needs independently with varying degrees of clinical utility. Caris Assure is a proprietary circulating nucleic acid sequencing platform that couples whole exome and transcriptome (WES/WTS) sequencing on white blood cells and plasma with advanced machine learning techniques to satisfy all three testing needs on one platform. This test detects SNVs, INDELs, structural variants, copy number, gene expression, tumor mutational burden (TMB), microsatellite instability (MSI), fragment length, and aneuploidy of both somatic (tumor and clonal hematopoiesis) and germline origin. Caris’ extensive database of over 350,000 tissue WES/WTS from solid malignancies was used to train deep learning neural networks to identify the molecular underpinnings of cancer. These networks were then deployed on WES/WTS data from plasma and buffy coat in pursuit of signals that can inform early detection, MRD and therapy selection. Validation studies were performed to characterize the analytic and clinical performance of Assure on over 3000 patient blood samples. These samples include ~1000 non-cancer patients (controls), ~1700 newly diagnosed patients where blood was collected at surgery (early detection), ~500 early-stage patients during adjuvant therapy at multiple time points (MRD), and ~200 locally advanced/metastatic patients where matched tissue testing was also performed (therapy selection). For early detection, stratification of blood samples from patients with stage I-IV cancer versus those with no reported cancer resulted in an AUC > 0.99 and included over 30 types of solid tumors. Notably, at 99.5% specificity, the sensitivities for stages I-IV (n= 119, 54, 50, 27) were 73%, 80%, 76%, and 89%. In the MRD setting for high-risk patients, the disease-free survival of patients whose cancers were predicted to recur was significantly shorter (39.6 mo) than those predicted not to recur (93.4 mo) (HR: 5.18, 95%CI: 2.94-9.09, p<.00001). This performance was observed across multiple lineages of cancer including but not limited to breast, colon, lung, and bladder. Lastly, for therapy selection, detection of driver mutations where blood was collected within 30 days of matched tissue demonstrated high concordance with a PPA of 93.8% and PPV of 96.8%. CHIP correction proved to be essential as ~35% percent of patients had CHIP mutations, including KRAS, BRAF, ATM, BRCA1/2, findings that could lead to improper therapy selection. Herein, we demonstrate for the first time a single liquid biopsy assay that addresses the entire continuum of care in clinical oncology with optimal diagnostic, prognostic, and predictive utility for patients and physicians. Citation Format: Jim Abraham, Valeriy Domenyuk, Maria Perdigones Borderias, Takayuki Yoshino, Elisabeth I. Heath, Emil Lou, Stephen Liu, John Marshall, Wafik S. El-Deiry, Anthony Shields, Martin Dietrich, Yoshiaki Nakamura, Takao Fujisawa, David D. Halbert, Dominic Sacchetti, Seth Stahl, Adam Stark, Sergey Klimov, Sourabh Antani, Chadi Nabhan, Jeffrey Swensen, George Poste, Matt Oberley, Milan Radovich, George W. Sledge, David Spetzler. AI enabled whole exome& transcriptome liquid biopsy addressing MCED, MRD, and therapy selection on a single platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2300.

Abstract 5017: Analytical performance of contrived samples for validation of liquid biopsy assays

