Genomic and epigenomic alterations involved in initiation, progression, and metastasis of cancer
Regulation of gene expression and splicing and their association with cancer
Expression and post-translational regulation of proteins in the context of tumor development and treatment
We develop software that uses state-of-the-art sequencing technology to identify variants that contribute to disease, including small mutations, structural variations, epigenetic modifications, and gene-protein-phosphoprotein expression changes. We then validate computational predictions using cell-based assays and high throughput screenings. By looking at thousands of tumors across many forms of cancer, we gain novel insight into the initiation, progression, metastasis, and treatment of cancer at the gene, pathway, and cell level. Ultimately, our work contributes to a deeper understanding cancer and more effective treatments.
Cancer Genomics and Proteomics Projects
Collaboration projects our group participates in:
The Cancer Genome Atlas (TCGA): A national initiative to catalog the genetic changes found in cancer
Pediatric Cancer Genome Project (PCGP): A collaboration between St. Jude Children's Research Hospital and Washington University, aimed at understanding the genetic origins of childhood cancers
International Cancer Genome Consortium (ICGC): A project that obtains a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe
Clinical Proteomic Tumor Analysis Consortium (CPTAC): A comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows
1000 Genomes Structural Variation Project: A collaboration to characterize and detect genomic structural variants existing in the human genome
Multiple Myeloma Research Foundation CoMMpass Study: A longitudinal tissue and data collection effort to study myeloma as it develops over time and responds to treatment
Human Tumor Atlas Network (HTAN): Extending TCGA and part of the Cancer Moonshot initiative, the HTAN project seeks to uncover the subtle dynamics of cancer by building a large collection of human tumor atlases, each consisting of complimentary molecular, cellular, space/time, and morphological data to facilitate new types of analysis and visualization of components and their interactions within the tumor ecosystem.
Patient-Derived Xenograft Development and Trial Centers Research Network (PDXNet): This NCI-established project is a consortium aimed at accelerating translational medicine by developing new patient-derived xenograft (PDX) mouse models and the associated methods and bioinformatics tools to test drug combinations and novel therapeutics.
Tools in Active Development
VarScan: Detect viruses from next-generation sequencing data [github]
MiSplice: Discover mutation-induced splice sites from integration of DNA and RNA sequence data [github]
SciClone: Infer the subclonal architecture of tumors [github]
Hotspot3D: Identify mutation-mutation and mutation-drug clusters using 3D protein structures and correlate them with known or potentially interacting functional variants, domains, and proteins [pubmed] [github]
GenomeVIP: Cloud-enabled variant discovery [github]
PepScan: Protein quantification and peptide identification from mass spectra data [github]
CharGer: Characterization of the clinical significance of germline variants [github]
Breakpoint Surveyor: Visualization of breakpoints and copy-number variation
For more information on all of our tools, see Tools page.