A5014457595- Cancer Genomics and Diagnostics
- Pediatric health and respiratory diseases
- Gut microbiota and health
- Asthma and respiratory diseases
- Cancer Diagnosis and Treatment
- Cancer Immunotherapy and Biomarkers
- Molecular Biology Techniques and Applications
- Genetic Associations and Epidemiology
- Gene expression and cancer classification
- RNA modifications and cancer
- Tumors and Oncological Cases
- IL-33, ST2, and ILC Pathways
- Ferroptosis and cancer prognosis
- RNA Research and Splicing
- Effects of Environmental Stressors on Livestock
- Radiomics and Machine Learning in Medical Imaging
- Chromosomal and Genetic Variations
- DNA Repair Mechanisms
- Genomic variations and chromosomal abnormalities
- Melanoma and MAPK Pathways
- Genomics and Rare Diseases
- Probiotics and Fermented Foods
- Cutaneous Melanoma Detection and Management
- Immunotherapy and Immune Responses
- Epigenetics and DNA Methylation
Tempus Labs (United States)
2018-2025
University of Chicago
2015-2022
University of Washington
2010
The Amish and Hutterites are U.S. agricultural populations whose lifestyles remarkably similar in many respects but farming practices, particular, distinct; the former follow traditional practices whereas latter use industrialized practices. also show striking disparities prevalence of asthma, little is known about immune responses underlying these disparities.We studied environmental exposures, genetic ancestry, profiles among 60 Hutterite children, measuring levels allergens endotoxins...
Patient-derived tumor organoids (TOs) are emerging as high-fidelity models to study cancer biology and develop novel precision medicine therapeutics. However, utilizing TOs for systems-biology-based approaches has been limited by a lack of scalable reproducible methods profile these models. We describe robust pan-cancer TO platform with chemically defined media optimized on cultures acquired from over 1,000 patients. Crucially, we demonstrate genetic transcriptomic concordance this approach...
Abstract Introduction Variants in the tau gene ( MAPT ) region are associated with breast cancer women and Alzheimer's disease (AD) among persons lacking apolipoprotein E ε4 (ε4–). Methods To identify novel genes tau‐related pathology, we conducted two genome‐wide association studies (GWAS) for AD, one 10,340 ε4– Disease Genetics Consortium (ADGC) another 31 members (22 women) of a consanguineous Hutterite kindred. Results We identified associations AD MGMT variants ADGC (rs12775171, odds...
The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a mapping study of the microbiome two accessible upper airway sites, nasopharynx and nasal vestibule, during seasons 144 adult members founder population European decent. We estimated relative abundances (RAs) genus level bacteria from 16S rRNA gene sequences examined associations with 148,653 variants (linkage disequilibrium [LD] r 2 < 0.5) selected among all...
Abstract Common variants at many loci have been robustly associated with asthma but explain little of the overall genetic risk. Here we investigate role rare (<1%) and low-frequency (1–5%) using Illumina HumanExome BeadChip array in 4,794 cases, 4,707 non-asthmatic controls 590 case–parent trios representing European Americans, African Americans/African Caribbeans Latinos. Our study reveals one missense mutation GRASP gene that is Latino sample ( P =4.31 × 10 −6 ; OR=1.25; MAF=1.21%) two...
Recent molecular studies of spitzoid neoplasms have identified mutually exclusive kinase fusions involving ROS1, ALK, RET, BRAF, NTRK1, MET, and NTRK3 as early initiating genomic events. Pigmented spindle cell nevus (PSCN) Reed is a morphologic variant Spitz may be very diagnostically challenging, having histologic features concerning for melanoma. Their occurrence in younger patients, lack association to sun exposure, rapid growth phase similar nevi suggest also play significant role these...
With the introduction of DNA-damaging therapies into standard care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following strong clinical evidence utility DNA-sequencing-based HRD testing in ovarian cancer, and breast we present analytical validation Tempus HRD-DNA test. We further developed, validated, explored HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to...