Abstract Introduction: Cell-free DNA (cfDNA) extracted from plasma is critical for the analytical validation of liquid biopsy assays. cfDNA is comprised of genetic material from tumor and non-tumor cells, which can be highly variable across tumor types and disease stage. Relative to tumor tissue, cfDNA yield is lower and may not always capture all clinically relevant variants (e.g. gene fusions). Supplementing analytical validation studies with contrived samples prepared from cell line derived DNA to mimic the features of cfDNA allows for more robust testing of rare variants in clinical samples. To determine the commutability of contrived sample DNA to clinical plasma sample cfDNA, a retrospective analysis of sensitivity studies using two methods of contrived sample preparation was performed. Methods: The PGDx elio Plasma Focus assay was used to compare sample base size post library preparation and limit of detection (LoD) of clinically relevant variants. Both methods used fragmented cell line DNA with a variant of interest and for method #1, cell line DNA was spiked into noncancerous donor plasma, which was then extracted resulting in a cfDNA and cell line DNA mixture. This contrived sample was diluted using wild-type (WT) DNA extracted from noncancerous donor plasma to obtain a target variant allele frequency (VAF). Method #2 used fragmented cell line DNA diluted with fragmented WT cell line DNA to obtain a target VAF. This retrospective data analysis will include a minimum of 28 samples run in replicate (3-20) across multiple studies. Results: Data obtained from a DNA fragment analyzer post library preparation show similarities between fragmented cell line DNA spiked into plasma, fragmented cell line DNA, and clinical plasma cfDNA, with fragment peaks ranging from 290-320 base pair (bp). The median LoDs across the three sample types (n=28) were also similar for single nucleotide variants (SNVs) at VAFs of 0.70%, 0.76%, 0.72%, indels at VAFs of 0.70%, 1.0%, 0.78%, amplifications at folds of 1.4, 1.3, 1.5, and translocations at fusion read fractions of 0.5%, 0.61%, 0.55%. When comparing the same variants in a contrived sample functional characterization study, the call rates of various dilution levels were similar. A Fisher’s Exact Test of the Hit Rate showed no significant difference for KRAS G12V SNV, ERBB2 amplification, and RET translocation between cell line DNA and clinical cfDNA. Conclusions: This data demonstrates that contrived samples perform with general equivalence to and may be an appropriate substitute for clinical plasma samples, though certain DNA sources may influence overall performance. Overall, fragmented cell line DNA spiked into plasma and fragmented cell line DNA diluted with WT fragmented cell line DNA performed similarly to clinical cfDNA samples representative of the intended use population. Citation Format: Amanda E. Harvey, Cindy K. Maddox, Sonomi O. Dillon, Omar T. Khawar, Ellen L. Verner, Amy Greer, Kenneth C. Valkenburg, Brian J. Caveney, Shakti Ramkissoon. Analytical performance of contrived samples for validation of liquid biopsy assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5017.

Abstract 7487: Construction of a reliable CTC detection method and validity evaluation of CTC markers in colorectal cancer

Abstract Even in modern times when medical technology has advanced, cancer remains a life-threatening disease, and recurrence and metastasis are major issues in cancer treatment. The characteristics of cancer cells change with progression and treatment. Therefore, timely evaluation on their characteristics and decision on the treatment strategy are required. Circulating tumor cells (CTCs) are released into blood vessels in solid tumors and promote metastasis by circulating in the blood. CTCs are thus attractive targets for liquid biopsy and can provide useful information for selection of appropriate treatment. To obtain reliable results from CTC testing, it is important to prove that the detected cells are derived from cancerous tissue. In molecular tests targeting CTCs, it is still unclear whether the detected cells are derived from cancer tissue displaying genetic mutations. Aiming to establish reliable CTC testing, we have developed a simple method using molecular imaging flow cytometry to detect APC gene mutation together with Cytokeratin and Vimentin, which are epithelial-mesenchymal transition markers. Since, abnormalities in the APC gene are detected in 60-70% of colorectal cancer patients, detecting such mutations provides strong evidence that the detected cells are derived from cancerous tissue. Here, we show that upon evaluation of analytical performance of our method using cells isolated from cancerous tissue, our method showed high concordance rate against APC gene mutation. A clinical proof-of-concept using 5 mL of whole blood from colorectal cancer patients revealed that counts of cells with APC mutation in blood and cells with Cytokeratin and/or Vimentin expression in blood are highly correlated. Our results demonstrated a pathological stage-dependent increase in the count and frequency of Cytokeratin and/or Vimentin positive CTCs. We believe that our study not only establishes a practical approach for identifying CTCs in cancer patients but also provides potential implications in clinical practice, prognostic evaluation, and selection of treatment strategies. Citation Format: Yusuke Takahashi, Yuichi Ijiri, Shiki Fujino, Nakhaei Elnaz, Ayuko Kishimoto, Kentaro Shirai, Shigeki Iwanaga, Masatoshi Yanagida, Ali Asgar Bhagat, Norikatsu Miyoshi. Construction of a reliable CTC detection method and validity evaluation of CTC markers in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7487.

