Scaling Clinical Trial Matching Using Large Language Models: A Case Study in Oncology

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.Comment: 24 pages, 5 figures, accepted at Machine Learning for Healthcare (MLHC) 202

Next-Generation Sequencing-Based Assay Shows High Clonal Characterization Success Rate for Plasma Cell Neoplasms, and Concordance with Flow Cytometry in Minimal Residual Disease Detection

Abstract Introduction After therapy or stem cell transplantation, multiple myeloma patients achieving complete response (CR) or stringent complete response (sCR) can still have a significant risk of disease relapse, illustrating the importance of using highly sensitive methods for minimal residual disease (MRD) detection and prognostication. Two techniques used clinically for MRD detection include multiparametric flow cytometry (FC), which has a sensitivity down to 2-6 X 10-6 of cells, and next-generation sequencing (NGS)-based assay for detection of patient-specific clonal IGH VDJ gene sequences associated with the neoplastic plasma cells (PC). We determined the clonal characterization success rate of plasma cell neoplasm samples from a single institution in a clinical lab, using a commercially available NGS-based assay, Lymphotrack® (Invivoscribe, San Diego, CA). The characterized clonal sequences were used for MRD detection in subsequent monitoring samples, and the results were compared to concurrent FC findings. Methods DNA was extracted from fresh marrow or formalin-fixed paraffin-embedded (FFPE) tissue, and amplified by PCR reactions using primers sets for IGH Leader, FR1, FR2, FR3 regions, and IGK. Sequencing was performed on the Illumina MiSeqTM Platform, and sequence analyses were performed using the Lymphotrack® software, and MSK-Lymphoclone, a software developed at our institution. Disease-associated clonal sequences were characterized based on predefined clonal calling criteria and stored. In subsequent samples sent for disease monitoring, a search for sequencing reads with high homology (>99%) to the patient-specific sequences was performed for MRD detection. 10-color FC for PC analyses were also performed on the same samples at our institution (Roshal M, et al. Blood Adv 2017;1(12):728-32), with a target minimum of 3 million cells for MRD analyses. Results Overall, clonal characterization was successful in 235/251 cases (93.6%), with no difference in number of sequencing reads between the successful and unsuccessful cases (p=0.24). Higher success rate was observed among cases with higher aspirate PC counts: ≥5% (95.6% success rate) and ≥10% (98.1% success rate). IGH FR1 and Leader primers together characterized 214/251 cases (85.3%), while the remaining cases required additional primers. The characterized clones showed high median somatic hypermutation (SHM) rate of 8.1% (range: 0.0-29.0%), as well as IGH V and J segment usage bias: V3 (50.2%), followed by V4 (20.3%); J4 (43.4%), followed by J6 (27.5%), concordant with prior literature. 187 samples from 124 unique patients were tested by the Lymphotrack® assay for monitoring purposes, of which the diagnostic clones were detected in 147/187 samples (78.6%), with no difference in number of sequencing reads between cases with and without detectable clone (p=0.35). Within the short median time interval of 9.5 months between the characterization and monitoring samples, most clonal sequences remained stable. In 2 cases, new clonal sequences emerged in subsequent samples. Overall, FC and Lymphotrack® showed high concordance rate for MRD detection (92.9%) (See figures). All discordant cases showed <5% PC by aspirate differential counts and CD138 immunostains. FC+/NGS- cases (9/184, 4.9%) showed abnormal PC comprising a median of 0.00095% of WBC by FC, while FC-/NGS+ cases (4/184, 2.2%) showed detectable clone at a median of 0.0405% of sequencing reads. Sampling differences might have contributed to the discrepancies. Additionally, in the FC+/NGS- cases, neoplastic subclones might be present at very low level in the characterization samples, below threshold for clonal calling, and therefore could not be specifically tracked in subsequent samples. Conclusions Our study demonstrated high clonal characterization success rate for plasma cell neoplasms using the Lymphotrack® assay when multiple primers sets were used, and the assay showed concordance with FC in MRD detection for the majority of cases. MRD detection sensitivity can be limited by low sample concentration/volume. Furthermore, the presence of very low level neoplastic subclones in the characterization samples might hamper clonal calling and detection in subsequent samples. Disclosures Ho: Invivoscribe, Inc.: Honoraria. Landgren:Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy; Karyopharm: Consultancy. Arcila:Invivoscribe, Inc.: Consultancy, Honoraria

Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms

Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kits. Data were analyzed by commercial and in-house–developed bioinformatics pipelines. Performance characteristics were evaluated directly comparing with capillary electrophoresis (CE) assays (BIOMED-2 primers). Assays were monitored after implementation (>1.5 years), concurrently testing by CE methods. A total of 1189 clinical samples were studied (94 validation, 1095 postimplementation). NGS showed superior performance compared with CE assays. For initial assessment, clonality detection rate was >97% for all malignancy types. Concordance with CE was 96%; discordances were related to higher sensitivity/resolution of NGS and improved detection in cases with high somatic hypermutation. Routine NGS clonality assessment is feasible and superior to existing assays, enabling accurate and specific index clone assessment and future tracking of all rearrangements in a patient sample. Successful implementation requires new standardization, validation, and implementation processes, which should be performed as a multicenter and multidisciplinary collaboration

Plasma Cell Myeloma Residual Disease Quantitation Using a Next-Generation Sequencing-Based IGH Clonal Rearrangement Assay with the Aid of a "Spike-in" Clonal Sequence

Introduction: Next-generation sequencing (NGS)-based IGH clonal rearrangement assays can characterize and subsequently track disease-associated clonal sequences for lymphoid and plasma cell neoplasms, even at very low levels. As IGH PCR primers are used, the detected clonal sequences are usually reported as % of sequencing reads, roughly corresponding to % of B and plasma cells (PC) in samples, rather than % of total cellularity, hampering accurate disease burden assessment. In this study, we evaluated a method for calculating residual disease burden as % of total cellularity, with the aid of adding a known quantity of "spike-in" clonal sequence to the samples, and compared to concurrent 10-color flow cytometry (FC) quantitation of abnormal PC. Methods: DNA was extracted from 40 plasma cell myeloma patient marrow biopsies sent for disease monitoring purposes at Memorial Sloan Kettering Cancer Center (MSKCC), with previously-characterized clonal sequences specific to the patients' myelomas. All samples had concurrent FC analyses and aspirate differential counts performed. 100 cell equivalent of DNA with a known clonal sequence (LymphoQuant®, LQ) was added to 700ng of patient DNA (~100,000 cell equivalent), and testing was performed using LymphotrackTM, a NGS-based assay. Following PCR amplification using IGH FR1 primers, sequencing was performed on the Illumina MiSeqTM instruments at the molecular laboratory of MSKCC. Reproducibility studies were conducted on a subset of samples at the laboratory of Invivoscribe, Inc. using identical methodology. LymphoTrack MRD data analysis tool (MRDDAT) v.1.0.3 was used to search for both the myeloma-specific and LQ clonal sequences. Disease as # of cell equivalent was calculated as: (% reads for myeloma clonal sequence/% reads for LQ) X 100 cells. Disease as % of total cellularity was calculated as: (# of cell equivalent/100,000 cells) X 100%. Results: Disease as % of total cellularity calculated by LQ showed a median of 0.7576% cells (range: 0.000614% to 39.89%), compared to abnormal PC as % of total WBC by FC with a median of 0.355% cells (range: 0.00061% to 44.70%). Overall, a good correlation between disease quantitation by LQ and FC could be observed for cases with ≤10% total PC by aspirate count (r=0.79), while the correlation is lower for cases with >10% total PC (r=0.51). 12/40 samples were tested in two different laboratories, and showed excellent correlation in disease quantitation by LQ (r=0.94). As expected, detectable clonal sequences as % of sequencing reads (rather than as % of total cellularity) showed poor correlation with FC quantitation (r=0.32), due to variability of total B and plasma cell content in different samples. Conclusions: Disease as % of total cellularity calculated with the aid of a known "spike-in" sequence in the NGS-based assay showed good correlation with the quantitation of abnormal PC by FC, when total PC was ≤10% by aspirate count. The correlation between the two declines when total PC was >10%. When patient samples contain a high number of B and/or plasma cells, the PCR amplification efficiency of the very small amount of the admixed "spike-in" clonal sequence may be hampered, affecting accurate quantitation. Furthermore, FR1 primers may not anneal optimally to some patients' clonal sequences due to somatic hypermutations in binding sites, underestimating the % of disease clone. Utilization of a second "spike-in" sequence and other primer sets (FR2, FR3) may improve disease % calculations in some cases. Disclosures Ho: Invivoscribe, Inc.: Honoraria. Roshal:Celgene: Other: Provision of Services; Auron Therapeutics: Equity Ownership, Other: Provision of services; Physicians' Education Resource: Other: Provision of services. Huang:Invivoscribe, Inc.: Employment. Hutt:Invivoscribe, Inc.: Employment. Miller:Invivoscribe, Inc.: Employment. Landgren:Theradex: Other: IDMC; Abbvie: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Merck: Other: IDMC; Adaptive: Honoraria, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Arcila:Invivoscribe, Inc.: Consultancy, Honoraria

Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

Liquid biopsies allow the non-invasive detection of somatic mutations from tumours. Here, the authors develop and test MSK-ACCESS, an NGS-based clinical assay for identifying low frequency mutations in 129 genes and describe how it benefits patients in the clinic