A5058907044- Advanced Breast Cancer Therapies
- Lung Cancer Treatments and Mutations
- Head and Neck Cancer Studies
- Cervical Cancer and HPV Research
- Cancer Genomics and Diagnostics
- HER2/EGFR in Cancer Research
- Cancer Treatment and Pharmacology
- Genomics and Rare Diseases
- Clinical Laboratory Practices and Quality Control
- Estrogen and related hormone effects
- Genetic factors in colorectal cancer
- Biomedical Text Mining and Ontologies
- Meta-analysis and systematic reviews
- PI3K/AKT/mTOR signaling in cancer
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Artificial Intelligence in Healthcare and Education
- Cancer Immunotherapy and Biomarkers
- Sepsis Diagnosis and Treatment
- Computational Drug Discovery Methods
- AI in cancer detection
- Ovarian cancer diagnosis and treatment
- Pharmacogenetics and Drug Metabolism
- RNA modifications and cancer
- Bone health and treatments
University of Utah
2024-2025
ARUP Laboratories (United States)
2024-2025
Washington University in St. Louis
2013-2024
Jewish Hospital
2024
Barnes-Jewish Hospital
2019-2024
Saint Louis University
2024
Medical College of Wisconsin
2024
James S. McDonnell Foundation
2015-2023
The University of Texas Southwestern Medical Center
2022
Altor BioScience (United States)
2019
The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents interactions gene druggability information from papers, databases web resources. DGIdb normalizes content 30 disparate sources allows for user-friendly advanced browsing, searching filtering ease of access through an intuitive user interface, application programming interface (API) public cloud-based server image. v3.0 represents a major update the database. Nine previously included 24 were...
The Drug–Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that consolidates disparate data sources describing drug–gene interactions and gene druggability. It provides an intuitive graphical user interface documented application programming (API) for querying these data. DGIdb was assembled through extensive manual curation effort, reflecting the combined information of twenty-seven sources. For 2.0, substantial updates have been made to increase content improve its...
Abstract Purpose: Cyclin-dependent kinase (CDK) 4/6 drives cell proliferation in estrogen receptor–positive (ER+) breast cancer. This single-arm phase II neoadjuvant trial (NeoPalAna) assessed the antiproliferative activity of CDK4/6 inhibitor palbociclib primary cancer as a prelude to adjuvant studies. Experimental Design: Eligible patients with clinical stage II/III ER+/HER2− received anastrozole 1 mg daily for 4 weeks (cycle 0; goserelin if premenopausal), followed by adding (125 on days...
Pembrolizumab improved survival in patients with recurrent or metastatic head and neck squamous-cell carcinoma (HNSCC). The aims of this study were to determine if pembrolizumab would be safe, result pathologic tumor response (pTR), lower the relapse rate resectable human papillomavirus (HPV)-unrelated HNSCC.Neoadjuvant (200 mg) was administered followed 2 3 weeks later by surgical ablation. Postoperative (chemo)radiation planned. Patients high-risk pathology (positive margins and/or...
Nearly all patients with small cell lung cancer (SCLC) eventually relapse chemoresistant disease. The molecular mechanisms driving chemoresistance in SCLC remain un-characterized. Here, we describe whole-exome sequencing of paired tumor samples procured at diagnosis and from 12 patients, unpaired 18 additional patients. Multiple somatic copy number alterations, including gains ABCC1 deletions MYCL, MSH2, MSH6, are identifiable relapsed samples. Relapse also exhibit recurrent mutations loss...
Here we report targeted sequencing of 83 genes using DNA from primary breast cancer samples 625 postmenopausal (UBC-TAM series) and 328 premenopausal (MA12 trial) hormone receptor-positive (HR+) patients to determine interactions between somatic mutation prognosis. Independent validation prognostic was achieved data the METABRIC study. Previously established associations MAP3K1 PIK3CA mutations with luminal A status/favorable prognosis TP53 Luminal B/non-luminal tumors/poor were observed,...
Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology informatics concepts. We make available open-access tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential alternative splicing analysis methods....
This trial was conducted to determine the maximum tolerated dose (MTD) and preliminary efficacy of buparlisib, an oral pan-class I PI3K inhibitor, plus fulvestrant in postmenopausal women with metastatic estrogen receptor positive (ER(+)) breast cancer.Phase IA employed a 3+3 design MTD buparlisib daily fulvestrant. Subsequent cohorts (phase IB cohort C) evaluated intermittent (5/7-day) continuous dosing (100 mg daily). No more than 3 prior systemic treatments setting were allowed these...
Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list somatic variants. Despite widespread use in analyzing sequence data, methods standardize have not been described, resulting high inter- and intralab variability.This standard operating procedure (SOP) consists annotate variants with four different calls 19 tags. The indicate reviewer's confidence each the tags commonly observed sequencing patterns artifacts that inform...
Abstract High-grade serous ovarian cancer (HGSC) is the most lethal histotype of and majority cases present with metastasis late-stage disease. Over last few decades, overall survival for patients has not significantly improved, there are limited targeted treatment options. We aimed to better characterize distinctions between primary metastatic tumors based on short- or long-term survival. characterized 39 matched by whole exome RNA sequencing. Of these, 23 were short-term (ST) survivors...
•Extensive genomic analyses were performed in an adult with post-allo relapsed B-ALL.•Mutations found EP300, NF1, IKZF1, SETD2, RB1, PAX5, ETV6, and ZNF384.•Transcriptome analysis identified aberrant overexpression of the FLT3 gene.•Treatment inhibitor sunitinib induced a rapid clinical molecular response.•Comprehensive studies can sometimes reveal unexpected therapeutic targets. The events responsible for pathogenesis B-lymphoblastic leukemia (B-ALL) are not yet clear. We integrative...
Abstract CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed literature-derived evidence characterizing the clinical utility cancer variants. As sequencing becomes more prevalent management, need for variant interpretation has grown beyond capability any single institution. contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally...
Measuring parathyroid hormone-related peptide (PTHrP) helps diagnose the humoral hypercalcemia of malignancy, but is often ordered for patients with low pretest probability, resulting in poor test utilization. Manual review results to identify inappropriate PTHrP orders a cumbersome process.Using dataset 1330 from single institute, we developed machine learning (ML) model predict abnormal results. We then evaluated performance on two external datasets. Different strategies (model...
Abstract Patients with multiple myeloma (MM) who are treated lenalidomide rarely develop a secondary B-cell acute lymphoblastic leukemia (B-ALL). The clonal and biological relationship between these sequential malignancies is not yet clear. We identified 17 patients MM lenalidomide, subsequently developed B-ALL. Patient samples were evaluated through sequencing, cytogenetics/fluorescence in situ hybridization (FISH), immunohistochemical (IHC) staining, immunoglobulin heavy chain (IgH)...
Abstract Background Intravenous (IV) fluid contamination is a common cause of preanalytical error that can delay or misguide treatment decisions, leading to patient harm. Current approaches for detecting rely on delta checks, which require prior result, manual technologist intervention, inefficient and vulnerable human error. Supervised machine learning may provide means detect contamination, but its implementation hindered by reliance expert-labeled training data. An automated approach...