Poster

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 [...]

2021 SITC: Extensively validated HLA LOH algorithm demonstrates an association between HLA LOH and genomic instability Background Human Leukocyte Antigen (HLA) genes are critical for the presentation of neoantigens to the immune system by cancer cells. Deletion of HLA alleles, known as HLA loss of heterozygosity (LOH), has been highlighted as a key immune [...]

2021 SITC: Exome-scale liquid biopsy characterization of emerging immune resistance mechanisms in treatment-resistant GIST Background Metastatic gastrointestinal stromal tumors (GIST) are lethal tumors of the GI tract characterized by gain of function mutations in KIT or PDGFRɑ. Transient first-line control is achieved through the inhibition of tyrosine kinase signaling using the KIT inhibitor imatinib, [...]

2021 AACR: Longitudinal Exome-Scale Liquid Biopsy Monitoring of Evolving Therapeutic Resistance Mechanisms in Head and Neck Squamous Cell Carcinoma Patients Receiving Anti-PD-1 Therapy Typical liquid biopsy panels capture a relatively small number of variants, and likely under-represent the heterogeneity of resistance in late-stage cancers. To address the challenges associated with identifying multiple concurrent heterogeneous [...]