Obi L. Griffith
A5001076376- Cancer Genomics and Diagnostics
- Lymphoma Diagnosis and Treatment
- Genomics and Rare Diseases
- Genetic factors in colorectal cancer
- Genomics and Phylogenetic Studies
- Immunotherapy and Immune Responses
- Lung Cancer Treatments and Mutations
- RNA modifications and cancer
- Advanced Breast Cancer Therapies
- Estrogen and related hormone effects
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Head and Neck Cancer Studies
- vaccines and immunoinformatics approaches
- Cancer Immunotherapy and Biomarkers
- Monoclonal and Polyclonal Antibodies Research
- Cervical Cancer and HPV Research
- Hippo pathway signaling and YAP/TAZ
- RNA Research and Splicing
- Immune Cell Function and Interaction
- Cancer-related gene regulation
- HER2/EGFR in Cancer Research
- CAR-T cell therapy research
- Genetics, Bioinformatics, and Biomedical Research
Washington University in St. Louis
2016-2025
James S. McDonnell Foundation
2016-2025
Canada's Michael Smith Genome Sciences Centre
2005-2023
University of British Columbia
2003-2023
Alvin J. Siteman Cancer Center
2015-2023
Jewish Hospital
2022-2023
Barnes-Jewish Hospital
2022-2023
University of Winnipeg
2003-2020
National Human Genome Research Institute
2016-2019
Altor BioScience (United States)
2019
We sequenced the 29,751-base genome of severe acute respiratory syndrome (SARS)âassociated coronavirus known as Tor2 isolate. The sequence reveals that this is only moderately related to other coronaviruses, including two human HCoV-OC43 and HCoV-229E. Phylogenetic analysis predicted viral proteins indicates virus does not closely resemble any three previously groups coronaviruses. will aid in diagnosis SARS infection humans potential animal hosts (using polymerase chain reaction...
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 provides information on drug-gene interactions and druggable genes from publications, databases, other web-based sources. Drug, gene, interaction data are normalized merged into conceptual groups. contained in this available to users through straightforward search interface, an application programming interface (API), TSV downloads. DGIdb 4.0 the latest major version release of database. A primary focus update...
To characterize patient-derived xenografts (PDXs) for functional studies, we made whole-genome comparisons with originating breast cancers representative of the major intrinsic subtypes. Structural and copy number aberrations were found to be retained high fidelity. However, at single-nucleotide level, variable numbers PDX-specific somatic events documented, although they only rarely functionally significant. Variant allele frequencies often preserved in PDXs, demonstrating that clonal...
The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing complete open reading frame (ORF) for every human mouse gene. initially used random strategy select clones from large number libraries diverse tissues. Candidate were chosen based on 5′-EST sequences, then fully sequenced high accuracy analyzed by algorithms developed this project. Currently, more than 11,000 10,000 genes are...
The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations neoplastic cells harboring distinct mutations. A fine resolution view this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all which may have clinical implications. Single analysis already contributes to understanding these phenomena. However, cryptic subclones frequently revealed by additional patient samples (e.g., collected...
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...
Cancer immunotherapy has gained significant momentum from recent clinical successes of checkpoint blockade inhibition. Massively parallel sequence analysis suggests a connection between mutational load and response to this class therapy. Methods identify which tumor-specific mutant peptides (neoantigens) can elicit anti-tumor T cell immunity are needed improve predictions therapy targets for vaccines adoptive therapies. Here, we present flexible, streamlined computational workflow...
Tests that predict outcomes for patients with acute myeloid leukemia (AML) are imprecise, especially those intermediate risk AML.To determine whether genomic approaches can provide novel prognostic information adult de novo AML.Whole-genome or exome sequencing was performed on samples obtained at disease presentation from 71 AML (mean age, 50.8 years) treated standard induction chemotherapy a single site starting in March 2002, follow-up through January 2015. In addition, deep digital paired...
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...
First-generation molecular profiles for human breast cancers have enabled the identification of features that can predict therapeutic response; however, little is known about how various data types best be combined to yield optimal predictors. Collections cancer cell lines mirror many aspects pathobiology, and measurements their omic biological responses are well-suited development strategies identify most predictive feature sets. We used least squares-support vector machines random forest...
Abstract Summary: Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. provides rapid easy-to-use suite of visualization tools, while maintaining high degree flexibility leveraging abilities ggplot2 Bioconductor. Availability Implementation: is an R available via Bioconductor...
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...
Efficient tools for data management and integration are essential many aspects of high-throughput biology. In particular, annotations genes human genetic variants commonly used but highly fragmented across resources. Here, we describe MyGene.info MyVariant.info, high-performance web services querying gene variant annotation information. These currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model organizing biological MyVariant.info...
Identification of neoantigens is a critical step in predicting response to checkpoint blockade therapy and design personalized cancer vaccines. This cross-disciplinary challenge, involving genomics, proteomics, immunology, computational approaches. We have built framework called pVACtools that, when paired with well-established genomics pipeline, produces an end-to-end solution for neoantigen characterization. supports identification altered peptides from different mechanisms, including...
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical genomic data through both harmonized aggregation federated approaches. decreasing cost sequencing (along with other genome-wide molecular assays) increasing evidence its utility will soon drive generation sequence from tens millions humans, levels diversity. In this perspective, we present GA4GH strategies addressing major challenges revolution. We...