3.5 Publications

August 11, 2020

Real-world Evidence of Diagnostic Testing and Treatment Patterns in U.S. Breast Cancer Patients with Implications for Treatment Biomarkers from RNA-sequencing Data

medRxiv, Tempus-authored — We performed a retrospective analysis of longitudinal real-world data (RWD) from breast cancer patients to replicate results from clinical studies and demonstrate the feasibility of generating real-world evidence. We also assessed the value of transcriptome profiling as a complementary tool for determining molecular subtypes. PATIENTS AND...

June 11, 2020

Molecular Analysis of Atypical Deep Penetrating Nevus Progressing to Melanoma

Journal of Cutaneous Pathology, Tempus-authored — Deep penetrating nevi (DPN) are dermal‐based, heavily pigmented melanocytic proliferations primarily resulting from mutations in B‐catenin and BRAF or, less commonly, NRAS. DPNs are considered to be intermediate grade tumors which are stable with low risk of malignant tra...

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....

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