Abstract 5632: Advancing transcriptome insights during RNA-Seq library construction of FFPE samples in a novel workflow

Abstract Formalin-fixed, paraffin-embedded (FFPE) tumor tissue has significant clinical benefits in oncology research and is considered vital for studying tumor gene expression through RNA sequencing (RNA-Seq). However, RNA extracted from FFPE samples tends to be severely degraded, making it suboptimal for constructing high-quality RNA-Seq libraries. The RNA-Seq workflow can further impair data quality, as traditional library preparation and pre-library ribodepletion workflows may result in the loss of valuable information due to rare transcripts being not captured or washed away. Moreover, small, degraded fragments are a challenging template for ligases, and the resulting adapter addition may be inadequate. Here we assessed a novel workflow employing a proprietary enzyme to overcome the limitations and biases of cDNA synthesis using reverse transcriptase (RT) and ligases. This innovative RNA-Seq library preparation approach, coupled with a post-library ribodepletion strategy, aims to capture a more complete transcriptome profile from RNA extracted from FFPE breast cancer samples, and can also be used for evaluation of gene regulation through intronic and intergenic bases. The study also compared two commercially available kits, RecoverAll and PureLink, for FFPE RNA extraction, evaluating quality metrics such as RNA integrity number (RIN), DV200, recovery of small RNAs during NGS library construction, and transcriptome coverage. A parallel fresh frozen RNA sample, extracted using a phenol-based reagent, served as a benchmark. Our findings demonstrate that the novel workflow yields a richer dataset, encompassing a wider range of transcriptomic elements, including both small and long RNAs from FFPE samples. Performing ribodepletion after the library preparation procedure led to increased detection of small RNAs compared to pre-library ribodepletion. The robust analytical performance of this streamlined library preparation protocol enables its suitability for RNA-Seq analysis of archived FFPE specimens, offering substantial utility for oncology research. Citation Format: Cissy Jiang, Elizabeth Jordan Dreskin, Angelica Olcott, Linda Lingelbach, Srikanth Perike. Advancing transcriptome insights during RNA-Seq library construction of FFPE samples in a novel workflow [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5632.

A novel split-type photoelectrochemical biosensor based on liposome-induced in situ formation of Bi2S3@BiOI/Ag2S heterojunction for the sensitive detection of CEA

A novel split-type photoelectrochemical (PEC) biosensor was constructed for the sensitive detection of carcinoembryonic antigen (CEA) based on the Ag+-liposome (ALL) signal amplification strategy and Bi2S3@BiOI heterojunction as the substrate material. The split-type sensing mode effectively avoids the complex fixation of biomolecules on the electrode surface and preserves the activity of biomolecules. The sandwich complex was formed between CEA and aptamer-anchored streptavidin-functionalized magnetic beads (SMB-Apt) and ALL-labeled aptamer (ALL-Apt). After the methanol was added, a large amount of Ag+ was released from the liposome. The released Ag+ was transferred to the Bi2S3@BiOI modified electrode surface for incubation and then soaked in Na2S solution to form a narrow band gap photosensitive material Ag2S on the electrode surface. Bi2S3@BiOI/Ag2S ternary heterojunction in situ was formed due to the band gap matching relationship between Ag2S and the Bi2S3@BiOI heterojunction, which effectively expanded the light absorption range and enhanced the photocurrent signal. Under the optimal experimental conditions, the constructed PEC sensing platform exhibited good analytical performance for CEA with a linear range of 0.005 ∼ 50 ng mL−1 and a detection limit of 1.21 pg mL−1. Additionally, the PEC sensor had good selectivity, reproducibility, and stability, which provided a new research idea for the detection of clinical tumor biomarkers.

Abstract 7295: A novel XNA technology-based assay to detect JAK2 V617F mutation by real-time PCR

