Poster

2022 AACR Poster #146: Transcriptome augmentation provides accurate and sensitive quantification of genes associated with the tumor microenvironment Overview Tumors harbor a complex and dynamic ecosystem of malignant, immune, and stromal cells. While malignant cells dictate much of the tumor biology, there is evidence that the tumor microenvironment (TME) also plays a significant role [...]

2022 SITC Poster #51: A combination of antigen presentation and T-cell recognition features improves neoantigen immunogenicity predictions Overview Tumor neoantigen burden outperforms tumor mutational burden (TMB) in prediction of patient response to immune checkpoint blockade (ICB) therapy by better capturing the biological mechanism underlying response [1]. However, immune recognition of neoantigens by T-cells requires [...]

2022 SITC Poster #119: Sensitive prediction of immunotherapy response by integrating immune infiltration and neoantigen presentation score in late-stage melanoma Overview Single-modality biomarkers such as tumor mutational burden (TMB) often fail to reliably predict response to immune checkpoint blockade (ICB), likely due to incomplete characterization of the complex tumor-immune interactions that influence treatment efficacy. We [...]

2022 AACR: Applying NeXT Liquid Biopsy™, an exome-scale platform, to monitor and discover somatic variants in a broad set of cancer types Overview Circulating tumor cell-free DNA (ctDNA) has become a biomarker for prognosis and disease monitoring. However, studies typically utilize assays limited to a small set of genes that may miss biologically important [...]

2022 AACR: Accurate quantification of infiltrating B cell composition and clone diversity in tumor samples Overview The role of B cells as a prognostic biomarker remains elusive. For instance, infiltrating B cells in colorectal cancer have both positive and negative prognostic value. Thus, a scalable approach to quantify B cells and the B-cell receptor [...]

2022 AACR: Exome-scale longitudinal tracking of emerging therapeutic resistance in GIST via analysis of circulating tumor DNA Overview Gastrointestinal stromal tumors (GIST) are lethal tumors characterized by constitutively activating mutations to KIT or PDGFRA. Transient disease control in the first-line setting is achieved via inhibition of tyrosine kinase signaling using the KIT inhibitor imatinib. [...]

2022 AACR: A high sensitivity, tumor-informed liquid biopsy platform, designed to detect minimal residual disease at part per million resolution Overview Tumor-informed liquid biopsy approaches have proven promising for detecting minimal residual disease (MRD) and recurrence of cancer following surgical resection or other therapy. However, current liquid biopsy MRD assays typically detect ctDNA in a [...]

2022 AACR: Mono-allelic immunopeptidomics data from 109 MHC-I alleles reveals variability in binding preferences and improves neoantigen prediction algorithm Overview  This study extends the previously published MHC-I, pan-allelic neoantigen prediction algorithm, SHERPA™, with immunopeptidomics from 84 additional mono-allelic transfected cell lines, totaling data from 109 unique alleles. SHERPA achieves model generalizability and 98% population [...]

2021 SITC: Tumor-informed liquid biopsy monitoring of evolving therapeutic resistance mechanisms in head and neck squamous cell carcinoma patients receiving anti-PD-1 therapy Background Typical liquid biopsy panels offer a limited understanding of tumor biology, potentially under-representing the heterogeneity of resistance in late-stage cancers. Here, diminished scope can result in undetected, therapeutically-relevant biomarkers which respond [...]

2021 SITC: Comprehensive profiling of the tumor-immune microenvironment using an augmented transcriptome Introduction Comprehensive profiling of both the tumor and tumor microenvironment (TME) can help further our understanding of tumor progression and response to treatment. Many immune features can be extracted from transcriptomic data, including characterization of the immune infiltrate and profiling of the [...]