Poster

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 [...]

2021 AACR: Accurate modeling of antigen processing and MHC peptide presentation using large-scale immunopeptidomes and a novel machine learning framework Neoantigens, which are antigens specific to cancer cells, can be harnessed to develop personalized cancer vaccines and prognostic biomarkers for checkpoint blockade inhibition. Next generation sequencing technologies have enabled comprehensive profiling of putative neoantigens [...]

2021 AACR: Pan-cancer survey of HLA loss of heterozygosity using a robustly validated NGS based machine learning algorithm HLA loss of heterozygosity (LOH) is increasingly being recognized as an important immune escape mechanism in response to checkpoint inhibitor therapy. HLA LOH reduces the repertoire of neoantigens displayed on the cell surface of cancer cells, [...]

2021 AACR: Pan-cancer shedding patterns of tumor circulating cell-free DNA Tumor circulating cell-free DNA (ctDNA) comprises DNA molecules cast from tumors that reach and circulate in a patient's bloodstream. Given its non-invasive nature, the liquid biopsy of ctDNA has remarkable potential for diagnosis, prognosis, disease progression tracking, and treatment monitoring. Nonetheless, little is known [...]

2021 AACR: Profiling tumor-infiltrating immune cells using an augmented transcriptome Due to the complexity of tumor-immune interactions, comprehensive profiling of both the tumor and tumor microenvironment (TME) can help further our understanding of tumor progression and response to treatment. One significant application is quantification of the immune infiltrate, which has the potential to characterize [...]