Abstract The Janus kinase 2 (JAK2) gene is located on chromosome 9p24.1 and encodes a non-receptor tyrosine kinase that plays a central role in cytokine and growth factor signaling. The JAK2 protein is especially important for controlling the production of blood cells from hematopoietic stem cells. In fact, the JAK2 mutation at amino acid 617 (Valine 617 to Phenylalanine, V617F) is the most frequently detected mutation in myeloproliferative neoplasms (MPN), including essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (PMF). This dominant gain-of-function V617F mutation results in constitutive tyrosine phosphorylation activity, leading to uncontrolled blood cell production, including increased numbers of erythrocytes, neutrophils, and platelets. To detect the JAK2 V617F mutation in DNA from patient blood samples, we developed a unique real-time PCR assay using our proprietary XNA technology that enables the assay to selectively amplify the mutant sequence by using a synthetic DNA analog XNA (Xenonucleic Acid). The JAK2 V617F mutation detection assay is designed to detect a valine-to-phenylalanine mutation at amino acid 617 (V617F). PCR primers, TaqMan probes, and XNA were designed for the JAK2 V617F mutation, along with primers and probes for an internal control gene in the duplex setting. The analytical performance of the assay was verified and validated using a variety of control samples. The results revealed that the XNA completely suppressed the amplification of wildtype sequence while only the V617F mutant sequence was amplified. The JAK2 V617F mutation detection assay is highly reproducible with intra- and inter-assay coefficients of variation of less than 10%. Results for the assay’s analytical sensitivity indicated that V617F could be detected with about 0.25% mutant allele frequency in 10 ng DNA input. In addition, no significant cross-amplification between V617F and V617I was observed. Thus, the JAK2 V617F mutation detection assay is specific for the V617F mutation. The JAK2 V617F mutation detection assay, using XNA-based technology, provides high sensitivity and specificity to detect the JAK2 V617F mutation. Thus, this assay would be a useful tool for clinical decision-making in determining the presence of the JAK2 V617F mutation in DNA from patient blood samples. Citation Format: Shuo Shen, Robert Brown, Daniel Kim, Larry Pastor, Andrew Y. Fu, Pushpinder Kaur, Alisha Babu, Wei Liu, Aiguo Zhang, Hiromi Tanaka, Michael Y. Sha. A novel XNA technology-based assay to detect JAK2 V617F mutation by real-time PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7295.

Abstract 7408: Robust profiling of cancer-related gene fusions: Analytical validation of PANCARNA for multiple cancer types

Abstract The impact of examining gene fusion presence in cancer patients is often overlooked, and as such, no well-established workflow currently exists for robust profiling of tumor samples in this area. We established a targeted RNA sequencing panel (PANCARNA) for investigating gene fusions across multiple cancer types and performed analytical validation to confirm performance. Furthermore, we report on the applicability of using targeted RNA sequencing for the purposes of gene expression profiling. This panel covers 117 genes associated with solid tumors. Thirty-nine FFPE samples with gene fusion status validated using an orthogonal method were used to evaluate analytical performance. Of the 39 standard samples, 33 samples were positive for gene translocation events and 6 were negative controls. Samples were collected from across 10 cancer types. To examine the robustness of the panel, 12 samples with known fusions were selected to undergo testing. Each sample was tested in triplicate across two experimental batches. Seraseq Fusion RNA Mix V4 (SeraCare, Cat. 0710-0497) standard samples were used to test the limit of detection for PANCARNA. Additionally, we explored a cohort of 22 samples with over expressed genes and 4 samples without overexpressed genes to test the expression profiling capabilities of PANCARNA and compared the results to immunohistochemistry stains. Of the 39 samples tested using the orthogonal method and targeted RNA-Seq, 38 were found to have concordant fusion calls in both methods (Positive percent agreement = 97.0%, 32/33; Negative percent agreement = 100%, 6/6; Overall percent agreement = 97.4%, 38/39). In reproducibility studies, the assay produced consistent intrarun and interrun results in all samples (Repeatability = 100%, 12/12; Reproducibility = 100%, 12/12). The limit of detection for multiple fusions of interest, such as EML4-ALK, CD74-ROS1, TPM3-NTRK1, and SLC34A2-BRAF, is found to be 0.5-1 copies per ng of RNA. ETV6-NTRK1 can be reliably detected at 2-4 copies per ng of RNA. MET ex14 skipping events can also be detected in a few as 1-2 copies per ng of RNA. To validate the capability of PANCARNA to quantify gene expression, we tested 26 samples with known gene expression levels for three genes of interest (ERBB2, EGFR, MET). ERBB2, EGFR and MET amplification detection through PANCARNA was found to have a high concordance to IHC results (Sensitivity = 96.2%, 100%, 94.7%, respectively). In conclusion, PANCARNA demonstrated highly accurate and sensitive detection of clinically relevant gene fusions. This assay produces reliable results when detecting fusions and offers high concordance to results obtained through IHC/FISH, indicating that targeted RNA seq analysis can assist with profiling gene fusion events in a clinical setting. Citation Format: Haimeng Tang, Hua Bao, Rui Liu, Shuyu Wu, Sisi Liu, Xue Wu, Yang Shao. Robust profiling of cancer-related gene fusions: Analytical validation of PANCARNA for multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7408.