Cancers assume a variety of distinct histologies, and may originate from myriad sites including solid organs, hematopoietic cells, connective tissue. Clinical decision-making based on consensus guidelines such as the National Comprehensive Cancer Network (NCCN) is often predicated specific histologic anatomic diagnosis, supported by clinical features pathologist interpretation morphology immunohistochemical (IHC) staining patterns. However, in patients with nonspecific morphologic IHC...
Abstract Background: PRAME (Preferentially Expressed Antigen in Melanoma) is an intracellular cancer-testis antigen over-expressed across solid tumor types. Elevated expression associated with poor prognosis, particularly lung cancer. Further, its selective cells and ability to induce robust T-cell-mediated immune responses make it a promising pan-cancer immunotherapy target. This study investigates the influence of histological subtypes on impact outcome first line (1L) cancer patients....
Abstract Founder populations are ideally suited for studies on the clinical effects of alleles that rare in general but occur at higher frequencies these isolated populations. Whole genome sequencing 98 Hutterites, a founder population European descent, and subsequent imputation revealed 660,238 single nucleotide polymorphisms (<1%) or absent populations, >1% Hutterites. We examined variants plasma lipid levels 828 Hutterites applied Bayesian hierarchical framework to prioritize...
Abstract While whole‐genome resequencing remains expensive, genomic partitioning provides an affordable means of targeting sequence efforts towards regions high interest. There are several competitive methods for targeted capture; these include molecular inversion probes, microdroplet‐segregated multiplex PCR, and on‐array or in‐solution capture‐by‐hybridization. Enrichment the human exome by array hybridization has been successfully applied to pinpoint causative allele Mendelian disorders....
Abstract Tumor genome sequencing has emerged as a powerful tool for identifying biomarkers targeted cancer therapies. While DNA is well-established method and considered gold standard, RNA (RNA-seq) can identify anomalies in gene transcription, regulation of expression, fusions, which have critical diagnostic therapeutic impacts. Tempus Labs CLIA-certified, CAP-accredited offers several clinically validated NGS assays solid tumor hematological malignancy testing, including the xT 648-gene...
3081 Background: Tumors of unknown origin occur in approximately 5% newly diagnosed cancers and are difficult to treat without establishing the tissue type from which they derive. Establishing tumor guides standard care treatment for several NCCN targeted therapy guidelines. Leveraging specificity gene expression profiles, classification models based on RNA offer a promising approach identify likely primary cancer site tumors origin. Methods: In this study, we developed transcriptome-based...
Abstract Introduction: Understanding the molecular underpinnings of vulvar squamous cell carcinoma (vSCC) has strong potential for clinical impact, given unmet need this rare cancer. vSCCs have two main etiologies, including human papillomavirus (HPV) infection or skin conditions such as lichen sclerosis. Clinically, few treatment options with limited efficacy are available recurrent and large whole transcriptome disease subtyping studies due to rarity cancer type. Here, we present a study...
<h3>Background</h3> Mutations in DNA polymerases <i>POLE</i> and <i>POLD1</i> are associated with tumor development certain hereditary cancers characterized by hyper-mutated genomic phenotypes, leading to high mutation burden (TMB). Similar mismatch repair instability (MSI), increased TMB confers significant prognostic benefits immunotherapy due higher immune microenvironment activation. The current study utilizes Tempus' multimodal, real-world database, encompassing molecular clinical...
<h3>Background</h3> Immuno-oncology (IO) therapies have demonstrated effective and durable benefits in multiple cancer indications but responses are variable. Discovery validation of better biomarkers treatment response, ability to modulate immunological states, selection optimal drug combinations, identification new IO targets top priorities maximize the clinical impacts immunotherapy. While immune tumor microenvironment been well-characterized primary tumors,<sup>1</sup> large-scale...
Abstract Laboratories conducting high volumes of RNA sequencing must be extremely wary technical batch effects if samples are to compared across extended time periods, which is imperative for the most well-powered analyses cancer transcriptomes. Changes in reagents, protocols, or technologies used nucleic acid extraction, library preparation, and can alter transcriptomes ways that invalidate complicate comparisons from different batches, necessitating continuous monitoring. This monitoring...