3.5 Publications

May 15, 2020

Recurrent Transcriptionally Active ESR1 Fusions Render Therapeutic Vulnerabilities to Kinase Inhibition in Advanced Breast Cancer

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Background: We recently reported two ESR1 fusions (ESR1-YAP1 and ESR1-PCDH11X) that drive endocrine therapy (ET) resistance and metastasis in estrogen receptor positive (ER+) metastatic breast cancer (MBC) (PMC6171747). Here we report additional ESR1 fusions wit...

May 15, 2020

Accurate Estimation of Circulating Tumor DNA Fraction From Ultra Low-pass Whole-genome Sequencing

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Early detection of recurrence is critical to improve the survival of cancer patients. Blood-based “liquid biopsies” provide a minimally invasive method to detect variants, and ultra low-pass whole-genome sequencing (LPWGS) can accurately and sensitively detect low fractions of circulating tumor...

May 15, 2020

Universal Genetic and Transcriptomic Concordance Metrics to Validate Patient-derived Tumor Organoid Models

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Background: Patient derived tumor organoids (TOs) are emerging as potential models to elucidate mechanisms of tumor biology and therapeutic response. Here, we establish pan-cancer metrics for validation of genetic and transcriptomic recapitulation, and concordance of an organoid to its native tumor...

May 15, 2020

Multimodal Prediction of Diagnosis for Cancers of Unknown Primary

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Background: Tumors of unknown origin account for up to 5% of newly diagnosed cancers and the average survival time is 9 to 12 months from diagnosis. Establishing tumor type and subtype guides standard of care treatment for several NCCN targeted therapy guidelines. Metho...

May 15, 2020

Identification of Novel Druggable Fusions Enabled Through the Use of an Automated RNA Fusion Prioritization Pipeline

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Gene fusions can serve as key drivers in the development of various cancers and represent important therapeutic targets and diagnostic biomarkers. Due to high detection of candidate fusions from RNA-sequencing data, there is a recognized need to build tools that...

May 15, 2020

Large Scale Ultradeep Phenotypic Analysis of Patient Derived Tumor Organoids Unveils Intra- and Inter-tumor Heterogeneity of Drug Response

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Patient derived Tumor Organoids (TOs) are emerging as patient-representative models that recapitulate clinical responses to candidate therapeutics. Yet standard methods of interpreting in vitro treatments of TOs have been developed from monoclonal, rapidly proliferating 2D cell lines that are not...

May 15, 2020

Robust Detection of Sequencing Batch Effects in RNA Through Low Dimensional Embedding With Subtype-Matched Reference Samples

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Laboratories conducting high volumes of RNA sequencing must be extremely wary of technical batch effects if samples are to be compared across extended time periods, which is imperative for the most well-powered analyses of cancer transcriptomes. Changes in reagents, protocols,...

May 15, 2020

Transcriptome Background Tissue Correction in Metastatic Cancers Using a Correlated Composition Admixture Model

American Association for Cancer Research Annual Meeting 2020, Tempus-authored — Transcriptome profiling of tumors by standard RNA-seq measures the average effect of the tumor microenvironment. This expression profile is largely shaped by the tumor architecture where tumor purity can directly influence the genomic interpretation and consequent associations with clinical outcomes....

May 13, 2020

Learning Relevant H&E Slide Morphologies for Prediction of Colorectal Cancer Tumor Mutational Burden Using Weakly Supervised Deep Learning

American Society of Clinical Oncology Annual Meeting 2020, Tempus-authored — Background: Tumor mutation burden (TMB) is the number of non-synonymous mutations present in a cancer exome. In colorectal cancer (CRC), high TMB is associated with microsatellite instability (MSI), POLE mutations, and response to immunotherapy. TMB prediction from whole-sli...

May 13, 2020

Greater Than Two Coexisting Mutations in KRAS and NRAS Identified in the Circulating Tumor DNA Fraction of Liquid Biopsies by NGS and Confirmed With ddPCR

American Society of Clinical Oncology Annual Meeting 2020, Tempus-authored — Background: Liquid biopsies are increasingly utilized as a non-invasive tool in precision oncology to assess tumor mutational profiles in order to select targeted therapies, detect treatment resistance, and monitor disease progression in cancer patients. Additionally, liquid biopsies may provide...

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