Abstract 3671: Analytical performance of the Oncomine™ Dx Express Test, a CE-IVD NGS liquid biopsy assay for identification of clinically relevant variants

Abstract For in vitro Diagnostic use only. Not available in all regions including the United States. Introduction Minimally invasive blood-based liquid biopsy using cell-free total nucleic acid (cfTNA) and next generation sequencing (NGS) has substantially evolved in the field of clinical diagnostics for oncology, for detection of molecular therapeutic targets in non-small cell lung cancer (NSCLC). Here we describe analytical validation results for cfTNA using the CE-IVD Oncomine™ Dx Express Test (ODxET) assay, a qualitative in vitro diagnostic test that uses targeted NGS technology, the Ion Torrent Genexus™ Dx Integrated Sequencer to detect SNV, indel and copy number gain present in 42 genes and fusions in 7 genes from cfTNA isolated from NSCLC plasma samples. Methods Plasma samples from NSCLC patients were screened for variants of interest on several important gene loci. Screening involved isolation of cfTNA from K2-EDTA-derived plasma using the Genexus™ Cell-Free Total Nucleic Acid Purification kit on an automated purification system and sequencing was performed on the Genexus™ Dx integrated sequencer using the ODxET assay. Plasma samples having clinically relevant variants from the set of screened plasma samples were used to perform the validation studies. Results Analytical sensitivity and specificity of NSCLC plasma samples were characterized through determination of limit of detection (LOD) and limit of blank (LOB), respectively. The LOD level tested for DNA SNVs, and indels at 5 ng (minimum) input level ranged from 0.62% to 1.82% allelic frequency (AF), while 30 ng (maximum) input shows the LOD level ranging from 0.23% to 0.42% AF. The LOD for the tested RNA fusions ranged from 4.2 to 19.6 molecular counts for 5ng input and 4.9 to 8.0 molecular counts for 30ng input. Furthermore, LOB for the ODxET assay was determined by testing wild type (WT) cfTNA extracted from 30 healthy donor blood plasma samples, which were confirmed to be negative at all variant locations. The analytical accuracy study shows the false positive rate at 0.20% for SNVs, 0% for indel locations and fusion targets. In addition, the analytical reproducibility study shows 99.64% intra-run repeatability call rate for DNA variants and 98.75% for RNA variants. Conclusion In conclusion, we establish that the ODxET assay on Ion Torrent Genexus Dx Integrated Sequencer, is fast and efficient while demonstrating high sensitivity, specificity, and reproducibility for testing NSCLC liquid biopsy samples. Citation Format: Madhuri Jasti, Swasti Raut, Diarra Hassell, Nader Ezzedine, Daniela Garcia, Stephen Wunsch, Nick Siepert, Elliott Martinez, Emilia Ostrowska, Jeff Schagemann, Jian Gu, Thilanka Jayaweera, Luming He, Angie Cheng. Analytical performance of the Oncomine™ Dx Express Test, a CE-IVD NGS liquid biopsy assay for identification of clinically relevant variants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3671.

Abstract 3492: Comprehensive analysis of hematological malignancies with optical genome mapping and Bionano VIA™Software

Abstract The current standard for analysis of samples with suspected hematological cancer is karyotyping, fluorescence in situ hybridization (FISH), and/or chromosomal microarray (CMA). However, these methods have several limitations for the detection of structural variants (SVs) or copy number variants (CNV) that are smaller than 5 Mbp (karyotyping). Additionally, they are limited in their ability to detect low allele fraction (LAF) events and cannot detect the absence of heterozygosity (AOH) or the loss of heterozygosity (AOH/LOH - FISH and karyotyping). Optical genome mapping (OGM) from Bionano can enable accurate detection of SV and CNV events of sizes down to 5 kbp, with high sensitivity to detect LAF events down to 5% variant allele fraction. Bionano’s VIA™ software provides visualization and analysis support for OGM SV events including an improved Circos plot and ideogram for whole genome review. VIA incorporates CNV calling from OGM data using the SNP-FASST3 algorithm which also allows for accurate copy number calling at allele fractions as low as 10%. CNV detection performance was evaluated using 280 CNV events ranging in size from 175 kbp to 8 Mbp on the 22 autosomal chromosomes. Sensitivity and PPV were calculated for each size range separately. Using SNP-FASST3, VIA also adds the ability to detect AOH/LOH events from OGM data. By analyzing locations where known SNPs disrupt the specific nucleotide sequence motif used by the DLE-1 labeling enzyme, a B-allele frequency can be calculated and enable AOH/LOH detection at low allelic fractions. AOH/LOH performance using SNP-FASST3 was evaluated using a cohort of constitutional and cancer samples analyzed with orthogonal methods as well as with simulated events. Sensitivity for 20-25 Mbp AOH events was 92% with PPV greater than 90% at 25% aberrant cell fraction. The VIA 7.0 release also includes the ability to create a customizable decision tree using supplied reference annotation files for CNV, AOH and SV event pre-classification. VIA resources include a panel of target variants derived from various medical societies for clinical analysis guidelines specific to Acute Myeloid Leukemia (AML), Myelodysplastic Syndrome (MDS) and an aggregation of all hematological malignancy guidelines (pan-heme). These methods, combined with tools for expert review and reclassification of variants, allow users to conduct whole genome interpretation and report results. These new features in VIA provide a streamlined workflow for analyzing heterogeneous hematological cancer samples and demonstrate the analytical performance of updated approaches for detection of CNV and AOH/LOH regions at low allele fractions using optical genome mapping alone. Citation Format: Jacob Wisotsky, Aliz Raski, Westley Sherman, Megan Roytman, Samer Al-Saffar, Jen Hauenstein, Andy Wing Chun Pang, Viren Wasnikar, Neil Miller. Comprehensive analysis of hematological malignancies with optical genome mapping and Bionano VIA™Software [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3492.

Abstract 2506: Novel biomarkers that predict response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer

Abstract Background: Neoadjuvant chemoradiotherapy (nCRT) followed by surgery is standard of care for locally advanced rectal cancer (LARC). About 20% patients receiving nCRT alone experience a pathologic complete response (pCR), while up to 25% patients exhibit a poor response. Currently, there is no biomarker to predict response to nCRT. We hypothesized that inherited ability to recognize and repair DNA damage, especially lethal double-strand breaks (DSBs), manifest in lymphocytes, would yield a reproducible test predicting therapeutic response to nCRT. Methods: Expression of DNA damage response (DDR) proteins was studied using peripheral blood lymphocytes (PBLs) from LARC patients and healthy controls. PBLs from LARC patients collected either before nCRT or after a standard course of ~5.5 weeks of nCRT were assessed by immunofluorescence (IF) for phospho-γH2AXSer139 and by Luminex multi-analyte platform (xMAP) approaches. The xMAP assay was modified from a qualitative to a semi-quantitative assay that measures the following DDR-associated proteins- total ATR, phospho-γH2AXSer139, total MDM2, phospho-Chk1S345, phospho-Chk2T68, phospho-p53S15, total p21. The analytical performance of the assay was assessed with vendor-provided reference controls and banked PBLs from healthy controls (n=50). LARC patients were segregated by neoadjuvant rectal (NAR) score to determine if tested biomarkers correlated with nCRT response. We used two independent sets of LARC biospecimens for xMAP analysis (set 1, n=48; set 2, n=44). Results: IF-based assessment: Using PBLs from LARC patients, we found that poor responders (PoR; NAR score>14; n=21) had significantly lower γH2AX foci than complete responders (CR; NAR score<1; n=21) (P<0.0001, logistic regression). No significant difference was observed in positive γH2AX foci from PBLs drawn pre-nCRT versus post-nCRT from the same patient (p=0.4961, n=11, Wilcoxon test). xMAP assay performance: The performance assessment showed linear sample curves, precision with acceptable inter- and intra-assay coefficients of variability, and high reproducibility with ~1% outliers identified in replicates. Clinical associations using xMAP assay: levels of six proteins (ATR, p-γH2AXSer139, MDM2, p-Chk1S345, p-Chk2T68, p-p53S15) significantly differentiated CRs from PoRs (p-values and False Discovery Rate ⇐ 1e-5). The strongest associations with nCRT response were observed for: ATR, MDM2 and γH2AX. Conclusion: 1) we standardized an xMAP assay to assess DDRs in human PBLs, and 2) found novel biomarkers that predict response to nCRT in LARC patients using minimally invasive PBL biospecimen. In ongoing work, we are using a larger biospecimen set to establish clinical validity parameters. Citation Format: Adria Hasan, Elena V. Demidova, Philip Czyzewicz, Karthik Devarajan, Margret B. Einarson, Donald Baldwin, Erica A. Golemis, Joshua E. Meyer, Sanjeevani Arora. Novel biomarkers that predict response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2506.